diff --git a/docs/validation_reporting.md b/docs/validation_reporting.md new file mode 100644 index 0000000..323f541 --- /dev/null +++ b/docs/validation_reporting.md @@ -0,0 +1,59 @@ +# Validation & Reporting + +This add-on summarizes how the AMICA agent performed after a CXG run completes. It +inspects the grounded outputs written under `output/raw_output/**/groundings.tsv` +and the curated match-type tables from `output/pandasaurus_cxg_outputs_30/*.tsv`. + +## Usage + +```bash +uv run scripts/generate_validation_reports.py \ + --output-root ./output \ + --log-level INFO +``` + +By default the script writes three Markdown summaries into `output/reports/`: + +| File | Description | +|------|-------------| +| `filtered_granularity_report.md` | Aggregated stats that ignore `Broad term` / `Overlaps` rows.| +| `raw_stats_report.md` | Unfiltered counts (improved / identical / regressions / no-match) for every grounding row. | +| `granularity_report.md` | Narrative examples showcasing rows where the agent improved on the author label. | + + +## CLI options + +``` +usage: scripts/generate_validation_reports.py [-h] [--output-root OUTPUT_ROOT] + [--raw-output-dir RAW_OUTPUT_DIR] + [--match-type-dir MATCH_TYPE_DIR] + [--reports-dir REPORTS_DIR] + [--skip-filtered] + [--skip-examples] + [--skip-raw-stats] + [--skip-ontology] + [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] +``` + +Key flags: + +- `--output-root`: base directory that contains `raw_output/`, `pandasaurus_cxg_outputs_30/`, and `reports/`. Defaults to `resources/cxg/output`. Set this when your outputs sit under a different base (e.g., top-level ./output) +- `--raw-output-dir`: direct path to per-dataset `groundings.tsv` (AMICA raw outputs). Overrides `--output-root` for groundings. Use when groundings live outside the standard layout. **If missing:** script exits with `FileNotFoundError`. +- `--match-type-dir`: direct path to the Pandasaurus match-type TSV/CSV files. Use when those files live elsewhere; overrides `--output-root` for match types only. **If missing:** script exits with `FileNotFoundError`; missing individual dataset files are tolerated (that dataset runs without Broad/Overlap filtering). +- `--reports-dir`: output directory for markdown reports (auto-created if needed). Defaults to `/reports`. + +## Skip toggles + +- `--skip-filtered`, `--skip-raw-stats`, `--skip-examples`: toggle which reports are generated. +- `--skip-filtered`: do not generate the filtered granularity report (excludes "Broad term"/"Overlaps"). Use when only raw stats are needed. +- `--skip-raw-stats`: do not generate the unfiltered aggregate stats report. Use when only filtered or example reports are needed. +- `--skip-examples`: do not generate the “improved examples” report. Use when only aggregate statistics are required. +- `--skip-ontology`: runs without Cell Ontology lookups. This prevents network calls and allows offline runs, but any metric that depends on the hierarchy (improved vs regression, example extraction) will be degraded: rows that should be "improved" or "regression" are instead categorized as "other", and no examples are extracted. Reports include a warning banner. For accurate stats, leave ontology enabled or point to a local ontology via `--ontology-adapter` (e.g., `pronto:/path/to/cl.owl`). +- `--ontology-adapter`: use a custom oaklib adapter string (e.g., `pronto:/path/to/cl.owl`) for offline runs. Defaults to `ols:cl`. + +## Dependencies + +The script reuses AMICA's `oaklib` dependency to talk to the Cell Ontology +through OLS. Make sure the machine has outbound network access when you want +hierarchy-aware stats; otherwise pass `--skip-ontology` to generate degraded +reports without ontology calls. diff --git a/output/pandasaurus_cxg_outputs_30/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique.tsv new file mode 100644 index 0000000..a293702 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique.tsv @@ -0,0 +1,46 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +SI_earlyAE enterocyte of epithelium of small intestine CL:1000334 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_AE2 enterocyte of epithelium of small intestine CL:1000334 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_tuft intestinal tuft cell CL:0019032 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_earlyACC enterocyte of epithelium of large intestine CL:0002071 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_goblet colon goblet cell CL:0009039 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_matureAE enterocyte of epithelium of small intestine CL:1000334 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_BEST4 BEST4+ enterocyte CL:4030026 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_intermAE enterocyte of epithelium of small intestine CL:1000334 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_lateACC enterocyte of epithelium of large intestine CL:0002071 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_goblet small intestine goblet cell CL:1000495 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_EEC enteroendocrine cell of colon CL:0009042 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_tuft tuft cell of colon CL:0009041 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_ISC intestinal crypt stem cell of colon CL:0009043 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_ISC intestinal crypt stem cell of small intestine CL:0009017 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_BEST4 epithelial cell of small intestine CL:0002254 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_TA transit amplifying cell of small intestine CL:0009012 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_TA transit amplifying cell of colon CL:0009011 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_secretory_prog progenitor cell CL:0011026 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_secretory_prog progenitor cell CL:0011026 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_EEC enteroendocrine cell of small intestine CL:0009006 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_TA2 transit amplifying cell of small intestine CL:0009012 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_paneth paneth cell of epithelium of small intestine CL:1000343 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_FAE microfold cell of epithelium of small intestine CL:1000353 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +absorptive enterocyte of epithelium of small intestine CL:1000334 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +tuft intestinal tuft cell CL:0019032 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +absorptive enterocyte of epithelium of large intestine CL:0002071 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +goblet colon goblet cell CL:0009039 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +BEST4+ BEST4+ enterocyte CL:4030026 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +goblet small intestine goblet cell CL:1000495 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +EEC enteroendocrine cell of colon CL:0009042 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +tuft tuft cell of colon CL:0009041 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +ISC intestinal crypt stem cell of colon CL:0009043 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +ISC intestinal crypt stem cell of small intestine CL:0009017 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +BEST4+ epithelial cell of small intestine CL:0002254 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +TA transit amplifying cell of small intestine CL:0009012 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +TA transit amplifying cell of colon CL:0009011 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +secretory_prog progenitor cell CL:0011026 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +EEC enteroendocrine cell of small intestine CL:0009006 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +paneth paneth cell of epithelium of small intestine CL:1000343 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +FAE microfold cell of epithelium of small intestine CL:1000353 exact https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_6-? enterocyte of epithelium of small intestine CL:1000334 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_earlyCC enterocyte of epithelium of large intestine CL:0002071 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +C_lateCC enterocyte of epithelium of large intestine CL:0002071 more specific term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_secretory small intestine goblet cell CL:1000495 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad +SI_secretory paneth cell of epithelium of small intestine CL:1000343 broad term https://doi.org/10.1016/j.jcmgh.2022.02.007 https://datasets.cellxgene.cziscience.com/45a7d3bd-dc1a-4565-8881-25f8975247a6.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique.tsv new file mode 100644 index 0000000..56ef02d --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique.tsv @@ -0,0 +1,46 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +cvLSEC endothelial cell of pericentral hepatic sinusoid CL:0019022 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +LAM-like macrophage CL:0000235 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +lrNK hepatic pit cell CL:2000054 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +C-Hepato2 centrilobular region hepatocyte CL:0019029 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Arterial endothelial cell of artery CL:1000413 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +I-Hepato midzonal region hepatocyte CL:0019028 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +CD8T CD8-positive, alpha-beta T cell CL:0000625 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +P-Hepato periportal region hepatocyte CL:0019026 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +ppLSEC endothelial cell of periportal hepatic sinusoid CL:0019021 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Kupffer Kupffer cell CL:0000091 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +ActMac macrophage CL:0000235 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +CD4T CD4-positive, alpha-beta T cell CL:0000624 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +CD3T-lrNK hepatic pit cell CL:2000054 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +C-Hepato centrilobular region hepatocyte CL:0019029 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +MHCII macrophage CL:0000235 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +CD8T-cNK natural killer cell CL:0000623 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Stellate hepatic stellate cell CL:0000632 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Kupffer--LSEC-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Tcell T cell CL:0000084 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Neutrophil neutrophil CL:0000775 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Chol intrahepatic cholangiocyte CL:0002538 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +cNK natural killer cell CL:0000623 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +cDC conventional dendritic cell CL:0000990 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Hepato hepatocyte CL:0000182 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +P-Hepato2 periportal region hepatocyte CL:0019026 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +cvLSEC--T-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +cvEndo vein endothelial cell CL:0002543 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Monocyte monocyte CL:0000576 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Prolif unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +AntiB plasma cell CL:0000786 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +NKT--Mac-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +CholMucus intrahepatic cholangiocyte CL:0002538 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +MatB mature B cell CL:0000785 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Fibroblast fibroblast CL:0000057 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Hepato--Mac unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +pDC plasmacytoid dendritic cell CL:0000784 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Mac--Fibro-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +RBC erythrocyte CL:0000232 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +MAST mast cell CL:0000097 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +MatB--CD4T-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +Mac--B-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +MatB--RBC unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +CD4T--RBC-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +cNK--RBC-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad +NKT natural killer cell CL:0000623 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/7d4d0da4-655e-438a-a2ec-b4371e2b80fc.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique.tsv new file mode 100644 index 0000000..8174f96 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique.tsv @@ -0,0 +1,203 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +epithelial cells epithelial cell of proximal tubule CL:0002306 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +stroma cells kidney interstitial fibroblast CL:1000692 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells kidney loop of Henle thick ascending limb epithelial cell CL:1001106 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells lymphocyte CL:0000542 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells kidney collecting duct intercalated cell CL:1001432 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +endothelial cells endothelial cell CL:0000115 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells kidney interstitial alternatively activated macrophage CL:1000695 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells kidney loop of Henle thin descending limb epithelial cell CL:1001111 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells neutrophil CL:0000775 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells podocyte CL:0000653 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells kidney loop of Henle thin ascending limb epithelial cell CL:1001107 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells mononuclear phagocyte CL:0000113 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells kidney collecting duct principal cell CL:1001431 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells T cell CL:0000084 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells plasma cell CL:0000786 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells kidney connecting tubule epithelial cell CL:1000768 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells kidney distal convoluted tubule epithelial cell CL:1000849 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +stroma cells renal interstitial pericyte CL:1001318 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +neural cells neural cell CL:0002319 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells non-classical monocyte CL:0000875 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells conventional dendritic cell CL:0000990 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells mast cell CL:0000097 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells B cell CL:0000236 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells parietal epithelial cell CL:1000452 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +immune cells plasmacytoid dendritic cell, human CL:0001058 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +epithelial cells papillary tips cell CL:1000597 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Proximal Tubule Epithelial Cell epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Adaptive / Maladaptive / Repairing Proximal Tubule Epithelial Cell epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Medullary Fibroblast kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Macula Densa Cell kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Natural Killer Cell / Natural Killer T Cell lymphocyte CL:0000542 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Transitional Principal-Intercalated Cell kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Descending Vasa Recta Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Medullary Thick Ascending Limb Cell kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cortical Collecting Duct Intercalated Cell Type A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Medullary Thick Ascending Limb Cell kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Ascending Vasa Recta Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +M2 Macrophage kidney interstitial alternatively activated macrophage CL:1000695 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cycling Proximal Tubule Epithelial Cell epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Outer Medullary Collecting Duct Intercalated Cell Type A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Adaptive / Maladaptive / Repairing Thick Ascending Limb Cell kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Afferent / Efferent Arteriole Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Descending Thin Limb Cell Type 2 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Neutrophil neutrophil CL:0000775 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Podocyte podocyte CL:0000653 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Ascending Thin Limb Cell kidney loop of Henle thin ascending limb epithelial cell CL:1001107 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Descending Thin Limb Cell Type 1 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Monocyte-derived Cell mononuclear phagocyte CL:0000113 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cortical Collecting Duct Principal Cell kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Peritubular Capilary Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Proximal Tubule Epithelial Cell Segment 1 / Segment 2 epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Proximal Tubule Epithelial Cell Segment 3 epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cortical Thick Ascending Limb Cell kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Outer Medullary Collecting Duct Principal Cell kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Fibroblast kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Outer Medullary Collecting Duct Principal Cell kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +T Cell T cell CL:0000084 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Plasma Cell plasma cell CL:0000786 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Connecting Tubule Principal Cell kidney connecting tubule epithelial cell CL:1000768 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Distal Convoluted Tubule Cell Type 1 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Fibroblast kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Cortical Thick Ascending Limb Cell kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Vascular Smooth Muscle Cell renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Schwann Cell / Neural neural cell CL:0002319 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Descending Thin Limb Cell Type 3 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Glomerular Capillary Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Vascular Smooth Muscle Cell / Pericyte renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cycling Mononuclear Phagocyte mononuclear phagocyte CL:0000113 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Myofibroblast kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Peritubular Capilary Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Non-classical Monocyte non-classical monocyte CL:0000875 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cycling Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Classical Dendritic Cell conventional dendritic cell CL:0000990 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Lymphatic Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Distal Convoluted Tubule Cell Type 2 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Mesangial Cell renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Intercalated Cell Type B kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Connecting Tubule Cell kidney connecting tubule epithelial cell CL:1000768 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Mast Cell mast cell CL:0000097 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Vascular Smooth Muscle Cell renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Ascending Thin Limb Cell kidney loop of Henle thin ascending limb epithelial cell CL:1001107 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Renin-positive Juxtaglomerular Granular Cell renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +B Cell B cell CL:0000236 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Cortical Intercalated Cell Type A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Connecting Tubule Cell kidney connecting tubule epithelial cell CL:1000768 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Adaptive / Maladaptive / Repairing Fibroblast kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Parietal Epithelial Cell parietal epithelial cell CL:1000452 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cycling Connecting Tubule Cell kidney connecting tubule epithelial cell CL:1000768 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Inner Medullary Collecting Duct Cell kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Inner Medullary Collecting Duct Cell kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Endothelial Cell endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Medullary Fibroblast kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Connecting Tubule Intercalated Cell Type A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cycling Distal Convoluted Tubule Cell kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Podocyte podocyte CL:0000653 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Plasmacytoid Dendritic Cell plasmacytoid dendritic cell, human CL:0001058 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Descending Thin Limb Cell Type 3 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Degenerative Distal Convoluted Tubule Cell kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cycling Myofibroblast kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Papillary Tip Epithelial Cell papillary tips cell CL:1000597 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +Cycling Natural Killer Cell / Natural Killer T Cell lymphocyte CL:0000542 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +PT epithelial cell of proximal tubule CL:0002306 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +FIB kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM lymphocyte CL:0000542 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IC kidney collecting duct intercalated cell CL:1001432 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +EC endothelial cell CL:0000115 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM kidney interstitial alternatively activated macrophage CL:1000695 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +DTL kidney loop of Henle thin descending limb epithelial cell CL:1001111 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM neutrophil CL:0000775 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +POD podocyte CL:0000653 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +ATL kidney loop of Henle thin ascending limb epithelial cell CL:1001107 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM mononuclear phagocyte CL:0000113 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +PC kidney collecting duct principal cell CL:1001431 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM T cell CL:0000084 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM plasma cell CL:0000786 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +CNT kidney connecting tubule epithelial cell CL:1000768 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +DCT kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +VSM/P renal interstitial pericyte CL:1001318 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +NEU neural cell CL:0002319 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM non-classical monocyte CL:0000875 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM conventional dendritic cell CL:0000990 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM mast cell CL:0000097 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM B cell CL:0000236 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +PEC parietal epithelial cell CL:1000452 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMM plasmacytoid dendritic cell, human CL:0001058 broad term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +PapE papillary tips cell CL:1000597 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dPT epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +aPT epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +M-FIB kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +MD kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +NKC/T lymphocyte CL:0000542 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +tPC-IC kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +EC-DVR endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +M-TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +C-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dM-TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +EC-AVR endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +MAC-M2 kidney interstitial alternatively activated macrophage CL:1000695 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +cycPT epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +M-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +aTAL1 kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +EC-AEA endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +DTL2 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +N neutrophil CL:0000775 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +DTL1 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +MDC mononuclear phagocyte CL:0000113 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +C-PC kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +EC-PTC endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +PT-S1/2 epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +PT-S3 epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +C-TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +M-PC kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dM-PC kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +T T cell CL:0000084 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +PL plasma cell CL:0000786 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dFIB kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dC-TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +VSMC renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +SC/NEU neural cell CL:0002319 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +DTL3 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +EC-GC endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +VSMC/P renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +cycMNP mononuclear phagocyte CL:0000113 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +MYOF kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dEC-PTC endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +ncMON non-classical monocyte CL:0000875 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +cycEC endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +cDC conventional dendritic cell CL:0000990 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +EC-LYM endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +MC renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IC-B kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +MAST mast cell CL:0000097 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dVSMC renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dATL kidney loop of Henle thin ascending limb epithelial cell CL:1001107 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +REN renal interstitial pericyte CL:1001318 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +B B cell CL:0000236 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +aTAL2 kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dC-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dCNT kidney connecting tubule epithelial cell CL:1000768 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +aFIB kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +cycCNT kidney connecting tubule epithelial cell CL:1000768 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dIMCD kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +IMCD kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dEC endothelial cell CL:0000115 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dM-FIB kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +cycDCT kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dPOD podocyte CL:0000653 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +pDC plasmacytoid dendritic cell, human CL:0001058 exact https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dDTL3 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dDCT kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +cycMYOF kidney interstitial fibroblast CL:1000692 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +cycNKC/T lymphocyte CL:0000542 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +CCD-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +OMCD-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +CCD-PC kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +OMCD-PC kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +dOMCD-PC kidney collecting duct principal cell CL:1001431 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +CNT-PC kidney connecting tubule epithelial cell CL:1000768 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +DCT1 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +DCT2 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad +CNT-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://doi.org/10.1038/s41586-023-05769-3 https://datasets.cellxgene.cziscience.com/3f2bf1e8-75a6-4fa2-9f79-dd6bb54529a0.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique.tsv new file mode 100644 index 0000000..bad8d41 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique.tsv @@ -0,0 +1,20 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Inhibitory_4 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Oligodendrocytes oligodendrocyte CL:0000128 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_2 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Inhibitory_2 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_4 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_1 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Inhibitory_1 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Astrocytes astrocyte CL:0000127 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_3 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_5 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Microglia microglial cell CL:0000129 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +OPCs oligodendrocyte precursor cell CL:0002453 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Endo/Pericytes endothelial cell CL:0000115 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_8 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Inhibitory_3 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_9 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_6 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_10 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad +Excitatory_7 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/b279d4ec-2674-4c92-aad0-3786fa651fad.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique.tsv new file mode 100644 index 0000000..245c339 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique.tsv @@ -0,0 +1,17 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Fibroblasts ADAMDEC1 fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Endothelial cells CD36 endothelial cell CL:0000115 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Myofibroblasts HHIP NPNT myofibroblast cell CL:0000186 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Fibroblasts SMOC2 PTGIS fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Endothelial cells DARC endothelial cell CL:0000115 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Fibroblasts NPY SLITRK6 fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Myofibroblasts GREM1 GREM2 myofibroblast cell CL:0000186 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Endothelial cells CA4 CD36 endothelial cell CL:0000115 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Glial cells glial cell CL:0000125 exact https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Fibroblasts SFRP2 SLPI fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Endothelial cells LTC4S SEMA3G endothelial cell CL:0000115 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Pericytes HIGD1B STEAP4 pericyte CL:0000669 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Activated fibroblasts CCL19 ADAMADEC1 fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Lymphatics lymphocyte CL:0000542 exact https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Fibroblasts KCNN3 LY6H fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad +Pericytes RERGL NTRK2 pericyte CL:0000669 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/1a640ddc-ea3c-4711-ba8e-07084cc40a88.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique.tsv new file mode 100644 index 0000000..d3f8eca --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique.tsv @@ -0,0 +1,14 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +T cells T cell CL:0000084 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Diff. Keratinocytes keratinocyte CL:0000312 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Macrophages+DC macrophage CL:0000235 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +EpSC and undiff. progenitors stem cell of epidermis CL:1000428 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Secretory-reticular fibroblasts skin fibroblast CL:0002620 more specific term https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Pericytes pericyte CL:0000669 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Pro-inflammatory fibroblasts skin fibroblast CL:0002620 more specific term https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Secretory-papillary fibroblasts skin fibroblast CL:0002620 more specific term https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Mesenchymal fibroblasts skin fibroblast CL:0002620 more specific term https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Vascular EC endothelial cell of vascular tree CL:0002139 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Melanocytes melanocyte CL:0000148 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Lymphatic EC endothelial cell of lymphatic vessel CL:0002138 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad +Erythrocytes erythrocyte CL:0000232 exact https://doi.org/10.1038/s42003-020-0922-4 https://datasets.cellxgene.cziscience.com/ba0fb2d9-28c9-4149-8591-694e0b7d9c31.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique.tsv new file mode 100644 index 0000000..281fb5c --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique.tsv @@ -0,0 +1,31 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Hepato-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Kupffer Kupffer cell CL:0000091 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Stellate-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +P-Hepato periportal region hepatocyte CL:0019026 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +C-Hepato centrilobular region hepatocyte CL:0019029 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +cvLSEC endothelial cell of pericentral hepatic sinusoid CL:0019022 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Prolif-Mac macrophage CL:0000235 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +C-Hepato2 centrilobular region hepatocyte CL:0019029 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +I-Hepato midzonal region hepatocyte CL:0019028 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Chol intrahepatic cholangiocyte CL:0002538 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +ppLSEC endothelial cell of periportal hepatic sinusoid CL:0019021 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Monocyte monocyte CL:0000576 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Kupffer-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +P-Hepato2 periportal region hepatocyte CL:0019026 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +cvEndo vein endothelial cell CL:0002543 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Stellate hepatic stellate cell CL:0000632 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Prolif unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +CD4T CD4-positive, alpha-beta T cell CL:0000624 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +cvLSEC-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +aStellate hepatic stellate cell CL:0000632 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Chol-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +cvLSEC--Mac unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Tcell-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +VSMC vascular associated smooth muscle cell CL:0000359 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +lrNK hepatic pit cell CL:2000054 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Chol--Kupffer-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +AntiB plasma cell CL:0000786 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Fibroblast fibroblast CL:0000057 exact https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +Chol--Stellate-Doublet unknown unknown more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad +CholMucus intrahepatic cholangiocyte CL:0002538 more specific term https://doi.org/10.1016/j.jhep.2023.12.023 https://datasets.cellxgene.cziscience.com/4b5895d7-6d92-471a-b13a-5c59a000ddc4.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique.tsv new file mode 100644 index 0000000..fd6c062 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique.tsv @@ -0,0 +1,15 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +naive B cell naive B cell CL:0000788 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +memory B cell memory B cell CL:0000787 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +gamma-delta T cell gamma-delta T cell CL:0000798 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +plasmablast plasmablast CL:0000980 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +regulatory T cell regulatory T cell CL:0000815 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +CD4-positive, alpha-beta memory T cell CD4-positive, alpha-beta memory T cell CL:0000897 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +CD8-positive, alpha-beta memory T cell CD8-positive, alpha-beta memory T cell CL:0000909 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +naive CD8+ T cell naive thymus-derived CD8-positive, alpha-beta T cell CL:0000900 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +naive CD4+ T cell naive thymus-derived CD4-positive, alpha-beta T cell CL:0000895 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +mucosal invariant T cell (MAIT) mucosal invariant T cell CL:0000940 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +TissueResMemT memory T cell CL:0000813 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +double-positive T cell (DPT) double-positive, alpha-beta thymocyte CL:0000809 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +double negative T cell (DNT) double negative thymocyte CL:0002489 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad +TCRVbeta13.1pos T cell CL:0000084 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/e6ef9f09-bf7f-49bf-900c-457c02675411.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique.tsv new file mode 100644 index 0000000..b0a1ebe --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique.tsv @@ -0,0 +1,26 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +B cell IgA Plasma IgA plasma cell CL:0000987 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +B cell memory memory B cell CL:0000787 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +CD8 T CD8-positive, alpha-beta T cell CL:0000625 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +gd T gamma-delta T cell CL:0000798 more specific term https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Mast mast cell CL:0000097 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +ILC innate lymphoid cell CL:0001065 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Macrophage colon macrophage CL:0009038 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +NK natural killer cell CL:0000623 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Follicular B cell follicular B cell CL:0000843 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +B cell IgG Plasma B cell CL:0000236 more specific term https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Tcm memory T cell CL:0000813 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +B cell cycling B cell CL:0000236 more specific term https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Treg regulatory T cell CL:0000815 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +LYVE1 Macrophage macrophage CL:0000235 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Th1 T-helper 1 cell CL:0000545 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Th17 T-helper 17 cell CL:0000899 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +cDC2 conventional dendritic cell CL:0000990 more specific term https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +cycling gd T gamma-delta T cell CL:0000798 more specific term https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Monocyte monocyte CL:0000576 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +cDC1 conventional dendritic cell CL:0000990 more specific term https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Activated CD4 T CD4-positive, alpha-beta T cell CL:0000624 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +pDC plasmacytoid dendritic cell CL:0000784 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Tfh T follicular helper cell CL:0002038 exact https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +Lymphoid DC dendritic cell CL:0000451 more specific term https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad +cycling DCs dendritic cell CL:0000451 more specific term https://doi.org/10.1038/s41590-020-0602-z https://datasets.cellxgene.cziscience.com/9a696bfb-7cd5-4c27-89f5-f7979ae12111.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique.tsv new file mode 100644 index 0000000..6bfc5f7 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique.tsv @@ -0,0 +1,11 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +non-classical monocyte non-classical monocyte CL:0000875 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +classical monocyte classical monocyte CL:0000860 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +NK_CD16hi CD16-positive, CD56-dim natural killer cell, human CL:0000939 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +NK_CD56loCD16lo natural killer cell CL:0000623 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +plasmacytoid dendritic cell plasmacytoid dendritic cell CL:0000784 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +conventional dendritic cell conventional dendritic cell CL:0000990 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +platelet platelet CL:0000233 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +NK_CD56hiCD16lo CD16-negative, CD56-bright natural killer cell, human CL:0000938 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +granulocyte granulocyte CL:0000094 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad +intermediate monocyte intermediate monocyte CL:0002393 exact https://doi.org/10.1016/j.cell.2021.02.018 https://datasets.cellxgene.cziscience.com/73024e1c-c5e4-48d2-9ca4-49d2f845c8b9.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique.tsv new file mode 100644 index 0000000..c8c501e --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique.tsv @@ -0,0 +1,43 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Plasma cells plasma cell CL:0000786 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Doublets unknown unknown more specific term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +T cells alpha-beta T cell CL:0000789 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +ILC innate lymphoid cell CL:0001065 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Progenitors progenitor cell CL:0011026 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +B cells B cell CL:0000236 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +CD36+ endothelium endothelial cell CL:0000115 more specific term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +MNP mononuclear phagocyte CL:0000113 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Cycling unknown unknown more specific term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Mast cells mast cell CL:0000097 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +TA transit amplifying cell of small intestine CL:0009012 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Enterocytes enterocyte of epithelium proper of ileum CL:1000342 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +SM smooth muscle fiber of ileum CL:1000278 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Goblets ileal goblet cell CL:1000326 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Fibs fibroblast CL:0000057 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +ACKR1+ endothelium endothelial cell CL:0000115 more specific term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Pericytes pericyte CL:0000669 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Enteroendocrines enteroendocrine cell of small intestine CL:0009006 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Paneth cells paneth cell of epithelium of small intestine CL:1000343 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Glial cells glial cell CL:0000125 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Lymphatics endothelial cell of lymphatic vessel CL:0002138 exact https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Immune cells plasma cell CL:0000786 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Immune cells alpha-beta T cell CL:0000789 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Immune cells innate lymphoid cell CL:0001065 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Immune cells B cell CL:0000236 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Endothelium endothelial cell CL:0000115 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Immune cells mononuclear phagocyte CL:0000113 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Immune cells mast cell CL:0000097 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Endothelium endothelial cell of lymphatic vessel CL:0002138 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma progenitor cell CL:0011026 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma endothelial cell CL:0000115 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma unknown unknown https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma transit amplifying cell of small intestine CL:0009012 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma enterocyte of epithelium proper of ileum CL:1000342 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma smooth muscle fiber of ileum CL:1000278 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma ileal goblet cell CL:1000326 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma fibroblast CL:0000057 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma pericyte CL:0000669 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma enteroendocrine cell of small intestine CL:0009006 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma paneth cell of epithelium of small intestine CL:1000343 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma glial cell CL:0000125 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad +Stroma endothelial cell of lymphatic vessel CL:0002138 broad term https://doi.org/10.1016/j.cell.2019.08.008 https://datasets.cellxgene.cziscience.com/73904545-a97e-4b0b-9599-a8636359ef00.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique.tsv new file mode 100644 index 0000000..ff7eefa --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique.tsv @@ -0,0 +1,15 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +alpha pancreatic A cell CL:0000171 exact https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +beta_major type B pancreatic cell CL:0000169 more specific term https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +endothelial endothelial cell CL:0000115 exact https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +delta pancreatic D cell CL:0000173 exact https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +stellates pancreatic stellate cell CL:0002410 exact https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +beta_minor type B pancreatic cell CL:0000169 more specific term https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +duct_major pancreatic ductal cell CL:0002079 more specific term https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +immune_stellates unknown unknown more specific term https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +acinar_minor_mhcclassII pancreatic acinar cell CL:0002064 more specific term https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +hybrid unknown unknown more specific term https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +acinar pancreatic acinar cell CL:0002064 more specific term https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +epsilon pancreatic epsilon cell CL:0005019 exact https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +duct_acinar_related pancreatic ductal cell CL:0002079 more specific term https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad +pp PP cell CL:0000696 exact https://doi.org/10.1038/s42255-022-00531-x https://datasets.cellxgene.cziscience.com/111d6e7d-d3d2-48fd-907a-4d3f8c77ee93.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique.tsv new file mode 100644 index 0000000..94c0d5d --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique.tsv @@ -0,0 +1,18 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Oligodendrocytes oligodendrocyte CL:0000128 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +L3-L5 Intratelencephalic Type 1 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +Astrocytes astrocyte CL:0000127 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +L6 Intratelencephalic - Type 1 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +SV2C LAMP5 Interneurons neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +L6 Corticothalamic / L6B neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +L2-L3 Intratelencephalic neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +L3-L5 Intratelencephalic Type 2 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +L6 Intratelencephalic - Type 2 neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +OPCs oligodendrocyte precursor cell CL:0002453 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +L5-L6 Near Projecting neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +Somatostatin Interneurons neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +Microglia microglial cell CL:0000129 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +VIP Interneurons neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +L5 Extratelencephalic neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +Endothelial endothelial cell CL:0000115 exact https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad +Parvalbumin interneurons neuron CL:0000540 more specific term https://doi.org/10.1007/s00401-023-02599-5 https://datasets.cellxgene.cziscience.com/8ec7b265-1c95-4c33-9df3-45c850b8b6b5.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique.tsv new file mode 100644 index 0000000..5c19c1e --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique.tsv @@ -0,0 +1,70 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Plasmablast plasmablast CL:0000980 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +NK natural killer cell CL:0000623 more specific term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +B memory memory B cell CL:0000787 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +B naive naive B cell CL:0000788 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +cDC conventional dendritic cell CL:0000990 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +HSPC hematopoietic stem cell CL:0000037 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ T naive naive thymus-derived CD4-positive, alpha-beta T cell CL:0000895 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Platelet platelet CL:0000233 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD8+ Tem effector memory CD8-positive, alpha-beta T cell CL:0000913 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ CTL CD4-positive, alpha-beta cytotoxic T cell CL:0000934 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Classical Monocyte classical monocyte CL:0000860 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +pDC plasmacytoid dendritic cell, human CL:0001058 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +T/NK proliferative lymphocyte CL:0000542 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Non-classical Monocyte non-classical monocyte CL:0000875 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +NK CD56bright CD16-negative, CD56-bright natural killer cell, human CL:0000938 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ Tcm central memory CD4-positive, alpha-beta T cell CL:0000904 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Treg regulatory T cell CL:0000815 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +RBC erythrocyte CL:0000232 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +B intermediate transitional stage B cell CL:0000818 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ T activated activated CD4-positive, alpha-beta T cell, human CL:0001043 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD8+ T naive naive thymus-derived CD8-positive, alpha-beta T cell CL:0000900 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD8+ T activated activated CD8-positive, alpha-beta T cell, human CL:0001049 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +NK activated natural killer cell CL:0000623 more specific term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +MAIT mucosal invariant T cell CL:0000940 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Neutrophil neutrophil CL:0000775 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +immature Neutrophil immature neutrophil CL:0000776 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +NK cell natural killer cell CL:0000623 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +B cell memory B cell CL:0000787 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +B cell naive B cell CL:0000788 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ T cell naive thymus-derived CD4-positive, alpha-beta T cell CL:0000895 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD8+ T cell effector memory CD8-positive, alpha-beta T cell CL:0000913 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ T cell CD4-positive, alpha-beta cytotoxic T cell CL:0000934 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD14+ Monocyte classical monocyte CL:0000860 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Other T lymphocyte CL:0000542 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD16+ Monocyte non-classical monocyte CL:0000875 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +NK cell CD16-negative, CD56-bright natural killer cell, human CL:0000938 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ T cell central memory CD4-positive, alpha-beta T cell CL:0000904 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ T cell regulatory T cell CL:0000815 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +B cell transitional stage B cell CL:0000818 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD4+ T cell activated CD4-positive, alpha-beta T cell, human CL:0001043 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD8+ T cell naive thymus-derived CD8-positive, alpha-beta T cell CL:0000900 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD8+ T cell activated CD8-positive, alpha-beta T cell, human CL:0001049 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +CD8+ T cell mucosal invariant T cell CL:0000940 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Neutrophil immature neutrophil CL:0000776 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_P plasmablast CL:0000980 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK natural killer cell CL:0000623 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_B memory B cell CL:0000787 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_B naive B cell CL:0000788 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Myeloid conventional dendritic cell CL:0000990 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Hematopoietic_SC hematopoietic stem cell CL:0000037 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK naive thymus-derived CD4-positive, alpha-beta T cell CL:0000895 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Hematopoietic_Mega platelet CL:0000233 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK effector memory CD8-positive, alpha-beta T cell CL:0000913 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK CD4-positive, alpha-beta cytotoxic T cell CL:0000934 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Myeloid classical monocyte CL:0000860 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Myeloid plasmacytoid dendritic cell, human CL:0001058 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK lymphocyte CL:0000542 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Myeloid non-classical monocyte CL:0000875 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK CD16-negative, CD56-bright natural killer cell, human CL:0000938 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK central memory CD4-positive, alpha-beta T cell CL:0000904 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK regulatory T cell CL:0000815 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Hematopoietic_R erythrocyte CL:0000232 exact https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_B transitional stage B cell CL:0000818 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK activated CD4-positive, alpha-beta T cell, human CL:0001043 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK naive thymus-derived CD8-positive, alpha-beta T cell CL:0000900 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK activated CD8-positive, alpha-beta T cell, human CL:0001049 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Lymphoid_T/NK mucosal invariant T cell CL:0000940 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Myeloid_G neutrophil CL:0000775 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad +Myeloid_G immature neutrophil CL:0000776 broad term https://doi.org/10.1016/j.isci.2021.103115 https://datasets.cellxgene.cziscience.com/767750a4-5bb1-4093-9882-639bf4d285fd.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique.tsv new file mode 100644 index 0000000..162c607 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique.tsv @@ -0,0 +1,52 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +RPE retinal pigment epithelial cell CL:0002586 exact https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_01 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_Y_03 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_17 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_04 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_06 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_16 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_12 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_Y_01 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_08 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +37- unknown unknown more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +38- unknown unknown more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_11 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_15 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_09 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +rod retinal rod cell CL:0000604 exact https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +L/M cone retinal cone cell CL:0000573 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +S cone retinal cone cell CL:0000573 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +HC_02 retina horizontal cell CL:0000745 exact https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +5- unknown unknown more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +CdBC_01 ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +CdBC_02 ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +ChBC_04 OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +ChBC_01 OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +ChBC_03 OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +RBC rod bipolar cell CL:0000751 exact https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +CdBC_03 ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +CdBC_05 ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +ChBC_02 OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +CdBC_04 OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_18 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_05 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_13 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +MC_01 Mueller cell CL:0000636 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +MC_02 Mueller cell CL:0000636 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +MC_03 Mueller cell CL:0000636 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_10 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_07 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +AC_B_02 amacrine cell CL:0000561 more specific term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +Ast astrocyte CL:0000127 exact https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +pigmented retinal pigment epithelial cell CL:0002586 exact https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +amacrine amacrine cell CL:0000561 broad term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +amacrine unknown unknown https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +cone retinal cone cell CL:0000573 exact https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +horizontal retina horizontal cell CL:0000745 broad term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +horizontal unknown unknown https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +bipolar ON-bipolar cell CL:0000749 broad term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +bipolar OFF-bipolar cell CL:0000750 broad term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +bipolar rod bipolar cell CL:0000751 broad term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +macroglia Mueller cell CL:0000636 broad term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad +macroglia astrocyte CL:0000127 broad term https://doi.org/10.1016/j.cell.2020.08.013 https://datasets.cellxgene.cziscience.com/228fc052-e279-4253-92f6-593ac3d32c58.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique.tsv new file mode 100644 index 0000000..b1ab619 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique.tsv @@ -0,0 +1,13 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +IMB ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +FMB OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +DB5* ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +DB3b OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +DB3a OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +BB+GB* ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +DB4 ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +DB2 OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +DB1 OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +OFFx OFF-bipolar cell CL:0000750 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +DB6 ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad +RB1 ON-bipolar cell CL:0000749 more specific term https://doi.org/10.1038/s41598-020-66092-9 https://datasets.cellxgene.cziscience.com/e5c05222-061f-47fd-9555-26f8a160bb81.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique.tsv new file mode 100644 index 0000000..7880b68 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique.tsv @@ -0,0 +1,42 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +CD4 T cell CD4-positive, alpha-beta T cell CL:0000624 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +TA transit amplifying cell CL:0009010 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +IgA plasma cell IgA plasma cell CL:0000987 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Goblet cell intestine goblet cell CL:0019031 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +IgG plasma cell IgG plasma cell CL:0000985 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Cycling B cell B cell CL:0000236 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +S4 fibroblasts fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +crypt intestinal crypt stem cell CL:0002250 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +early enterocyte enterocyte CL:0000584 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Memory B cell memory B cell CL:0000787 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +FCER2 B cell B cell CL:0000236 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Tfh T follicular helper cell CL:0002038 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +cDC2 conventional dendritic cell CL:0000990 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Arterial endothelial cell endothelial cell of artery CL:1000413 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +IL2RG+ enterocyte (M cell) M cell of gut CL:0000682 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +enterocyte enterocyte CL:0000584 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +enteroendocrine enteroendocrine cell CL:0000164 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Venous endothelial cell vein endothelial cell CL:0002543 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Activated T activated CD4-positive, alpha-beta T cell, human CL:0001043 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Monocyte monocyte CL:0000576 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +S1 fibroblasts fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +cDC1 conventional dendritic cell CL:0000990 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +myofibroblast myofibroblast cell CL:0000186 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +pericyte pericyte CL:0000669 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Treg regulatory T cell CL:0000815 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Lymphatic endothelial cell endothelial cell of lymphatic vessel CL:0002138 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +B cell B cell CL:0000236 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Activated B cell B cell CL:0000236 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +pDC plasmacytoid dendritic cell CL:0000784 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Cycling plasma cell plasma cell CL:0000786 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +gd T/NK cell gamma-delta T cell CL:0000798 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +mast cells mast cell CL:0000097 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Paneth cell glial cell CL:0000125 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +BEST4 enterocyte enterocyte CL:0000584 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +activated DC dendritic cell, human CL:0001056 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +S2 fibroblasts fibroblast CL:0000057 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +CD8 T cell CD8-positive, alpha-beta T cell CL:0000625 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Macrophage glial cell CL:0000125 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Glial cell glial cell CL:0000125 more specific term https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Cycling myeloid cells myeloid cell CL:0000763 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad +Tuft intestinal tuft cell CL:0019032 exact https://doi.org/10.1016/j.devcel.2020.11.010 https://datasets.cellxgene.cziscience.com/5790e30c-cc55-449f-bf80-62f5c12efe40.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique.tsv new file mode 100644 index 0000000..e098c7a --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique.tsv @@ -0,0 +1,10 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Iris_PPE pigmented epithelial cell CL:0000529 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad +Uveal_Melanocyte melanocyte CL:0000148 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad +Iris_Fibro fibroblast CL:0000057 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad +Iris_APE pigmented epithelial cell CL:0000529 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad +Macrophage macrophage CL:0000235 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad +Iris_Sphincter smooth muscle cell of sphincter of pupil CL:0002243 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad +Schwann Schwann cell CL:0002573 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad +Lymphocyte lymphocyte CL:0000542 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad +Vasc_Endo blood vessel endothelial cell CL:0000071 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/518aaebf-2678-4141-b063-16c5979be995.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique.tsv new file mode 100644 index 0000000..46ad767 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique.tsv @@ -0,0 +1,16 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +PC renal principal cell CL:0005009 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +PT epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +DCT2 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +DCT1 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +ICA renal alpha-intercalated cell CL:0005011 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +ICB renal beta-intercalated cell CL:0002201 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +PEC parietal epithelial cell CL:1000452 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +CNT kidney connecting tubule epithelial cell CL:1000768 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +ENDO kidney capillary endothelial cell CL:1000892 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +MES mesangial cell CL:0000650 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +PODO podocyte CL:0000653 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +PT_VCAM1 epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +LEUK leukocyte CL:0000738 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad +FIB fibroblast CL:0000057 exact https://doi.org/10.1038/s41467-021-22368-w https://datasets.cellxgene.cziscience.com/ff2e21de-0848-4346-8f8b-4e1741ec4b39.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique.tsv new file mode 100644 index 0000000..fc5116e --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique.tsv @@ -0,0 +1,38 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Thick ascending limb of Loop of Henle kidney loop of Henle thick ascending limb epithelial cell CL:1001106 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Peritubular capillary endothelium 2 capillary endothelial cell CL:0002144 more specific term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Proximal tubule epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +NK cell natural killer cell CL:0000623 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Proliferating Proximal Tubule epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +CD4 T cell CD4-positive, alpha-beta T cell CL:0000624 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Podocyte podocyte CL:0000653 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Transitional urothelium urothelial cell CL:0000731 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +B cell B cell CL:0000236 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Ascending vasa recta endothelium vasa recta ascending limb cell CL:1001131 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Type A intercalated cell renal alpha-intercalated cell CL:0005011 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Peritubular capillary endothelium 1 capillary endothelial cell CL:0002144 more specific term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Pelvic epithelium kidney epithelial cell CL:0002518 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Glomerular endothelium glomerular endothelial cell CL:0002188 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Indistinct intercalated cell renal intercalated cell CL:0005010 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Type B intercalated cell renal beta-intercalated cell CL:0002201 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Descending vasa recta endothelium vasa recta descending limb cell CL:1001285 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +CD8 T cell CD8-positive, alpha-beta T cell CL:0000625 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Epithelial progenitor cell progenitor cell CL:0011026 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +MNP-a/classical monocyte derived classical monocyte CL:0000860 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Neutrophil neutrophil CL:0000775 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Connecting tubule kidney connecting tubule epithelial cell CL:1000768 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Myofibroblast myofibroblast cell CL:0000186 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +MNP-c/dendritic cell dendritic cell CL:0000451 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +NKT cell mature NK T cell CL:0000814 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +MNP-d/Tissue macrophage kidney resident macrophage CL:1000698 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Fibroblast kidney interstitial fibroblast CL:1000692 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Distinct proximal tubule 1 epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +MNP-b/non-classical monocyte derived non-classical monocyte CL:0000875 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Distinct proximal tubule 2 epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Principal cell renal principal cell CL:0005009 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Plasmacytoid dendritic cell plasmacytoid dendritic cell CL:0000784 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Mast cell mast cell CL:0000097 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Peritubular capillary endothelium capillary endothelial cell CL:0002144 exact https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Intercalated cell renal alpha-intercalated cell CL:0005011 broad term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Intercalated cell renal intercalated cell CL:0005010 broad term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad +Intercalated cell renal beta-intercalated cell CL:0002201 broad term https://doi.org/10.1126/science.aat5031 https://datasets.cellxgene.cziscience.com/7dafa492-6129-4dff-a794-17bdefde3575.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/a12ccb9b-4fbe-457d-8590-ac78053259ef_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/a12ccb9b-4fbe-457d-8590-ac78053259ef_cxg_dataset_unique.tsv new file mode 100644 index 0000000..11caa50 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/a12ccb9b-4fbe-457d-8590-ac78053259ef_cxg_dataset_unique.tsv @@ -0,0 +1,98 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +IMM kidney interstitial alternatively activated macrophage CL:1000695 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +DCT kidney distal convoluted tubule epithelial cell CL:1000849 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +PT epithelial cell of proximal tubule CL:0002306 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM T cell CL:0000084 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IC kidney collecting duct intercalated cell CL:1001432 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +FIB kidney interstitial fibroblast CL:1000692 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +CNT kidney connecting tubule epithelial cell CL:1000768 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +PC kidney collecting duct principal cell CL:1001431 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +EC endothelial cell CL:0000115 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM B cell CL:0000236 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM mature NK T cell CL:0000814 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM mononuclear phagocyte CL:0000113 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +POD podocyte CL:0000653 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +PEC parietal epithelial cell CL:1000452 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM mast cell CL:0000097 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM plasmacytoid dendritic cell, human CL:0001058 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM plasma cell CL:0000786 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM non-classical monocyte CL:0000875 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM conventional dendritic cell CL:0000990 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +DTL kidney loop of Henle thin descending limb epithelial cell CL:1001111 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +VSM/P renal interstitial pericyte CL:1001318 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +ATL kidney loop of Henle thin ascending limb epithelial cell CL:1001107 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMM neutrophil CL:0000775 broad term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +PapE papillary tips cell CL:1000597 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +NEU neural cell CL:0002319 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +MAC-M2 kidney interstitial alternatively activated macrophage CL:1000695 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +DCT1 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +PT-S1 epithelial cell of proximal tubule CL:0002306 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +T T cell CL:0000084 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +aPT epithelial cell of proximal tubule CL:0002306 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +aTAL1 kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dC-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +CCD-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +MD kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +PT-S2 epithelial cell of proximal tubule CL:0002306 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +CNT-PC kidney connecting tubule epithelial cell CL:1000768 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dPT/DTL epithelial cell of proximal tubule CL:0002306 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +DCT2 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +PT-S3 epithelial cell of proximal tubule CL:0002306 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +CCD-PC kidney collecting duct principal cell CL:1001431 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +EC-GC endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +C-TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +B B cell CL:0000236 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +NKT mature NK T cell CL:0000814 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +MDC mononuclear phagocyte CL:0000113 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +EC-PTC endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IC-B kidney collecting duct intercalated cell CL:1001432 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +aFIB kidney interstitial fibroblast CL:1000692 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +EC-DVR endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +MAST mast cell CL:0000097 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dPT epithelial cell of proximal tubule CL:0002306 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dM-TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +EC-AEA endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dIMCD kidney collecting duct principal cell CL:1001431 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dOMCD-PC kidney collecting duct principal cell CL:1001431 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +EC-LYM endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dCNT kidney connecting tubule epithelial cell CL:1000768 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dDCT kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +pDC plasmacytoid dendritic cell, human CL:0001058 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +PL plasma cell CL:0000786 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dPOD podocyte CL:0000653 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +aTAL2 kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +cycMNP mononuclear phagocyte CL:0000113 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +ncMON non-classical monocyte CL:0000875 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +cDC conventional dendritic cell CL:0000990 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +DTL2 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +EC-AVR endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +M-TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +DTL1 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +VSMC/P renal interstitial pericyte CL:1001318 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dFIB kidney interstitial fibroblast CL:1000692 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +MC renal interstitial pericyte CL:1001318 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +cycPT epithelial cell of proximal tubule CL:0002306 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +MYOF kidney interstitial fibroblast CL:1000692 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +CNT-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +OMCD-IC-A kidney collecting duct intercalated cell CL:1001432 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +tPC-IC kidney collecting duct intercalated cell CL:1001432 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +N neutrophil CL:0000775 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +VSMC renal interstitial pericyte CL:1001318 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dATL kidney loop of Henle thin ascending limb epithelial cell CL:1001107 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +cycCNT kidney connecting tubule epithelial cell CL:1000768 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +cycDCT kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +SC/NEU neural cell CL:0002319 exact https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dVSMC renal interstitial pericyte CL:1001318 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +cycMYOF kidney interstitial fibroblast CL:1000692 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +REN renal interstitial pericyte CL:1001318 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +M-FIB kidney interstitial fibroblast CL:1000692 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +IMCD kidney collecting duct principal cell CL:1001431 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dEC-PTC endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +OMCD-PC kidney collecting duct principal cell CL:1001431 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +cycEC endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dDTL3 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +DTL3 kidney loop of Henle thin descending limb epithelial cell CL:1001111 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dM-FIB kidney interstitial fibroblast CL:1000692 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dEC endothelial cell CL:0000115 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad +dC-TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://datasets.cellxgene.cziscience.com/112a469f-6838-49f9-9f96-470744e79e8d.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique.tsv new file mode 100644 index 0000000..3b08b55 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique.tsv @@ -0,0 +1,8 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +K_Epi-Basal basal cell CL:0000646 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/9a25a459-dedc-45c0-b3b7-0e4be0a0b2c9.h5ad +K_Epi-Wing corneal epithelial cell CL:0000575 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/9a25a459-dedc-45c0-b3b7-0e4be0a0b2c9.h5ad +K_Fibro fibroblast CL:0000057 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/9a25a459-dedc-45c0-b3b7-0e4be0a0b2c9.h5ad +K_Epi-Superficial corneal epithelial cell CL:0000575 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/9a25a459-dedc-45c0-b3b7-0e4be0a0b2c9.h5ad +K_Endo corneal endothelial cell CL:0000132 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/9a25a459-dedc-45c0-b3b7-0e4be0a0b2c9.h5ad +K_Epi-TA transit amplifying cell CL:0009010 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/9a25a459-dedc-45c0-b3b7-0e4be0a0b2c9.h5ad +Immune leukocyte CL:0000738 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/9a25a459-dedc-45c0-b3b7-0e4be0a0b2c9.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique.tsv new file mode 100644 index 0000000..444e16c --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique.tsv @@ -0,0 +1,15 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +retinal rod cell type A retinal rod cell CL:0000604 more specific term https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +unannotated unknown unknown more specific term https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +retinal rod cell type B retinal rod cell CL:0000604 more specific term https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +retinal bipolar neuron type B OFF-bipolar cell CL:0000750 exact https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +retinal rod cell type C retinal rod cell CL:0000604 more specific term https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +unspecified unknown unknown more specific term https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +retinal bipolar neuron type C ON-bipolar cell CL:0000749 more specific term https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +Muller cell Mueller cell CL:0000636 exact https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +retinal cone cell retinal cone cell CL:0000573 exact https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +retinal bipolar neuron type A ON-bipolar cell CL:0000749 more specific term https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +amacrine cell amacrine cell CL:0000561 exact https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +retinal bipolar neuron type D ON-bipolar cell CL:0000749 more specific term https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +retinal ganglion cell retinal ganglion cell CL:0000740 exact https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad +microglial cell microglial cell CL:0000129 exact https://doi.org/10.15252/embj.2018100811 https://datasets.cellxgene.cziscience.com/74a5e56b-15f0-4965-b6de-7e8dd689d74f.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique.tsv new file mode 100644 index 0000000..75c3ae3 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique.tsv @@ -0,0 +1,29 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +K_Epi-Wing corneal epithelial cell CL:0000575 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Limbal_Epi-Superficial basal cell CL:0000646 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Conj_Epi-Superficial conjunctival epithelial cell CL:1000432 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Conj_Epi-Basal conjunctival epithelial cell CL:1000432 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +K_Epi-Superficial corneal epithelial cell CL:0000575 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +K_Epi-Basal basal cell CL:0000646 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Conj_Epi-Wing conjunctival epithelial cell CL:1000432 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Limbal_Epi-Basal basal cell CL:0000646 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Limbal_Epi-Wing basal cell CL:0000646 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +TM_Fibro fibroblast CL:0000057 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Conj_Melanocyte melanocyte CL:0000148 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Lymphatic_Endo endothelial cell of lymphatic vessel CL:0002138 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Uveal_Fibro fibroblast CL:0000057 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Schwann Schwann cell CL:0002573 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Sclera_Fibro fibroblast CL:0000057 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Uveal_Melanocyte melanocyte CL:0000148 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Ciliary_Muscle ciliary muscle cell CL:1000443 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +CC_VenEndo endothelial cell CL:0000115 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Lymphocyte lymphocyte CL:0000542 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +K_Endo corneal endothelial cell CL:0000132 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +VascEndo blood vessel endothelial cell CL:0000071 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Pericyte pericyte CL:0000669 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +K_Fibro fibroblast CL:0000057 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Goblet goblet cell CL:0000160 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Schlemm_Endo endothelial cell CL:0000115 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Macrophage macrophage CL:0000235 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +FibroX fibroblast CL:0000057 more specific term https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad +Mast mast cell CL:0000097 exact https://doi.org/10.1073/pnas.2200914119 https://datasets.cellxgene.cziscience.com/8b0c2c6a-902e-41dd-ad1c-60165d552360.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique.tsv new file mode 100644 index 0000000..d97d6db --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique.tsv @@ -0,0 +1,17 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +PT epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +TAL1 kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +DCT2 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +DCT1 kidney distal convoluted tubule epithelial cell CL:1000849 more specific term https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +TAL2 kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +ICA renal alpha-intercalated cell CL:0005011 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +ICB renal beta-intercalated cell CL:0002201 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +PEC parietal epithelial cell CL:1000452 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +ENDO endothelial cell CL:0000115 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +ATL kidney loop of Henle thin ascending limb epithelial cell CL:1001107 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +PTVCAM1 epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +PODO podocyte CL:0000653 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +PC renal principal cell CL:0005009 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +MES mesangial cell CL:0000650 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +FIB fibroblast CL:0000057 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad +LEUK leukocyte CL:0000738 exact https://doi.org/10.1038/s41467-022-32972-z https://datasets.cellxgene.cziscience.com/46d8d92b-32e0-4ca5-9907-4dbf519c7fc3.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique.tsv new file mode 100644 index 0000000..42b3be3 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique.tsv @@ -0,0 +1,11 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +spinous spinous cell of epidermis CL:0000649 exact https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +basal2 basal cell of epidermis CL:0002187 more specific term https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +melanocyte melanocyte CL:0000148 exact https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +mitotic keratinocyte CL:0000312 more specific term https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +channel Merkel cell CL:0000242 exact https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +basal1 basal cell of epidermis CL:0002187 more specific term https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +immune hematopoietic cell CL:0000988 exact https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +WNT1 keratinocyte CL:0000312 more specific term https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +folicular hair follicular keratinocyte CL:2000092 exact https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad +granular granular cell of epidermis CL:0002189 exact https://doi.org/10.1016/j.celrep.2018.09.006 https://datasets.cellxgene.cziscience.com/022b2aab-8abb-4972-92e2-750b7cadafa7.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique.tsv new file mode 100644 index 0000000..b96fc0c --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique.tsv @@ -0,0 +1,15 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +cone retinal cone cell CL:0000573 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +RGC retinal ganglion cell CL:0000740 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +Muller Mueller cell CL:0000636 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +cone-on-BC cone retinal bipolar cell CL:0000752 more specific term https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +cone-off-BC cone retinal bipolar cell CL:0000752 more specific term https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +amacrine amacrine cell CL:0000561 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +pericyte pericyte CL:0000669 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +endothelial retinal blood vessel endothelial cell CL:0002585 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +horizontal retina horizontal cell CL:0000745 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +rod retinal rod cell CL:0000604 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +astrocyte retinal astrocyte CL:4033015 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +rod-BC rod bipolar cell CL:0000751 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +cone-off-BC-BC3A cone retinal bipolar cell CL:0000752 more specific term https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad +microglia microglial cell CL:0000129 exact https://doi.org/10.1093/hmg/ddab140 https://datasets.cellxgene.cziscience.com/4d7c53aa-892b-4c73-8616-a97a5be4fb2c.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique.tsv new file mode 100644 index 0000000..f44be89 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique.tsv @@ -0,0 +1,26 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +PC renal principal cell CL:0005009 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +CNT kidney collecting duct cell CL:1001225 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +DCT kidney distal convoluted tubule epithelial cell CL:1000849 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +TAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +Macro macrophage CL:0000235 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +IC-A renal alpha-intercalated cell CL:0005011 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +PT-C epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +IC-B renal beta-intercalated cell CL:0002201 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +AVR vasa recta ascending limb cell CL:1001131 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +PT-B epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +Mono monocyte CL:0000576 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +tAL kidney loop of Henle thick ascending limb epithelial cell CL:1001106 more specific term https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +IC-PC columnar/cuboidal epithelial cell CL:0000075 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +vSMC vascular associated smooth muscle cell CL:0000359 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +GC glomerular capillary endothelial cell CL:1001005 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +AEA-DVR vasa recta descending limb cell CL:1001285 more specific term https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +NKcell natural killer cell CL:0000623 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +DL vasa recta descending limb cell CL:1001285 more specific term https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +Tcell T cell CL:0000084 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +UC unknown unknown exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +Peri pericyte CL:0000669 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +Bcell B cell CL:0000236 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +PT-A epithelial cell of proximal tubule CL:0002306 more specific term https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +Podo podocyte CL:0000653 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad +Mesangial mesangial cell CL:0000650 exact https://doi.org/10.1073/pnas.2103240118 https://datasets.cellxgene.cziscience.com/c0b7ba53-d527-44ae-aa8c-1b7eef19017e.h5ad diff --git a/output/pandasaurus_cxg_outputs_30/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique.tsv b/output/pandasaurus_cxg_outputs_30/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique.tsv new file mode 100644 index 0000000..f9a4208 --- /dev/null +++ b/output/pandasaurus_cxg_outputs_30/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique.tsv @@ -0,0 +1,18 @@ +author_cell_type CL_label CL_ID match_type reference dataset_version +Stem cells OLFM4 PCNA stem cell CL:0000034 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Enterocytes TMIGD1 MEP1A enterocyte CL:0000584 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Stem cells OLFM4 stem cell CL:0000034 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Goblet cells MUC2 TFF1- goblet cell CL:0000160 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Stem cells OLFM4 GSTA1 stem cell CL:0000034 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Goblet cells MUC2 TFF1 goblet cell CL:0000160 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Epithelial Cycling cells epithelial cell CL:0000066 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Stem cells OLFM4 LGR5 stem cell CL:0000034 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Enterocytes BEST4 enterocyte CL:0000584 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +L cells type L enteroendocrine cell CL:0002279 exact https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Epithelial cells METTL12 MAFB epithelial cell CL:0000066 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Paneth cells paneth cell CL:0000510 exact https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Enterocytes TMIGD1 MEP1A GSTA1 enterocyte CL:0000584 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Goblet cells SPINK4 goblet cell CL:0000160 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Epithelial HBB HBA epithelial cell CL:0000066 more specific term https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Tuft cells tuft cell CL:0002204 exact https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad +Enterochromaffin cells type EC enteroendocrine cell CL:0000577 exact https://doi.org/10.1016/j.immuni.2023.01.002 https://datasets.cellxgene.cziscience.com/b7c3c27c-97c2-4983-97df-1d537d138a43.h5ad diff --git a/output/raw_output/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..1d11e9b --- /dev/null +++ b/output/raw_output/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,46 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +BEST4+ CL:4030026 BEST4+ enterocyte DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'BEST4+', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030026 BEST4+ enterocyte +BEST4+ CL:0002254 epithelial cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'BEST4+', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030026 BEST4+ enterocyte +C_BEST4 CL:4030026 BEST4+ enterocyte DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_BEST4', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030026 BEST4+ enterocyte +C_EEC CL:0009042 enteroendocrine cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_EEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell +C_ISC CL:0009043 intestinal crypt stem cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_ISC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002250 intestinal crypt stem cell +C_TA CL:0009011 transit amplifying cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_TA', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0009010 transit amplifying cell +C_earlyACC CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_earlyACC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047018 early colonocyte +C_earlyCC CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_earlyCC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:4047018 early colonocyte +C_goblet CL:0009039 colon goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_goblet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell +C_lateACC CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_lateACC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000622 acinar cell +C_lateCC CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_lateCC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000064 ciliated cell +C_secretory_prog CL:0011026 progenitor cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_secretory_prog', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0011026 progenitor cell +C_tuft CL:0009041 tuft cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell +EEC CL:0009042 enteroendocrine cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'EEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell +EEC CL:0009006 enteroendocrine cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'EEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell +FAE CL:1000353 microfold cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'FAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4052011 follicle associated enterocyte +ISC CL:0009043 intestinal crypt stem cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'ISC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002250 intestinal crypt stem cell +ISC CL:0009017 intestinal crypt stem cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'ISC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002250 intestinal crypt stem cell +SI_6-? CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_6-?', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +SI_AE2 CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_AE2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +SI_BEST4 CL:0002254 epithelial cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_BEST4', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047051 small intestine BEST4+ enterocyte +SI_EEC CL:0009006 enteroendocrine cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_EEC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0009006 enteroendocrine cell of small intestine +SI_FAE CL:1000353 microfold cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_FAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4052011 follicle associated enterocyte +SI_ISC CL:0009017 intestinal crypt stem cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_ISC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009017 intestinal crypt stem cell of small intestine +SI_TA CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_TA', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0009012 transit amplifying cell of small intestine +SI_TA2 CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_TA2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009012 transit amplifying cell of small intestine +SI_earlyAE CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_earlyAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047019 early enterocyte +SI_goblet CL:1000495 small intestine goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_goblet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000495 small intestine goblet cell +SI_intermAE CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_intermAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000334 enterocyte of epithelium of small intestine +SI_matureAE CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_matureAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000334 enterocyte of epithelium of small intestine +SI_paneth CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_paneth', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000343 paneth cell of epithelium of small intestine +SI_secretory CL:1000495 small intestine goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_secretory', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1001598 small intestine secretory cell +SI_secretory CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_secretory', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1001598 small intestine secretory cell +SI_secretory_prog CL:0011026 progenitor cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_secretory_prog', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0011026 progenitor cell +SI_tuft CL:0019032 intestinal tuft cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009080 tuft cell of small intestine +TA CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'TA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009010 transit amplifying cell +TA CL:0009011 transit amplifying cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'TA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009010 transit amplifying cell +absorptive CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'absorptive', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} +absorptive CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'absorptive', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} +goblet CL:0009039 colon goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'goblet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} +goblet CL:1000495 small intestine goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'goblet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell +paneth CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'paneth', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000510 paneth cell +secretory_prog CL:0011026 progenitor cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'secretory_prog', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0011026 progenitor cell +tuft CL:0019032 intestinal tuft cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell +tuft CL:0009041 tuft cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell diff --git a/output/raw_output/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique/groundings.tsv b/output/raw_output/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..33be62d --- /dev/null +++ b/output/raw_output/019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,43 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +BEST4+ CL:4030026 BEST4+ enterocyte DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'BEST4+', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030026 BEST4+ enterocyte TRUE +BEST4+ CL:0002254 epithelial cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'BEST4+', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030026 BEST4+ enterocyte FALSE +C_BEST4 CL:4030026 BEST4+ enterocyte DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_BEST4', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030026 BEST4+ enterocyte TRUE +C_EEC CL:0009042 enteroendocrine cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_EEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell FALSE +C_ISC CL:0009043 intestinal crypt stem cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_ISC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002250 intestinal crypt stem cell FALSE +C_TA CL:0009011 transit amplifying cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_TA', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0009010 transit amplifying cell FALSE +C_earlyACC CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_earlyACC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047018 early colonocyte FALSE +C_earlyCC CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_earlyCC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:4047018 early colonocyte FALSE +C_goblet CL:0009039 colon goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_goblet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell FALSE +C_lateACC CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_lateACC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000622 acinar cell FALSE +C_lateCC CL:0002071 enterocyte of epithelium of large intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_lateCC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000064 ciliated cell FALSE +C_secretory_prog CL:0011026 progenitor cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_secretory_prog', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0011026 progenitor cell TRUE +C_tuft CL:0009041 tuft cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'C_tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell FALSE +EEC CL:0009042 enteroendocrine cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'EEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell FALSE +EEC CL:0009006 enteroendocrine cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'EEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell FALSE +FAE CL:1000353 microfold cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'FAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4052011 follicle associated enterocyte FALSE +ISC CL:0009043 intestinal crypt stem cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'ISC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002250 intestinal crypt stem cell FALSE +ISC CL:0009017 intestinal crypt stem cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'ISC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002250 intestinal crypt stem cell FALSE +SI_6-? CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_6-?', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +SI_AE2 CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_AE2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +SI_BEST4 CL:0002254 epithelial cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_BEST4', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047051 small intestine BEST4+ enterocyte FALSE +SI_EEC CL:0009006 enteroendocrine cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_EEC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0009006 enteroendocrine cell of small intestine TRUE +SI_FAE CL:1000353 microfold cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_FAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4052011 follicle associated enterocyte FALSE +SI_ISC CL:0009017 intestinal crypt stem cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_ISC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009017 intestinal crypt stem cell of small intestine TRUE +SI_TA CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_TA', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0009012 transit amplifying cell of small intestine TRUE +SI_TA2 CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_TA2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009012 transit amplifying cell of small intestine TRUE +SI_earlyAE CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_earlyAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047019 early enterocyte FALSE +SI_goblet CL:1000495 small intestine goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_goblet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000495 small intestine goblet cell TRUE +SI_intermAE CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_intermAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000334 enterocyte of epithelium of small intestine TRUE +SI_matureAE CL:1000334 enterocyte of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_matureAE', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000334 enterocyte of epithelium of small intestine TRUE +SI_paneth CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_paneth', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000343 paneth cell of epithelium of small intestine TRUE +SI_secretory CL:1000495 small intestine goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_secretory', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1001598 small intestine secretory cell FALSE +SI_secretory CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_secretory', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1001598 small intestine secretory cell FALSE +SI_secretory_prog CL:0011026 progenitor cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_secretory_prog', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0011026 progenitor cell TRUE +SI_tuft CL:0019032 intestinal tuft cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'SI_tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009080 tuft cell of small intestine FALSE +TA CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'TA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009010 transit amplifying cell FALSE +TA CL:0009011 transit amplifying cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'TA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009010 transit amplifying cell FALSE +goblet CL:1000495 small intestine goblet cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'goblet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell FALSE +paneth CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'paneth', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000510 paneth cell FALSE +secretory_prog CL:0011026 progenitor cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'secretory_prog', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0011026 progenitor cell TRUE +tuft CL:0019032 intestinal tuft cell DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell FALSE +tuft CL:0009041 tuft cell of colon DOI:10.1016/j.jcmgh.2022.02.007 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique {'name': 'tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell FALSE diff --git a/output/raw_output/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..9b99217 --- /dev/null +++ b/output/raw_output/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,46 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +ActMac CL:0000235 macrophage DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'ActMac', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage +AntiB CL:0000786 plasma cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'AntiB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000946 antibody secreting cell +Arterial CL:1000413 endothelial cell of artery DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Arterial', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1000413 endothelial cell of artery +C-Hepato CL:0019029 centrilobular region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'C-Hepato', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte +C-Hepato2 CL:0019029 centrilobular region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'C-Hepato2', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte +CD3T-lrNK CL:2000054 hepatic pit cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD3T-lrNK', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047101 liver-resident natural killer cell +CD4T CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD4T', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD4T--RBC-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD4T--RBC-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD8T CL:0000625 CD8-positive, alpha-beta T cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD8T', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell +CD8T-cNK CL:0000623 natural killer cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD8T-cNK', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell +Chol CL:0002538 intrahepatic cholangiocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Chol', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1000488 cholangiocyte +CholMucus CL:0002538 intrahepatic cholangiocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CholMucus', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047056 large mucus secreting cholangiocyte +Fibroblast CL:0000057 fibroblast DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Fibroblast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Hepato CL:0000182 hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Hepato', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte +Hepato--Mac unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Hepato--Mac', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +I-Hepato CL:0019028 midzonal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'I-Hepato', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte +Kupffer CL:0000091 Kupffer cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Kupffer', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000091 Kupffer cell +Kupffer--LSEC-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Kupffer--LSEC-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000091 Kupffer cell +LAM-like CL:0000235 macrophage DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'LAM-like', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:4033086 lipid-associated macrophage +MAST CL:0000097 mast cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MAST', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell +MHCII CL:0000235 macrophage DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MHCII', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000145 professional antigen presenting cell +Mac--B-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Mac--B-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +Mac--Fibro-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Mac--Fibro-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +MatB CL:0000785 mature B cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MatB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000785 mature B cell +MatB--CD4T-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MatB--CD4T-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +MatB--RBC unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MatB--RBC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte +Monocyte CL:0000576 monocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte +NKT CL:0000623 natural killer cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'NKT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000814 mature NK T cell +NKT--Mac-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'NKT--Mac-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +Neutrophil CL:0000775 neutrophil DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000775 neutrophil +P-Hepato CL:0019026 periportal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'P-Hepato', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte +P-Hepato2 CL:0019026 periportal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'P-Hepato2', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte +Prolif unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Prolif', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +RBC CL:0000232 erythrocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'RBC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte +Stellate CL:0000632 hepatic stellate cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Stellate', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +Tcell CL:0000084 T cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Tcell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000084 T cell +cDC CL:0000990 conventional dendritic cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cDC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000990 conventional dendritic cell +cNK CL:0000623 natural killer cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cNK', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000623 natural killer cell +cNK--RBC-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cNK--RBC-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +cvEndo CL:0002543 vein endothelial cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cvEndo', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +cvLSEC CL:0019022 endothelial cell of pericentral hepatic sinusoid DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cvLSEC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0019022 endothelial cell of pericentral hepatic sinusoid +cvLSEC--T-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cvLSEC--T-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +lrNK CL:2000054 hepatic pit cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'lrNK', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:4047101 liver-resident natural killer cell +pDC CL:0000784 plasmacytoid dendritic cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'pDC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell +ppLSEC CL:0019021 endothelial cell of periportal hepatic sinusoid DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'ppLSEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0019021 endothelial cell of periportal hepatic sinusoid diff --git a/output/raw_output/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique/groundings.tsv b/output/raw_output/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..b7fbfcc --- /dev/null +++ b/output/raw_output/02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,46 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +ActMac CL:0000235 macrophage DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'ActMac', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage TRUE +AntiB CL:0000786 plasma cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'AntiB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000946 antibody secreting cell FALSE +Arterial CL:1000413 endothelial cell of artery DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Arterial', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1000413 endothelial cell of artery TRUE +C-Hepato CL:0019029 centrilobular region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'C-Hepato', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte FALSE +C-Hepato2 CL:0019029 centrilobular region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'C-Hepato2', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte FALSE +CD3T-lrNK CL:2000054 hepatic pit cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD3T-lrNK', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047101 liver-resident natural killer cell FALSE +CD4T CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD4T', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell TRUE +CD4T--RBC-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD4T--RBC-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell FALSE +CD8T CL:0000625 CD8-positive, alpha-beta T cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD8T', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell TRUE +CD8T-cNK CL:0000623 natural killer cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CD8T-cNK', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell TRUE +Chol CL:0002538 intrahepatic cholangiocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Chol', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1000488 cholangiocyte FALSE +CholMucus CL:0002538 intrahepatic cholangiocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'CholMucus', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047056 large mucus secreting cholangiocyte FALSE +Fibroblast CL:0000057 fibroblast DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Fibroblast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +Hepato CL:0000182 hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Hepato', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte TRUE +Hepato--Mac unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Hepato--Mac', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +I-Hepato CL:0019028 midzonal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'I-Hepato', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte FALSE +Kupffer CL:0000091 Kupffer cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Kupffer', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000091 Kupffer cell TRUE +Kupffer--LSEC-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Kupffer--LSEC-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000091 Kupffer cell FALSE +LAM-like CL:0000235 macrophage DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'LAM-like', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:4033086 lipid-associated macrophage FALSE +MAST CL:0000097 mast cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MAST', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell TRUE +MHCII CL:0000235 macrophage DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MHCII', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000145 professional antigen presenting cell FALSE +Mac--B-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Mac--B-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +Mac--Fibro-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Mac--Fibro-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +MatB CL:0000785 mature B cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MatB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000785 mature B cell TRUE +MatB--CD4T-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MatB--CD4T-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell FALSE +MatB--RBC unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'MatB--RBC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte FALSE +Monocyte CL:0000576 monocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte TRUE +NKT CL:0000623 natural killer cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'NKT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000814 mature NK T cell FALSE +NKT--Mac-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'NKT--Mac-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +Neutrophil CL:0000775 neutrophil DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000775 neutrophil TRUE +P-Hepato CL:0019026 periportal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'P-Hepato', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte FALSE +P-Hepato2 CL:0019026 periportal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'P-Hepato2', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte FALSE +Prolif unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Prolif', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +RBC CL:0000232 erythrocyte DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'RBC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte TRUE +Stellate CL:0000632 hepatic stellate cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Stellate', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +Tcell CL:0000084 T cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'Tcell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000084 T cell TRUE +cDC CL:0000990 conventional dendritic cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cDC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000990 conventional dendritic cell TRUE +cNK CL:0000623 natural killer cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cNK', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000623 natural killer cell TRUE +cNK--RBC-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cNK--RBC-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +cvEndo CL:0002543 vein endothelial cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cvEndo', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell FALSE +cvLSEC CL:0019022 endothelial cell of pericentral hepatic sinusoid DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cvLSEC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0019022 endothelial cell of pericentral hepatic sinusoid TRUE +cvLSEC--T-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'cvLSEC--T-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +lrNK CL:2000054 hepatic pit cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'lrNK', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:4047101 liver-resident natural killer cell FALSE +pDC CL:0000784 plasmacytoid dendritic cell DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'pDC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell TRUE +ppLSEC CL:0019021 endothelial cell of periportal hepatic sinusoid DOI:10.1016/j.jhep.2023.12.023 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique {'name': 'ppLSEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0019021 endothelial cell of periportal hepatic sinusoid TRUE diff --git a/output/raw_output/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..fc2ea85 --- /dev/null +++ b/output/raw_output/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,203 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +ATL CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'ATL', 'full_name': 'ascending thin limbs', 'paper_synonyms': '', 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell +Adaptive / Maladaptive / Repairing Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Adaptive / Maladaptive / Repairing Fibroblast', 'full_name': 'adaptive fibroblast', 'paper_synonyms': 'aFIB', 'tissue_context': ''} CL:0000057 fibroblast +Adaptive / Maladaptive / Repairing Proximal Tubule Epithelial Cell CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Adaptive / Maladaptive / Repairing Proximal Tubule Epithelial Cell', 'full_name': 'adaptive proximal tubule (aPT) epithelial cell (successful or maladaptive tubular repair)', 'paper_synonyms': 'aPT; aEpi; Ad/Mal; PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +Adaptive / Maladaptive / Repairing Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Adaptive / Maladaptive / Repairing Thick Ascending Limb Cell', 'full_name': 'adaptive (successful or maladaptive repair) thick ascending limb cell (aTAL)', 'paper_synonyms': 'aTAL; adaptive epithelial (aEpi); Ad/Mal', 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell +Afferent / Efferent Arteriole Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Afferent / Efferent Arteriole Endothelial Cell', 'full_name': 'endothelial cell of the afferent/efferent arterioles (EC-AEA)', 'paper_synonyms': 'EC-AEA', 'tissue_context': ''} CL:1000412 endothelial cell of arteriole +Ascending Thin Limb Cell CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Ascending Thin Limb Cell', 'full_name': 'ascending thin limb cell', 'paper_synonyms': 'ATL', 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell +Ascending Vasa Recta Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Ascending Vasa Recta Endothelial Cell', 'full_name': 'ascending vasa recta endothelial cell', 'paper_synonyms': 'EC-AVR', 'tissue_context': ''} CL:1001131 vasa recta ascending limb cell +B CL:0000236 B cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'B', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +B Cell CL:0000236 B cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'B Cell', 'full_name': 'B cell', 'paper_synonyms': 'B', 'tissue_context': ''} CL:0000236 B cell +C-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'C-IC-A', 'full_name': 'cortical intercalated cell A', 'paper_synonyms': '', 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell +C-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'C-PC', 'full_name': 'cortical principal cell', 'paper_synonyms': 'PC; principal cells', 'tissue_context': ''} CL:1000714 kidney cortex collecting duct principal cell +C-TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'C-TAL', 'full_name': 'cortical thick ascending limb', 'paper_synonyms': 'thick ascending limb (TAL)', 'tissue_context': ''} CL:1001109 kidney loop of Henle cortical thick ascending limb epithelial cell +CCD-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CCD-IC-A', 'full_name': 'cortical collecting duct intercalated cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1000715 kidney cortex collecting duct intercalated cell +CCD-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CCD-PC', 'full_name': 'cortical collecting duct principal cell', 'paper_synonyms': 'CCD; cortical collecting duct; PC; principal cells', 'tissue_context': ''} CL:1000714 kidney cortex collecting duct principal cell +CNT CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CNT', 'full_name': 'connecting tubule', 'paper_synonyms': None, 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +CNT-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CNT-IC-A', 'full_name': 'connecting tubule intercalated cell', 'paper_synonyms': 'CNT-IC; IC', 'tissue_context': ''} CL:4030019 kidney connecting tubule intercalated cell +CNT-PC CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CNT-PC', 'full_name': 'connecting tubule principal cell', 'paper_synonyms': 'CNT; connecting tubule; PC; principal cells', 'tissue_context': ''} CL:4030018 kidney connecting tubule principal cell +Classical Dendritic Cell CL:0000990 conventional dendritic cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Classical Dendritic Cell', 'full_name': 'classical dendritic cell', 'paper_synonyms': 'cDC', 'tissue_context': ''} CL:0000990 conventional dendritic cell +Connecting Tubule Cell CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Connecting Tubule Cell', 'full_name': 'connecting tubule cell', 'paper_synonyms': 'CNT', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +Connecting Tubule Intercalated Cell Type A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Connecting Tubule Intercalated Cell Type A', 'full_name': 'Connecting Tubule Intercalated Cell Type A', 'paper_synonyms': 'CNT-IC; IC; CNT', 'tissue_context': ''} CL:4030020 kidney connecting tubule alpha-intercalated cell +Connecting Tubule Principal Cell CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Connecting Tubule Principal Cell', 'full_name': 'Connecting tubule principal cell', 'paper_synonyms': 'CNT-PC; CNT; PC', 'tissue_context': ''} CL:4030018 kidney connecting tubule principal cell +Cortical Collecting Duct Intercalated Cell Type A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cortical Collecting Duct Intercalated Cell Type A', 'full_name': 'Cortical collecting duct intercalated cell type A', 'paper_synonyms': 'CCD; IC; collecting duct (CD)', 'tissue_context': ''} CL:4030015 kidney collecting duct alpha-intercalated cell +Cortical Collecting Duct Principal Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cortical Collecting Duct Principal Cell', 'full_name': 'cortical collecting duct principal cell', 'paper_synonyms': 'C-PC; PC', 'tissue_context': ''} CL:1000714 kidney cortex collecting duct principal cell +Cortical Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cortical Thick Ascending Limb Cell', 'full_name': 'cortical thick ascending limb (C-TAL) cell', 'paper_synonyms': 'C-TAL; TAL', 'tissue_context': ''} CL:1001109 kidney loop of Henle cortical thick ascending limb epithelial cell +Cycling Connecting Tubule Cell CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Connecting Tubule Cell', 'full_name': 'cycling connecting tubule cell', 'paper_synonyms': 'CNT; Cyc', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +Cycling Distal Convoluted Tubule Cell CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Distal Convoluted Tubule Cell', 'full_name': 'Cycling Distal Convoluted Tubule Cell', 'paper_synonyms': 'DCT; DCT1; DCT2', 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell +Cycling Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Endothelial Cell', 'full_name': 'endothelial cell, cycling state', 'paper_synonyms': '', 'tissue_context': ''} CL:0000115 endothelial cell +Cycling Mononuclear Phagocyte CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Mononuclear Phagocyte', 'full_name': 'cycling mononuclear phagocyte', 'paper_synonyms': 'cycMNP', 'tissue_context': ''} CL:4033078 cycling mononuclear phagocyte +Cycling Myofibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Myofibroblast', 'full_name': 'cycling myofibroblast', 'paper_synonyms': 'cycMyoF', 'tissue_context': ''} CL:0000186 myofibroblast cell +Cycling Natural Killer Cell / Natural Killer T Cell CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Natural Killer Cell / Natural Killer T Cell', 'full_name': 'cycling natural killer cell / natural killer T cell', 'paper_synonyms': 'NKT', 'tissue_context': ''} CL:4033071 cycling natural killer cell +Cycling Proximal Tubule Epithelial Cell CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Proximal Tubule Epithelial Cell', 'full_name': 'cycling proximal tubule epithelial cell', 'paper_synonyms': 'PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +DCT CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DCT', 'full_name': 'distal convoluted tubule', 'paper_synonyms': None, 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell +DCT1 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DCT1', 'full_name': 'distal convoluted tubule cell 1', 'paper_synonyms': 'DCT; distal convoluted tubule', 'tissue_context': ''} CL:4030016 epithelial cell of early distal convoluted tubule +DCT2 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DCT2', 'full_name': 'distal convoluted tubule cell 2', 'paper_synonyms': 'DCT', 'tissue_context': ''} CL:4030017 epithelial cell of late distal convoluted tubule +DTL CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DTL', 'full_name': 'descending thin limb', 'paper_synonyms': None, 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +DTL1 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DTL1', 'full_name': 'descending thin limb 1', 'paper_synonyms': 'DTL; descending thin limb', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +DTL2 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DTL2', 'full_name': 'descending thin limb cell type 2', 'paper_synonyms': None, 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +DTL3 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DTL3', 'full_name': 'descending thin limb 3', 'paper_synonyms': 'DTL', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +Degenerative Ascending Thin Limb Cell CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Ascending Thin Limb Cell', 'full_name': 'Degenerative ascending thin limb cell', 'paper_synonyms': 'ATL', 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell +Degenerative Connecting Tubule Cell CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Connecting Tubule Cell', 'full_name': 'Degenerative connecting tubule cell', 'paper_synonyms': 'CNT', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +Degenerative Cortical Intercalated Cell Type A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Cortical Intercalated Cell Type A', 'full_name': 'Degenerative cortical intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:1000715 kidney cortex collecting duct intercalated cell +Degenerative Cortical Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Cortical Thick Ascending Limb Cell', 'full_name': 'degenerative cortical thick ascending limb cell', 'paper_synonyms': 'C-TAL; cortical TAL', 'tissue_context': ''} CL:1001109 kidney loop of Henle cortical thick ascending limb epithelial cell +Degenerative Descending Thin Limb Cell Type 3 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Descending Thin Limb Cell Type 3', 'full_name': 'degenerative descending thin limb cell type 3', 'paper_synonyms': 'DTL3', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +Degenerative Distal Convoluted Tubule Cell CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Distal Convoluted Tubule Cell', 'full_name': 'degenerative distal convoluted tubule cell', 'paper_synonyms': 'DCT', 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell +Degenerative Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Endothelial Cell', 'full_name': 'Degenerative Endothelial Cell', 'paper_synonyms': 'EC-AEA; EC-GC; EC-LYM; EC-AVR; EC-DVR; EC', 'tissue_context': ''} CL:0000115 endothelial cell +Degenerative Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Fibroblast', 'full_name': 'degenerative fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:0000057 fibroblast +Degenerative Inner Medullary Collecting Duct Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Inner Medullary Collecting Duct Cell', 'full_name': 'degenerative inner medullary collecting duct cell', 'paper_synonyms': 'IMCD; CD', 'tissue_context': ''} CL:1000547 kidney inner medulla collecting duct epithelial cell +Degenerative Medullary Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Medullary Fibroblast', 'full_name': 'Degenerative Medullary Fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:4030022 renal medullary fibroblast +Degenerative Medullary Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Medullary Thick Ascending Limb Cell', 'full_name': 'degenerative medullary thick ascending limb cell', 'paper_synonyms': 'TAL; M-TAL', 'tissue_context': ''} CL:1001108 kidney loop of Henle medullary thick ascending limb epithelial cell +Degenerative Outer Medullary Collecting Duct Principal Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Outer Medullary Collecting Duct Principal Cell', 'full_name': 'Degenerative Outer Medullary Collecting Duct Principal Cell', 'paper_synonyms': 'OMCD; PC; degenerative medullary principal cells; dM-PCs', 'tissue_context': ''} CL:1000716 kidney outer medulla collecting duct principal cell +Degenerative Peritubular Capilary Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Peritubular Capilary Endothelial Cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell +Degenerative Podocyte CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Podocyte', 'full_name': 'Degenerative Podocyte', 'paper_synonyms': 'POD; PODs', 'tissue_context': ''} CL:0000653 podocyte +Degenerative Proximal Tubule Epithelial Cell CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Proximal Tubule Epithelial Cell', 'full_name': 'degenerative proximal tubule (PT) epithelial cell', 'paper_synonyms': 'PT; degen', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +Degenerative Vascular Smooth Muscle Cell CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Vascular Smooth Muscle Cell', 'full_name': 'degenerative vascular smooth muscle cell', 'paper_synonyms': 'VSMC; VSM/P', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell +Descending Thin Limb Cell Type 1 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Descending Thin Limb Cell Type 1', 'full_name': 'descending thin limb cell type 1', 'paper_synonyms': 'DTL1', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +Descending Thin Limb Cell Type 2 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Descending Thin Limb Cell Type 2', 'full_name': 'descending thin limb cell type 2 (DTL2)', 'paper_synonyms': 'DTL2', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +Descending Thin Limb Cell Type 3 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Descending Thin Limb Cell Type 3', 'full_name': 'descending thin limb cell type 3', 'paper_synonyms': 'DTL3; DTL', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +Descending Vasa Recta Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Descending Vasa Recta Endothelial Cell', 'full_name': 'Descending vasa recta endothelial cell', 'paper_synonyms': 'EC-DVR', 'tissue_context': ''} CL:1000892 kidney capillary endothelial cell +Distal Convoluted Tubule Cell Type 1 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Distal Convoluted Tubule Cell Type 1', 'full_name': 'Distal convoluted tubule cell type 1', 'paper_synonyms': 'DCT1', 'tissue_context': ''} CL:4030016 epithelial cell of early distal convoluted tubule +Distal Convoluted Tubule Cell Type 2 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Distal Convoluted Tubule Cell Type 2', 'full_name': 'distal convoluted tubule cell 2', 'paper_synonyms': 'DCT2', 'tissue_context': ''} CL:4030017 epithelial cell of late distal convoluted tubule +EC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC', 'full_name': 'endothelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +EC-AEA CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-AEA', 'full_name': 'endothelial cells of the afferent/efferent arterioles', 'paper_synonyms': None, 'tissue_context': ''} CL:1000412 endothelial cell of arteriole +EC-AVR CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-AVR', 'full_name': 'endothelial cell of the vasa recta', 'paper_synonyms': '', 'tissue_context': ''} CL:1000892 kidney capillary endothelial cell +EC-DVR CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-DVR', 'full_name': 'endothelial cells of the vasa recta', 'paper_synonyms': '', 'tissue_context': ''} CL:1000892 kidney capillary endothelial cell +EC-GC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-GC', 'full_name': 'glomerular capillaries', 'paper_synonyms': '', 'tissue_context': ''} CL:1001005 glomerular capillary endothelial cell +EC-LYM CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-LYM', 'full_name': 'endothelial cells of the lymphatics', 'paper_synonyms': None, 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel +EC-PTC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-PTC', 'full_name': 'endothelial cell PTC', 'paper_synonyms': 'EC; endothelial cells', 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell +FIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'FIB', 'full_name': 'fibroblast', 'paper_synonyms': 'fibroblast (FIB)', 'tissue_context': ''} CL:0000057 fibroblast +Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Fibroblast', 'full_name': 'fibroblast (FIB)', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:0000057 fibroblast +Glomerular Capillary Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Glomerular Capillary Endothelial Cell', 'full_name': 'glomerular capillary endothelial cell', 'paper_synonyms': 'EC-GC', 'tissue_context': ''} CL:1001005 glomerular capillary endothelial cell +IC CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IC', 'full_name': 'intercalated cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0005010 renal intercalated cell +IC-B CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IC-B', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC; CNT-IC', 'tissue_context': ''} CL:0005010 renal intercalated cell +IMCD CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMCD', 'full_name': 'inner medullary collecting duct cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1000547 kidney inner medulla collecting duct epithelial cell +IMM CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:1000695 kidney interstitial alternatively activated macrophage DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0000775 neutrophil DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0000084 T cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0000786 plasma cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0000875 non-classical monocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0000990 conventional dendritic cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0000097 mast cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0000236 B cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +IMM CL:0001058 plasmacytoid dendritic cell, human DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte +Inner Medullary Collecting Duct Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Inner Medullary Collecting Duct Cell', 'full_name': 'inner medullary collecting duct cell', 'paper_synonyms': 'IMCD', 'tissue_context': ''} CL:1000547 kidney inner medulla collecting duct epithelial cell +Intercalated Cell Type B CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Intercalated Cell Type B', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:0005010 renal intercalated cell +Lymphatic Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Lymphatic Endothelial Cell', 'full_name': 'endothelial cell of the lymphatics', 'paper_synonyms': 'EC-LYM', 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel +M-FIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M-FIB', 'full_name': 'medullary fibroblast', 'paper_synonyms': '', 'tissue_context': ''} CL:4030022 renal medullary fibroblast +M-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M-IC-A', 'full_name': 'medullary intercalated cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1001432 kidney collecting duct intercalated cell +M-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M-PC', 'full_name': 'medullary principal cell', 'paper_synonyms': 'principal cell (PC)', 'tissue_context': ''} CL:1001431 kidney collecting duct principal cell +M-TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M-TAL', 'full_name': 'medullary thick ascending limb', 'paper_synonyms': '', 'tissue_context': ''} CL:1001108 kidney loop of Henle medullary thick ascending limb epithelial cell +M2 Macrophage CL:1000695 kidney interstitial alternatively activated macrophage DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M2 Macrophage', 'full_name': 'M2 macrophage', 'paper_synonyms': 'MAC-M2', 'tissue_context': ''} CL:0000890 alternatively activated macrophage +MAC-M2 CL:1000695 kidney interstitial alternatively activated macrophage DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MAC-M2', 'full_name': 'M2 macrophage', 'paper_synonyms': 'M2 macrophages', 'tissue_context': ''} CL:0000890 alternatively activated macrophage +MAST CL:0000097 mast cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MAST', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell +MC CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell +MD CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MD', 'full_name': 'macula densa cells', 'paper_synonyms': 'Macula Densa', 'tissue_context': ''} CL:1000850 macula densa epithelial cell +MDC CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MDC', 'full_name': 'monocyte-derived cells', 'paper_synonyms': 'MDCs', 'tissue_context': ''} CL:0000782 myeloid dendritic cell +MYOF CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MYOF', 'full_name': 'myofibroblasts', 'paper_synonyms': 'MyoF', 'tissue_context': ''} CL:0000186 myofibroblast cell +Macula Densa Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Macula Densa Cell', 'full_name': 'macula densa cell', 'paper_synonyms': 'MD', 'tissue_context': ''} CL:1000850 macula densa epithelial cell +Mast Cell CL:0000097 mast cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Mast Cell', 'full_name': 'mast cell', 'paper_synonyms': 'MAST', 'tissue_context': ''} CL:0000097 mast cell +Medullary Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Medullary Fibroblast', 'full_name': 'medullary fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:0000057 fibroblast +Medullary Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Medullary Thick Ascending Limb Cell', 'full_name': 'Medullary thick ascending limb cell', 'paper_synonyms': 'M-TAL; thick ascending limb (TAL)', 'tissue_context': ''} CL:1001108 kidney loop of Henle medullary thick ascending limb epithelial cell +Mesangial Cell CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Mesangial Cell', 'full_name': 'mesangial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000650 mesangial cell +Monocyte-derived Cell CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Monocyte-derived Cell', 'full_name': 'monocyte-derived cell', 'paper_synonyms': 'MDCs', 'tissue_context': ''} NO MATCH found +Myofibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Myofibroblast', 'full_name': 'myofibroblast', 'paper_synonyms': 'MyoF', 'tissue_context': ''} CL:0000186 myofibroblast cell +N CL:0000775 neutrophil DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'N', 'full_name': 'neutrophils', 'paper_synonyms': 'MPO+ cells', 'tissue_context': ''} CL:0000775 neutrophil +NEU CL:0002319 neural cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'NEU', 'full_name': 'neuronal cell', 'paper_synonyms': 'SCI/NEU; Schwann/neuronal', 'tissue_context': ''} CL:0000540 neuron +NKC/T CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'NKC/T', 'full_name': 'T cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000084 T cell +Natural Killer Cell / Natural Killer T Cell CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Natural Killer Cell / Natural Killer T Cell', 'full_name': 'Natural killer cell / natural killer T cell', 'paper_synonyms': 'NKT', 'tissue_context': ''} CL:0000623 natural killer cell +Neutrophil CL:0000775 neutrophil DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': 'neutrophil', 'paper_synonyms': 'N', 'tissue_context': ''} CL:0000775 neutrophil +Non-classical Monocyte CL:0000875 non-classical monocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Non-classical Monocyte', 'full_name': 'non-classical monocyte', 'paper_synonyms': 'ncMON', 'tissue_context': ''} CL:0000875 non-classical monocyte +OMCD-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'OMCD-IC-A', 'full_name': 'outer medullary collecting duct intercalated cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1000717 kidney outer medulla collecting duct intercalated cell +OMCD-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'OMCD-PC', 'full_name': 'outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; outer medullary collecting duct; PC; principal cells', 'tissue_context': ''} CL:1000716 kidney outer medulla collecting duct principal cell +Outer Medullary Collecting Duct Intercalated Cell Type A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Outer Medullary Collecting Duct Intercalated Cell Type A', 'full_name': 'outer medullary collecting duct intercalated cell', 'paper_synonyms': 'OMCD; IC', 'tissue_context': ''} CL:1000717 kidney outer medulla collecting duct intercalated cell +Outer Medullary Collecting Duct Principal Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Outer Medullary Collecting Duct Principal Cell', 'full_name': 'outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; PC; M-PC', 'tissue_context': ''} CL:1000716 kidney outer medulla collecting duct principal cell +PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PC', 'full_name': 'principal cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0005009 renal principal cell +PEC CL:1000452 parietal epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PEC', 'full_name': 'parietal epithelial cells', 'paper_synonyms': '', 'tissue_context': ''} CL:1000452 parietal epithelial cell +PL CL:0000786 plasma cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PL', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +POD CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'POD', 'full_name': 'podocytes', 'paper_synonyms': 'PODs', 'tissue_context': ''} CL:0000653 podocyte +PT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PT', 'full_name': 'proximal tubule', 'paper_synonyms': 'proximal tubule (PT)', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +PT-S1/2 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PT-S1/2', 'full_name': 'proximal tubule S1/2', 'paper_synonyms': 'PT; proximal tubule', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +PT-S3 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PT-S3', 'full_name': 'proximal tubule S3', 'paper_synonyms': 'proximal tubule (PT)', 'tissue_context': ''} CL:4030011 epithelial cell of proximal tubule segment 3 +PapE CL:1000597 papillary tips cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PapE', 'full_name': 'papillary tip epithelial cells abutting the calyx', 'paper_synonyms': '', 'tissue_context': ''} CL:1000597 papillary tips cell +Papillary Tip Epithelial Cell CL:1000597 papillary tips cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Papillary Tip Epithelial Cell', 'full_name': 'papillary tip epithelial cell', 'paper_synonyms': 'PapE', 'tissue_context': ''} CL:1000597 papillary tips cell +Parietal Epithelial Cell CL:1000452 parietal epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Parietal Epithelial Cell', 'full_name': 'parietal epithelial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1000452 parietal epithelial cell +Peritubular Capilary Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Peritubular Capilary Endothelial Cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell +Plasma Cell CL:0000786 plasma cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Plasma Cell', 'full_name': 'Plasma cell', 'paper_synonyms': 'PL', 'tissue_context': ''} CL:0000786 plasma cell +Plasmacytoid Dendritic Cell CL:0001058 plasmacytoid dendritic cell, human DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Plasmacytoid Dendritic Cell', 'full_name': 'plasmacytoid dendritic cell', 'paper_synonyms': 'pDC', 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell +Podocyte CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Podocyte', 'full_name': 'podocyte (POD)', 'paper_synonyms': 'POD; PODs', 'tissue_context': ''} CL:0000653 podocyte +Proximal Tubule Epithelial Cell Segment 1 / Segment 2 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Proximal Tubule Epithelial Cell Segment 1 / Segment 2', 'full_name': 'proximal tubule (PT) epithelial cell, segment 1/segment 2', 'paper_synonyms': 'PT-S1; PT-S2; PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +Proximal Tubule Epithelial Cell Segment 3 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Proximal Tubule Epithelial Cell Segment 3', 'full_name': 'proximal tubule (PT) epithelial cell, segment 3', 'paper_synonyms': 'PT-S3; PT', 'tissue_context': ''} CL:4030011 epithelial cell of proximal tubule segment 3 +REN CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'REN', 'full_name': 'juxtaglomerular renin-producing granular cell', 'paper_synonyms': 'renin-producing granular cells; juxtaglomerular renin-producing granular cells', 'tissue_context': ''} CL:0000648 kidney granular cell +Renin-positive Juxtaglomerular Granular Cell CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Renin-positive Juxtaglomerular Granular Cell', 'full_name': 'Juxtaglomerular renin-producing granular cell', 'paper_synonyms': 'REN; renin-producing granular cell', 'tissue_context': ''} CL:0000648 kidney granular cell +SC/NEU CL:0002319 neural cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'SC/NEU', 'full_name': 'Schwann/neuronal', 'paper_synonyms': 'SCI/NEU', 'tissue_context': ''} CL:0002319 neural cell +Schwann Cell / Neural CL:0002319 neural cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Schwann Cell / Neural', 'full_name': 'Schwann/neuronal cell', 'paper_synonyms': 'Schwann/neuronal; SCI/NEU', 'tissue_context': ''} CL:0002319 neural cell +T CL:0000084 T cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'T', 'full_name': 'T cell', 'paper_synonyms': 'CD3+ cells', 'tissue_context': ''} CL:0000084 T cell +T Cell CL:0000084 T cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'T Cell', 'full_name': 'T cell', 'paper_synonyms': 'CD3+ cells; lymphoid (T) cells; T', 'tissue_context': ''} CL:0000084 T cell +TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'TAL', 'full_name': 'thick ascending limb', 'paper_synonyms': 'thick ascending limb (TAL)', 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell +Transitional Principal-Intercalated Cell CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Transitional Principal-Intercalated Cell', 'full_name': 'Transitional principal–intercalated cell', 'paper_synonyms': 'transitioning principal and intercalated cells; PC, principal cells; IC, intercalated cells', 'tissue_context': ''} CL:1001225 kidney collecting duct cell +VSM/P CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'VSM/P', 'full_name': 'vascular smooth muscle cell or pericyte', 'paper_synonyms': 'VSMC', 'tissue_context': ''} CL:0008034 mural cell +VSMC CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'VSMC', 'full_name': 'vascular smooth muscle cell', 'paper_synonyms': 'VSM/P', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell +VSMC/P CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'VSMC/P', 'full_name': 'vascular smooth muscle cell or pericyte', 'paper_synonyms': 'VSM/P', 'tissue_context': ''} CL:4033054 perivascular cell +Vascular Smooth Muscle Cell CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Vascular Smooth Muscle Cell', 'full_name': 'vascular smooth muscle cell', 'paper_synonyms': 'VSMC; VSM/P', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell +Vascular Smooth Muscle Cell / Pericyte CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Vascular Smooth Muscle Cell / Pericyte', 'full_name': 'vascular smooth muscle cell or pericyte', 'paper_synonyms': 'VSM/P; VSMC', 'tissue_context': ''} CL:4033054 perivascular cell +aFIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'aFIB', 'full_name': 'adaptive fibroblast', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +aPT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'aPT', 'full_name': 'adaptive proximal tubule', 'paper_synonyms': '', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +aTAL1 CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'aTAL1', 'full_name': 'adaptive thick ascending limb 1', 'paper_synonyms': 'aTAL', 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell +aTAL2 CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'aTAL2', 'full_name': 'adaptive thick ascending limb cell 2', 'paper_synonyms': 'adaptive TAL; aTAL', 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell +cDC CL:0000990 conventional dendritic cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cDC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000990 conventional dendritic cell +cycCNT CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycCNT', 'full_name': 'cycling connecting tubule cell', 'paper_synonyms': 'CNT', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +cycDCT CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycDCT', 'full_name': 'cycling distal convoluted tubule', 'paper_synonyms': 'DCT', 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell +cycEC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycEC', 'full_name': 'cycling endothelial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +cycMNP CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycMNP', 'full_name': 'cycling MNP', 'paper_synonyms': '', 'tissue_context': ''} CL:4033078 cycling mononuclear phagocyte +cycMYOF CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycMYOF', 'full_name': 'cycling myofibroblasts', 'paper_synonyms': 'cycMyoF; cycling MyoF', 'tissue_context': ''} CL:0000186 myofibroblast cell +cycNKC/T CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycNKC/T', 'full_name': 'cycling T cells', 'paper_synonyms': None, 'tissue_context': ''} CL:4033069 cycling T cell +cycPT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycPT', 'full_name': 'cycling proximal tubule cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +dATL CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dATL', 'full_name': 'ascending thin limb', 'paper_synonyms': 'ATL', 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell +dC-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dC-IC-A', 'full_name': 'degenerative cortical intercalated cell A', 'paper_synonyms': 'intercalated cells (IC)', 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell +dC-TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dC-TAL', 'full_name': 'degenerative cortical thick ascending limb cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1001109 kidney loop of Henle cortical thick ascending limb epithelial cell +dCNT CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dCNT', 'full_name': 'degenerative connecting tubule cell', 'paper_synonyms': 'connecting tubules (CNT)', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +dDCT CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dDCT', 'full_name': 'degenerative distal convoluted tubule cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell +dDTL3 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dDTL3', 'full_name': 'degenerative descending thin limb 3', 'paper_synonyms': 'DTL3; DTL; descending thin limb', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell +dEC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dEC', 'full_name': 'degenerative endothelial cell', 'paper_synonyms': 'EC', 'tissue_context': ''} CL:0000115 endothelial cell +dEC-PTC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dEC-PTC', 'full_name': 'degenerative endothelial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +dFIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dFIB', 'full_name': 'degenerative fibroblast', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +dIMCD CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dIMCD', 'full_name': 'degenerative inner medullary collecting duct cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1000547 kidney inner medulla collecting duct epithelial cell +dM-FIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dM-FIB', 'full_name': 'degenerative medullary fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:4030022 renal medullary fibroblast +dM-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dM-PC', 'full_name': 'degenerative medullary principal cell', 'paper_synonyms': 'degenerative medullary principal cells (dM-PCs)', 'tissue_context': ''} CL:1001431 kidney collecting duct principal cell +dM-TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dM-TAL', 'full_name': 'degenerative medullary thick ascending limb cell', 'paper_synonyms': '', 'tissue_context': ''} CL:1001108 kidney loop of Henle medullary thick ascending limb epithelial cell +dOMCD-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dOMCD-PC', 'full_name': 'degenerative outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; outer medullary collecting duct; PC; principal cells', 'tissue_context': ''} CL:1000716 kidney outer medulla collecting duct principal cell +dPOD CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dPOD', 'full_name': 'degenerative podocyte', 'paper_synonyms': 'PODs', 'tissue_context': ''} CL:0000653 podocyte +dPT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dPT', 'full_name': 'degenerative proximal tubule', 'paper_synonyms': '', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +dVSMC CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dVSMC', 'full_name': 'vascular smooth muscle cell', 'paper_synonyms': 'VSMC; VSM/P', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell +endothelial cells CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'endothelial cells', 'full_name': 'endothelial cells', 'paper_synonyms': 'EC; endothelium', 'tissue_context': ''} CL:0000115 endothelial cell +epithelial cells CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1000452 parietal epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +epithelial cells CL:1000597 papillary tips cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +immune cells CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:1000695 kidney interstitial alternatively activated macrophage DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0000775 neutrophil DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0000084 T cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0000786 plasma cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0000875 non-classical monocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0000990 conventional dendritic cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0000097 mast cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0000236 B cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +immune cells CL:0001058 plasmacytoid dendritic cell, human DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte +ncMON CL:0000875 non-classical monocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'ncMON', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000875 non-classical monocyte +neural cells CL:0002319 neural cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'neural cells', 'full_name': 'neural cells', 'paper_synonyms': 'NEU; SCI/NEU; Schwann/neuronal', 'tissue_context': ''} CL:0002319 neural cell +pDC CL:0001058 plasmacytoid dendritic cell, human DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'pDC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell +stroma cells CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'stroma cells', 'full_name': 'stromal cells', 'paper_synonyms': 'STR; stroma', 'tissue_context': ''} CL:0000499 stromal cell +stroma cells CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'stroma cells', 'full_name': 'stromal cells', 'paper_synonyms': 'STR; stroma', 'tissue_context': ''} CL:0000499 stromal cell +tPC-IC CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'tPC-IC', 'full_name': 'transitioning principal and intercalated cells', 'paper_synonyms': '', 'tissue_context': ''} CL:1001225 kidney collecting duct cell diff --git a/output/raw_output/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique/groundings.tsv b/output/raw_output/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..b6b46ab --- /dev/null +++ b/output/raw_output/0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,203 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +ATL CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'ATL', 'full_name': 'ascending thin limbs', 'paper_synonyms': '', 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell TRUE +Adaptive / Maladaptive / Repairing Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Adaptive / Maladaptive / Repairing Fibroblast', 'full_name': 'adaptive fibroblast', 'paper_synonyms': 'aFIB', 'tissue_context': ''} CL:0000057 fibroblast FALSE +Adaptive / Maladaptive / Repairing Proximal Tubule Epithelial Cell CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Adaptive / Maladaptive / Repairing Proximal Tubule Epithelial Cell', 'full_name': 'adaptive proximal tubule (aPT) epithelial cell (successful or maladaptive tubular repair)', 'paper_synonyms': 'aPT; aEpi; Ad/Mal; PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +Adaptive / Maladaptive / Repairing Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Adaptive / Maladaptive / Repairing Thick Ascending Limb Cell', 'full_name': 'adaptive (successful or maladaptive repair) thick ascending limb cell (aTAL)', 'paper_synonyms': 'aTAL; adaptive epithelial (aEpi); Ad/Mal', 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell TRUE +Afferent / Efferent Arteriole Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Afferent / Efferent Arteriole Endothelial Cell', 'full_name': 'endothelial cell of the afferent/efferent arterioles (EC-AEA)', 'paper_synonyms': 'EC-AEA', 'tissue_context': ''} CL:1000412 endothelial cell of arteriole FALSE +Ascending Thin Limb Cell CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Ascending Thin Limb Cell', 'full_name': 'ascending thin limb cell', 'paper_synonyms': 'ATL', 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell TRUE +Ascending Vasa Recta Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Ascending Vasa Recta Endothelial Cell', 'full_name': 'ascending vasa recta endothelial cell', 'paper_synonyms': 'EC-AVR', 'tissue_context': ''} CL:1001131 vasa recta ascending limb cell FALSE +B CL:0000236 B cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'B', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell TRUE +B Cell CL:0000236 B cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'B Cell', 'full_name': 'B cell', 'paper_synonyms': 'B', 'tissue_context': ''} CL:0000236 B cell TRUE +C-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'C-IC-A', 'full_name': 'cortical intercalated cell A', 'paper_synonyms': '', 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell FALSE +C-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'C-PC', 'full_name': 'cortical principal cell', 'paper_synonyms': 'PC; principal cells', 'tissue_context': ''} CL:1000714 kidney cortex collecting duct principal cell FALSE +C-TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'C-TAL', 'full_name': 'cortical thick ascending limb', 'paper_synonyms': 'thick ascending limb (TAL)', 'tissue_context': ''} CL:1001109 kidney loop of Henle cortical thick ascending limb epithelial cell FALSE +CCD-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CCD-IC-A', 'full_name': 'cortical collecting duct intercalated cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1000715 kidney cortex collecting duct intercalated cell FALSE +CCD-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CCD-PC', 'full_name': 'cortical collecting duct principal cell', 'paper_synonyms': 'CCD; cortical collecting duct; PC; principal cells', 'tissue_context': ''} CL:1000714 kidney cortex collecting duct principal cell FALSE +CNT CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CNT', 'full_name': 'connecting tubule', 'paper_synonyms': None, 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell TRUE +CNT-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CNT-IC-A', 'full_name': 'connecting tubule intercalated cell', 'paper_synonyms': 'CNT-IC; IC', 'tissue_context': ''} CL:4030019 kidney connecting tubule intercalated cell FALSE +CNT-PC CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'CNT-PC', 'full_name': 'connecting tubule principal cell', 'paper_synonyms': 'CNT; connecting tubule; PC; principal cells', 'tissue_context': ''} CL:4030018 kidney connecting tubule principal cell FALSE +Classical Dendritic Cell CL:0000990 conventional dendritic cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Classical Dendritic Cell', 'full_name': 'classical dendritic cell', 'paper_synonyms': 'cDC', 'tissue_context': ''} CL:0000990 conventional dendritic cell TRUE +Connecting Tubule Cell CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Connecting Tubule Cell', 'full_name': 'connecting tubule cell', 'paper_synonyms': 'CNT', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell TRUE +Connecting Tubule Intercalated Cell Type A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Connecting Tubule Intercalated Cell Type A', 'full_name': 'Connecting Tubule Intercalated Cell Type A', 'paper_synonyms': 'CNT-IC; IC; CNT', 'tissue_context': ''} CL:4030020 kidney connecting tubule alpha-intercalated cell FALSE +Connecting Tubule Principal Cell CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Connecting Tubule Principal Cell', 'full_name': 'Connecting tubule principal cell', 'paper_synonyms': 'CNT-PC; CNT; PC', 'tissue_context': ''} CL:4030018 kidney connecting tubule principal cell FALSE +Cortical Collecting Duct Intercalated Cell Type A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cortical Collecting Duct Intercalated Cell Type A', 'full_name': 'Cortical collecting duct intercalated cell type A', 'paper_synonyms': 'CCD; IC; collecting duct (CD)', 'tissue_context': ''} CL:4030015 kidney collecting duct alpha-intercalated cell FALSE +Cortical Collecting Duct Principal Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cortical Collecting Duct Principal Cell', 'full_name': 'cortical collecting duct principal cell', 'paper_synonyms': 'C-PC; PC', 'tissue_context': ''} CL:1000714 kidney cortex collecting duct principal cell FALSE +Cortical Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cortical Thick Ascending Limb Cell', 'full_name': 'cortical thick ascending limb (C-TAL) cell', 'paper_synonyms': 'C-TAL; TAL', 'tissue_context': ''} CL:1001109 kidney loop of Henle cortical thick ascending limb epithelial cell FALSE +Cycling Connecting Tubule Cell CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Connecting Tubule Cell', 'full_name': 'cycling connecting tubule cell', 'paper_synonyms': 'CNT; Cyc', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell TRUE +Cycling Distal Convoluted Tubule Cell CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Distal Convoluted Tubule Cell', 'full_name': 'Cycling Distal Convoluted Tubule Cell', 'paper_synonyms': 'DCT; DCT1; DCT2', 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell TRUE +Cycling Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Endothelial Cell', 'full_name': 'endothelial cell, cycling state', 'paper_synonyms': '', 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Cycling Mononuclear Phagocyte CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Mononuclear Phagocyte', 'full_name': 'cycling mononuclear phagocyte', 'paper_synonyms': 'cycMNP', 'tissue_context': ''} CL:4033078 cycling mononuclear phagocyte FALSE +Cycling Myofibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Myofibroblast', 'full_name': 'cycling myofibroblast', 'paper_synonyms': 'cycMyoF', 'tissue_context': ''} CL:0000186 myofibroblast cell FALSE +Cycling Natural Killer Cell / Natural Killer T Cell CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Natural Killer Cell / Natural Killer T Cell', 'full_name': 'cycling natural killer cell / natural killer T cell', 'paper_synonyms': 'NKT', 'tissue_context': ''} CL:4033071 cycling natural killer cell FALSE +Cycling Proximal Tubule Epithelial Cell CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Cycling Proximal Tubule Epithelial Cell', 'full_name': 'cycling proximal tubule epithelial cell', 'paper_synonyms': 'PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +DCT CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DCT', 'full_name': 'distal convoluted tubule', 'paper_synonyms': None, 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell TRUE +DCT1 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DCT1', 'full_name': 'distal convoluted tubule cell 1', 'paper_synonyms': 'DCT; distal convoluted tubule', 'tissue_context': ''} CL:4030016 epithelial cell of early distal convoluted tubule FALSE +DCT2 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DCT2', 'full_name': 'distal convoluted tubule cell 2', 'paper_synonyms': 'DCT', 'tissue_context': ''} CL:4030017 epithelial cell of late distal convoluted tubule FALSE +DTL CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DTL', 'full_name': 'descending thin limb', 'paper_synonyms': None, 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +DTL1 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DTL1', 'full_name': 'descending thin limb 1', 'paper_synonyms': 'DTL; descending thin limb', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +DTL2 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DTL2', 'full_name': 'descending thin limb cell type 2', 'paper_synonyms': None, 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +DTL3 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'DTL3', 'full_name': 'descending thin limb 3', 'paper_synonyms': 'DTL', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +Degenerative Ascending Thin Limb Cell CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Ascending Thin Limb Cell', 'full_name': 'Degenerative ascending thin limb cell', 'paper_synonyms': 'ATL', 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell TRUE +Degenerative Connecting Tubule Cell CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Connecting Tubule Cell', 'full_name': 'Degenerative connecting tubule cell', 'paper_synonyms': 'CNT', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell TRUE +Degenerative Cortical Intercalated Cell Type A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Cortical Intercalated Cell Type A', 'full_name': 'Degenerative cortical intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:1000715 kidney cortex collecting duct intercalated cell FALSE +Degenerative Cortical Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Cortical Thick Ascending Limb Cell', 'full_name': 'degenerative cortical thick ascending limb cell', 'paper_synonyms': 'C-TAL; cortical TAL', 'tissue_context': ''} CL:1001109 kidney loop of Henle cortical thick ascending limb epithelial cell FALSE +Degenerative Descending Thin Limb Cell Type 3 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Descending Thin Limb Cell Type 3', 'full_name': 'degenerative descending thin limb cell type 3', 'paper_synonyms': 'DTL3', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +Degenerative Distal Convoluted Tubule Cell CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Distal Convoluted Tubule Cell', 'full_name': 'degenerative distal convoluted tubule cell', 'paper_synonyms': 'DCT', 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell TRUE +Degenerative Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Endothelial Cell', 'full_name': 'Degenerative Endothelial Cell', 'paper_synonyms': 'EC-AEA; EC-GC; EC-LYM; EC-AVR; EC-DVR; EC', 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Degenerative Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Fibroblast', 'full_name': 'degenerative fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:0000057 fibroblast FALSE +Degenerative Inner Medullary Collecting Duct Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Inner Medullary Collecting Duct Cell', 'full_name': 'degenerative inner medullary collecting duct cell', 'paper_synonyms': 'IMCD; CD', 'tissue_context': ''} CL:1000547 kidney inner medulla collecting duct epithelial cell FALSE +Degenerative Medullary Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Medullary Fibroblast', 'full_name': 'Degenerative Medullary Fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:4030022 renal medullary fibroblast FALSE +Degenerative Medullary Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Medullary Thick Ascending Limb Cell', 'full_name': 'degenerative medullary thick ascending limb cell', 'paper_synonyms': 'TAL; M-TAL', 'tissue_context': ''} CL:1001108 kidney loop of Henle medullary thick ascending limb epithelial cell FALSE +Degenerative Outer Medullary Collecting Duct Principal Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Outer Medullary Collecting Duct Principal Cell', 'full_name': 'Degenerative Outer Medullary Collecting Duct Principal Cell', 'paper_synonyms': 'OMCD; PC; degenerative medullary principal cells; dM-PCs', 'tissue_context': ''} CL:1000716 kidney outer medulla collecting duct principal cell FALSE +Degenerative Peritubular Capilary Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Peritubular Capilary Endothelial Cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell FALSE +Degenerative Podocyte CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Podocyte', 'full_name': 'Degenerative Podocyte', 'paper_synonyms': 'POD; PODs', 'tissue_context': ''} CL:0000653 podocyte TRUE +Degenerative Proximal Tubule Epithelial Cell CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Proximal Tubule Epithelial Cell', 'full_name': 'degenerative proximal tubule (PT) epithelial cell', 'paper_synonyms': 'PT; degen', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +Degenerative Vascular Smooth Muscle Cell CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Degenerative Vascular Smooth Muscle Cell', 'full_name': 'degenerative vascular smooth muscle cell', 'paper_synonyms': 'VSMC; VSM/P', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell FALSE +Descending Thin Limb Cell Type 1 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Descending Thin Limb Cell Type 1', 'full_name': 'descending thin limb cell type 1', 'paper_synonyms': 'DTL1', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +Descending Thin Limb Cell Type 2 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Descending Thin Limb Cell Type 2', 'full_name': 'descending thin limb cell type 2 (DTL2)', 'paper_synonyms': 'DTL2', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +Descending Thin Limb Cell Type 3 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Descending Thin Limb Cell Type 3', 'full_name': 'descending thin limb cell type 3', 'paper_synonyms': 'DTL3; DTL', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +Descending Vasa Recta Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Descending Vasa Recta Endothelial Cell', 'full_name': 'Descending vasa recta endothelial cell', 'paper_synonyms': 'EC-DVR', 'tissue_context': ''} CL:1000892 kidney capillary endothelial cell FALSE +Distal Convoluted Tubule Cell Type 1 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Distal Convoluted Tubule Cell Type 1', 'full_name': 'Distal convoluted tubule cell type 1', 'paper_synonyms': 'DCT1', 'tissue_context': ''} CL:4030016 epithelial cell of early distal convoluted tubule FALSE +Distal Convoluted Tubule Cell Type 2 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Distal Convoluted Tubule Cell Type 2', 'full_name': 'distal convoluted tubule cell 2', 'paper_synonyms': 'DCT2', 'tissue_context': ''} CL:4030017 epithelial cell of late distal convoluted tubule FALSE +EC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC', 'full_name': 'endothelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +EC-AEA CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-AEA', 'full_name': 'endothelial cells of the afferent/efferent arterioles', 'paper_synonyms': None, 'tissue_context': ''} CL:1000412 endothelial cell of arteriole FALSE +EC-AVR CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-AVR', 'full_name': 'endothelial cell of the vasa recta', 'paper_synonyms': '', 'tissue_context': ''} CL:1000892 kidney capillary endothelial cell FALSE +EC-DVR CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-DVR', 'full_name': 'endothelial cells of the vasa recta', 'paper_synonyms': '', 'tissue_context': ''} CL:1000892 kidney capillary endothelial cell FALSE +EC-GC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-GC', 'full_name': 'glomerular capillaries', 'paper_synonyms': '', 'tissue_context': ''} CL:1001005 glomerular capillary endothelial cell FALSE +EC-LYM CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-LYM', 'full_name': 'endothelial cells of the lymphatics', 'paper_synonyms': None, 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel FALSE +EC-PTC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'EC-PTC', 'full_name': 'endothelial cell PTC', 'paper_synonyms': 'EC; endothelial cells', 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell FALSE +FIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'FIB', 'full_name': 'fibroblast', 'paper_synonyms': 'fibroblast (FIB)', 'tissue_context': ''} CL:0000057 fibroblast FALSE +Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Fibroblast', 'full_name': 'fibroblast (FIB)', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:0000057 fibroblast FALSE +Glomerular Capillary Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Glomerular Capillary Endothelial Cell', 'full_name': 'glomerular capillary endothelial cell', 'paper_synonyms': 'EC-GC', 'tissue_context': ''} CL:1001005 glomerular capillary endothelial cell FALSE +IC CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IC', 'full_name': 'intercalated cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0005010 renal intercalated cell FALSE +IC-B CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IC-B', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC; CNT-IC', 'tissue_context': ''} CL:0005010 renal intercalated cell FALSE +IMCD CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMCD', 'full_name': 'inner medullary collecting duct cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1000547 kidney inner medulla collecting duct epithelial cell FALSE +IMM CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:1000695 kidney interstitial alternatively activated macrophage DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0000775 neutrophil DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0000084 T cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0000786 plasma cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0000875 non-classical monocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0000990 conventional dendritic cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0000097 mast cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0000236 B cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +IMM CL:0001058 plasmacytoid dendritic cell, human DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'IMM', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes; immune cells', 'tissue_context': ''} CL:0000738 leukocyte FALSE +Inner Medullary Collecting Duct Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Inner Medullary Collecting Duct Cell', 'full_name': 'inner medullary collecting duct cell', 'paper_synonyms': 'IMCD', 'tissue_context': ''} CL:1000547 kidney inner medulla collecting duct epithelial cell FALSE +Intercalated Cell Type B CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Intercalated Cell Type B', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:0005010 renal intercalated cell FALSE +Lymphatic Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Lymphatic Endothelial Cell', 'full_name': 'endothelial cell of the lymphatics', 'paper_synonyms': 'EC-LYM', 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel FALSE +M-FIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M-FIB', 'full_name': 'medullary fibroblast', 'paper_synonyms': '', 'tissue_context': ''} CL:4030022 renal medullary fibroblast FALSE +M-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M-IC-A', 'full_name': 'medullary intercalated cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1001432 kidney collecting duct intercalated cell TRUE +M-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M-PC', 'full_name': 'medullary principal cell', 'paper_synonyms': 'principal cell (PC)', 'tissue_context': ''} CL:1001431 kidney collecting duct principal cell TRUE +M-TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M-TAL', 'full_name': 'medullary thick ascending limb', 'paper_synonyms': '', 'tissue_context': ''} CL:1001108 kidney loop of Henle medullary thick ascending limb epithelial cell FALSE +M2 Macrophage CL:1000695 kidney interstitial alternatively activated macrophage DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'M2 Macrophage', 'full_name': 'M2 macrophage', 'paper_synonyms': 'MAC-M2', 'tissue_context': ''} CL:0000890 alternatively activated macrophage FALSE +MAC-M2 CL:1000695 kidney interstitial alternatively activated macrophage DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MAC-M2', 'full_name': 'M2 macrophage', 'paper_synonyms': 'M2 macrophages', 'tissue_context': ''} CL:0000890 alternatively activated macrophage FALSE +MAST CL:0000097 mast cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MAST', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell TRUE +MC CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell FALSE +MD CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MD', 'full_name': 'macula densa cells', 'paper_synonyms': 'Macula Densa', 'tissue_context': ''} CL:1000850 macula densa epithelial cell FALSE +MDC CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MDC', 'full_name': 'monocyte-derived cells', 'paper_synonyms': 'MDCs', 'tissue_context': ''} CL:0000782 myeloid dendritic cell FALSE +MYOF CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'MYOF', 'full_name': 'myofibroblasts', 'paper_synonyms': 'MyoF', 'tissue_context': ''} CL:0000186 myofibroblast cell FALSE +Macula Densa Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Macula Densa Cell', 'full_name': 'macula densa cell', 'paper_synonyms': 'MD', 'tissue_context': ''} CL:1000850 macula densa epithelial cell FALSE +Mast Cell CL:0000097 mast cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Mast Cell', 'full_name': 'mast cell', 'paper_synonyms': 'MAST', 'tissue_context': ''} CL:0000097 mast cell TRUE +Medullary Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Medullary Fibroblast', 'full_name': 'medullary fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:0000057 fibroblast FALSE +Medullary Thick Ascending Limb Cell CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Medullary Thick Ascending Limb Cell', 'full_name': 'Medullary thick ascending limb cell', 'paper_synonyms': 'M-TAL; thick ascending limb (TAL)', 'tissue_context': ''} CL:1001108 kidney loop of Henle medullary thick ascending limb epithelial cell FALSE +Mesangial Cell CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Mesangial Cell', 'full_name': 'mesangial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000650 mesangial cell FALSE +Monocyte-derived Cell CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Monocyte-derived Cell', 'full_name': 'monocyte-derived cell', 'paper_synonyms': 'MDCs', 'tissue_context': ''} NO MATCH found FALSE +Myofibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Myofibroblast', 'full_name': 'myofibroblast', 'paper_synonyms': 'MyoF', 'tissue_context': ''} CL:0000186 myofibroblast cell FALSE +N CL:0000775 neutrophil DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'N', 'full_name': 'neutrophils', 'paper_synonyms': 'MPO+ cells', 'tissue_context': ''} CL:0000775 neutrophil TRUE +NEU CL:0002319 neural cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'NEU', 'full_name': 'neuronal cell', 'paper_synonyms': 'SCI/NEU; Schwann/neuronal', 'tissue_context': ''} CL:0000540 neuron FALSE +NKC/T CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'NKC/T', 'full_name': 'T cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000084 T cell FALSE +Natural Killer Cell / Natural Killer T Cell CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Natural Killer Cell / Natural Killer T Cell', 'full_name': 'Natural killer cell / natural killer T cell', 'paper_synonyms': 'NKT', 'tissue_context': ''} CL:0000623 natural killer cell FALSE +Neutrophil CL:0000775 neutrophil DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': 'neutrophil', 'paper_synonyms': 'N', 'tissue_context': ''} CL:0000775 neutrophil TRUE +Non-classical Monocyte CL:0000875 non-classical monocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Non-classical Monocyte', 'full_name': 'non-classical monocyte', 'paper_synonyms': 'ncMON', 'tissue_context': ''} CL:0000875 non-classical monocyte TRUE +OMCD-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'OMCD-IC-A', 'full_name': 'outer medullary collecting duct intercalated cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1000717 kidney outer medulla collecting duct intercalated cell FALSE +OMCD-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'OMCD-PC', 'full_name': 'outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; outer medullary collecting duct; PC; principal cells', 'tissue_context': ''} CL:1000716 kidney outer medulla collecting duct principal cell FALSE +Outer Medullary Collecting Duct Intercalated Cell Type A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Outer Medullary Collecting Duct Intercalated Cell Type A', 'full_name': 'outer medullary collecting duct intercalated cell', 'paper_synonyms': 'OMCD; IC', 'tissue_context': ''} CL:1000717 kidney outer medulla collecting duct intercalated cell FALSE +Outer Medullary Collecting Duct Principal Cell CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Outer Medullary Collecting Duct Principal Cell', 'full_name': 'outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; PC; M-PC', 'tissue_context': ''} CL:1000716 kidney outer medulla collecting duct principal cell FALSE +PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PC', 'full_name': 'principal cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0005009 renal principal cell FALSE +PEC CL:1000452 parietal epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PEC', 'full_name': 'parietal epithelial cells', 'paper_synonyms': '', 'tissue_context': ''} CL:1000452 parietal epithelial cell TRUE +PL CL:0000786 plasma cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PL', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +POD CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'POD', 'full_name': 'podocytes', 'paper_synonyms': 'PODs', 'tissue_context': ''} CL:0000653 podocyte TRUE +PT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PT', 'full_name': 'proximal tubule', 'paper_synonyms': 'proximal tubule (PT)', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +PT-S1/2 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PT-S1/2', 'full_name': 'proximal tubule S1/2', 'paper_synonyms': 'PT; proximal tubule', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +PT-S3 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PT-S3', 'full_name': 'proximal tubule S3', 'paper_synonyms': 'proximal tubule (PT)', 'tissue_context': ''} CL:4030011 epithelial cell of proximal tubule segment 3 FALSE +PapE CL:1000597 papillary tips cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'PapE', 'full_name': 'papillary tip epithelial cells abutting the calyx', 'paper_synonyms': '', 'tissue_context': ''} CL:1000597 papillary tips cell TRUE +Papillary Tip Epithelial Cell CL:1000597 papillary tips cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Papillary Tip Epithelial Cell', 'full_name': 'papillary tip epithelial cell', 'paper_synonyms': 'PapE', 'tissue_context': ''} CL:1000597 papillary tips cell TRUE +Parietal Epithelial Cell CL:1000452 parietal epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Parietal Epithelial Cell', 'full_name': 'parietal epithelial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1000452 parietal epithelial cell TRUE +Peritubular Capilary Endothelial Cell CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Peritubular Capilary Endothelial Cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell FALSE +Plasma Cell CL:0000786 plasma cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Plasma Cell', 'full_name': 'Plasma cell', 'paper_synonyms': 'PL', 'tissue_context': ''} CL:0000786 plasma cell TRUE +Plasmacytoid Dendritic Cell CL:0001058 plasmacytoid dendritic cell, human DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Plasmacytoid Dendritic Cell', 'full_name': 'plasmacytoid dendritic cell', 'paper_synonyms': 'pDC', 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell FALSE +Podocyte CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Podocyte', 'full_name': 'podocyte (POD)', 'paper_synonyms': 'POD; PODs', 'tissue_context': ''} CL:0000653 podocyte TRUE +Proximal Tubule Epithelial Cell Segment 1 / Segment 2 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Proximal Tubule Epithelial Cell Segment 1 / Segment 2', 'full_name': 'proximal tubule (PT) epithelial cell, segment 1/segment 2', 'paper_synonyms': 'PT-S1; PT-S2; PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +Proximal Tubule Epithelial Cell Segment 3 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Proximal Tubule Epithelial Cell Segment 3', 'full_name': 'proximal tubule (PT) epithelial cell, segment 3', 'paper_synonyms': 'PT-S3; PT', 'tissue_context': ''} CL:4030011 epithelial cell of proximal tubule segment 3 FALSE +REN CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'REN', 'full_name': 'juxtaglomerular renin-producing granular cell', 'paper_synonyms': 'renin-producing granular cells; juxtaglomerular renin-producing granular cells', 'tissue_context': ''} CL:0000648 kidney granular cell FALSE +Renin-positive Juxtaglomerular Granular Cell CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Renin-positive Juxtaglomerular Granular Cell', 'full_name': 'Juxtaglomerular renin-producing granular cell', 'paper_synonyms': 'REN; renin-producing granular cell', 'tissue_context': ''} CL:0000648 kidney granular cell FALSE +SC/NEU CL:0002319 neural cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'SC/NEU', 'full_name': 'Schwann/neuronal', 'paper_synonyms': 'SCI/NEU', 'tissue_context': ''} CL:0002319 neural cell TRUE +Schwann Cell / Neural CL:0002319 neural cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Schwann Cell / Neural', 'full_name': 'Schwann/neuronal cell', 'paper_synonyms': 'Schwann/neuronal; SCI/NEU', 'tissue_context': ''} CL:0002319 neural cell TRUE +T CL:0000084 T cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'T', 'full_name': 'T cell', 'paper_synonyms': 'CD3+ cells', 'tissue_context': ''} CL:0000084 T cell TRUE +T Cell CL:0000084 T cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'T Cell', 'full_name': 'T cell', 'paper_synonyms': 'CD3+ cells; lymphoid (T) cells; T', 'tissue_context': ''} CL:0000084 T cell TRUE +TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'TAL', 'full_name': 'thick ascending limb', 'paper_synonyms': 'thick ascending limb (TAL)', 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell TRUE +Transitional Principal-Intercalated Cell CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Transitional Principal-Intercalated Cell', 'full_name': 'Transitional principal–intercalated cell', 'paper_synonyms': 'transitioning principal and intercalated cells; PC, principal cells; IC, intercalated cells', 'tissue_context': ''} CL:1001225 kidney collecting duct cell FALSE +VSM/P CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'VSM/P', 'full_name': 'vascular smooth muscle cell or pericyte', 'paper_synonyms': 'VSMC', 'tissue_context': ''} CL:0008034 mural cell FALSE +VSMC CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'VSMC', 'full_name': 'vascular smooth muscle cell', 'paper_synonyms': 'VSM/P', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell FALSE +VSMC/P CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'VSMC/P', 'full_name': 'vascular smooth muscle cell or pericyte', 'paper_synonyms': 'VSM/P', 'tissue_context': ''} CL:4033054 perivascular cell FALSE +Vascular Smooth Muscle Cell CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Vascular Smooth Muscle Cell', 'full_name': 'vascular smooth muscle cell', 'paper_synonyms': 'VSMC; VSM/P', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell FALSE +Vascular Smooth Muscle Cell / Pericyte CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'Vascular Smooth Muscle Cell / Pericyte', 'full_name': 'vascular smooth muscle cell or pericyte', 'paper_synonyms': 'VSM/P; VSMC', 'tissue_context': ''} CL:4033054 perivascular cell FALSE +aFIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'aFIB', 'full_name': 'adaptive fibroblast', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast FALSE +aPT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'aPT', 'full_name': 'adaptive proximal tubule', 'paper_synonyms': '', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +aTAL1 CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'aTAL1', 'full_name': 'adaptive thick ascending limb 1', 'paper_synonyms': 'aTAL', 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell TRUE +aTAL2 CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'aTAL2', 'full_name': 'adaptive thick ascending limb cell 2', 'paper_synonyms': 'adaptive TAL; aTAL', 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell TRUE +cDC CL:0000990 conventional dendritic cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cDC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000990 conventional dendritic cell TRUE +cycCNT CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycCNT', 'full_name': 'cycling connecting tubule cell', 'paper_synonyms': 'CNT', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell TRUE +cycDCT CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycDCT', 'full_name': 'cycling distal convoluted tubule', 'paper_synonyms': 'DCT', 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell TRUE +cycEC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycEC', 'full_name': 'cycling endothelial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +cycMNP CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycMNP', 'full_name': 'cycling MNP', 'paper_synonyms': '', 'tissue_context': ''} CL:4033078 cycling mononuclear phagocyte FALSE +cycMYOF CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycMYOF', 'full_name': 'cycling myofibroblasts', 'paper_synonyms': 'cycMyoF; cycling MyoF', 'tissue_context': ''} CL:0000186 myofibroblast cell FALSE +cycNKC/T CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycNKC/T', 'full_name': 'cycling T cells', 'paper_synonyms': None, 'tissue_context': ''} CL:4033069 cycling T cell FALSE +cycPT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'cycPT', 'full_name': 'cycling proximal tubule cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +dATL CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dATL', 'full_name': 'ascending thin limb', 'paper_synonyms': 'ATL', 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell TRUE +dC-IC-A CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dC-IC-A', 'full_name': 'degenerative cortical intercalated cell A', 'paper_synonyms': 'intercalated cells (IC)', 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell FALSE +dC-TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dC-TAL', 'full_name': 'degenerative cortical thick ascending limb cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1001109 kidney loop of Henle cortical thick ascending limb epithelial cell FALSE +dCNT CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dCNT', 'full_name': 'degenerative connecting tubule cell', 'paper_synonyms': 'connecting tubules (CNT)', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell TRUE +dDCT CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dDCT', 'full_name': 'degenerative distal convoluted tubule cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell TRUE +dDTL3 CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dDTL3', 'full_name': 'degenerative descending thin limb 3', 'paper_synonyms': 'DTL3; DTL; descending thin limb', 'tissue_context': ''} CL:1001111 kidney loop of Henle thin descending limb epithelial cell TRUE +dEC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dEC', 'full_name': 'degenerative endothelial cell', 'paper_synonyms': 'EC', 'tissue_context': ''} CL:0000115 endothelial cell TRUE +dEC-PTC CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dEC-PTC', 'full_name': 'degenerative endothelial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +dFIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dFIB', 'full_name': 'degenerative fibroblast', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast FALSE +dIMCD CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dIMCD', 'full_name': 'degenerative inner medullary collecting duct cell', 'paper_synonyms': None, 'tissue_context': ''} CL:1000547 kidney inner medulla collecting duct epithelial cell FALSE +dM-FIB CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dM-FIB', 'full_name': 'degenerative medullary fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''} CL:4030022 renal medullary fibroblast FALSE +dM-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dM-PC', 'full_name': 'degenerative medullary principal cell', 'paper_synonyms': 'degenerative medullary principal cells (dM-PCs)', 'tissue_context': ''} CL:1001431 kidney collecting duct principal cell TRUE +dM-TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dM-TAL', 'full_name': 'degenerative medullary thick ascending limb cell', 'paper_synonyms': '', 'tissue_context': ''} CL:1001108 kidney loop of Henle medullary thick ascending limb epithelial cell FALSE +dOMCD-PC CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dOMCD-PC', 'full_name': 'degenerative outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; outer medullary collecting duct; PC; principal cells', 'tissue_context': ''} CL:1000716 kidney outer medulla collecting duct principal cell FALSE +dPOD CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dPOD', 'full_name': 'degenerative podocyte', 'paper_synonyms': 'PODs', 'tissue_context': ''} CL:0000653 podocyte TRUE +dPT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dPT', 'full_name': 'degenerative proximal tubule', 'paper_synonyms': '', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +dVSMC CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'dVSMC', 'full_name': 'vascular smooth muscle cell', 'paper_synonyms': 'VSMC; VSM/P', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell FALSE +endothelial cells CL:0000115 endothelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'endothelial cells', 'full_name': 'endothelial cells', 'paper_synonyms': 'EC; endothelium', 'tissue_context': ''} CL:0000115 endothelial cell TRUE +epithelial cells CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1001111 kidney loop of Henle thin descending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:0000653 podocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1001431 kidney collecting duct principal cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1000452 parietal epithelial cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +epithelial cells CL:1000597 papillary tips cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'epithelial cells', 'full_name': 'epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell FALSE +immune cells CL:0000542 lymphocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:1000695 kidney interstitial alternatively activated macrophage DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0000775 neutrophil DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0000113 mononuclear phagocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0000084 T cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0000786 plasma cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0000875 non-classical monocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0000990 conventional dendritic cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0000097 mast cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0000236 B cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +immune cells CL:0001058 plasmacytoid dendritic cell, human DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'immune cells', 'full_name': 'immune cells', 'paper_synonyms': 'leukocytes', 'tissue_context': ''} CL:0000738 leukocyte FALSE +ncMON CL:0000875 non-classical monocyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'ncMON', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000875 non-classical monocyte TRUE +neural cells CL:0002319 neural cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'neural cells', 'full_name': 'neural cells', 'paper_synonyms': 'NEU; SCI/NEU; Schwann/neuronal', 'tissue_context': ''} CL:0002319 neural cell TRUE +pDC CL:0001058 plasmacytoid dendritic cell, human DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'pDC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell FALSE +stroma cells CL:1000692 kidney interstitial fibroblast DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'stroma cells', 'full_name': 'stromal cells', 'paper_synonyms': 'STR; stroma', 'tissue_context': ''} CL:0000499 stromal cell FALSE +stroma cells CL:1001318 renal interstitial pericyte DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'stroma cells', 'full_name': 'stromal cells', 'paper_synonyms': 'STR; stroma', 'tissue_context': ''} CL:0000499 stromal cell FALSE +tPC-IC CL:1001432 kidney collecting duct intercalated cell DOI:10.1038/s41586-023-05769-3 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique {'name': 'tPC-IC', 'full_name': 'transitioning principal and intercalated cells', 'paper_synonyms': '', 'tissue_context': ''} CL:1001225 kidney collecting duct cell FALSE diff --git a/output/raw_output/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..634f8a9 --- /dev/null +++ b/output/raw_output/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,20 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Astrocytes CL:0000127 astrocyte DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Astrocytes', 'full_name': 'astrocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000127 astrocyte +Endo/Pericytes CL:0000115 endothelial cell DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Endo/Pericytes', 'full_name': 'endothelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +Excitatory_1 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_1', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_10 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_10', 'full_name': 'excitatory neuron 10', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_2 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_2', 'full_name': 'excitatory neurons', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_3 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_3', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_4 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_4', 'full_name': 'excitatory neurons', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_5 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_5', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_6 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_6', 'full_name': 'excitatory neuron 6', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_7 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_7', 'full_name': 'excitatory neuron 7', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_8 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_8', 'full_name': 'excitatory neurons', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron +Excitatory_9 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_9', 'full_name': 'excitatory neuron 9', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron +Inhibitory_1 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Inhibitory_1', 'full_name': 'inhibitory neuron', 'paper_synonyms': '', 'tissue_context': ''} CL:0000617 GABAergic neuron +Inhibitory_2 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Inhibitory_2', 'full_name': 'inhibitory neurons', 'paper_synonyms': '', 'tissue_context': ''} CL:0000617 GABAergic neuron +Inhibitory_3 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Inhibitory_3', 'full_name': 'inhibitory neurons', 'paper_synonyms': None, 'tissue_context': ''} CL:0000617 GABAergic neuron +Inhibitory_4 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Inhibitory_4', 'full_name': 'inhibitory neurons', 'paper_synonyms': '', 'tissue_context': ''} CL:0000617 GABAergic neuron +Microglia CL:0000129 microglial cell DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Microglia', 'full_name': 'microglia', 'paper_synonyms': None, 'tissue_context': ''} CL:0000129 microglial cell +OPCs CL:0002453 oligodendrocyte precursor cell DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'OPCs', 'full_name': 'oligodendrocyte progenitor cells', 'paper_synonyms': 'OPCs', 'tissue_context': ''} CL:0002453 oligodendrocyte precursor cell +Oligodendrocytes CL:0000128 oligodendrocyte DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Oligodendrocytes', 'full_name': 'oligodendrocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000128 oligodendrocyte diff --git a/output/raw_output/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique/groundings.tsv b/output/raw_output/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..f4c1a13 --- /dev/null +++ b/output/raw_output/0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,20 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Astrocytes CL:0000127 astrocyte DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Astrocytes', 'full_name': 'astrocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000127 astrocyte TRUE +Endo/Pericytes CL:0000115 endothelial cell DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Endo/Pericytes', 'full_name': 'endothelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Excitatory_1 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_1', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_10 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_10', 'full_name': 'excitatory neuron 10', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_2 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_2', 'full_name': 'excitatory neurons', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_3 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_3', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_4 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_4', 'full_name': 'excitatory neurons', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_5 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_5', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_6 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_6', 'full_name': 'excitatory neuron 6', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_7 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_7', 'full_name': 'excitatory neuron 7', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_8 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_8', 'full_name': 'excitatory neurons', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Excitatory_9 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Excitatory_9', 'full_name': 'excitatory neuron 9', 'paper_synonyms': None, 'tissue_context': ''} CL:0000679 glutamatergic neuron FALSE +Inhibitory_1 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Inhibitory_1', 'full_name': 'inhibitory neuron', 'paper_synonyms': '', 'tissue_context': ''} CL:0000617 GABAergic neuron FALSE +Inhibitory_2 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Inhibitory_2', 'full_name': 'inhibitory neurons', 'paper_synonyms': '', 'tissue_context': ''} CL:0000617 GABAergic neuron FALSE +Inhibitory_3 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Inhibitory_3', 'full_name': 'inhibitory neurons', 'paper_synonyms': None, 'tissue_context': ''} CL:0000617 GABAergic neuron FALSE +Inhibitory_4 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Inhibitory_4', 'full_name': 'inhibitory neurons', 'paper_synonyms': '', 'tissue_context': ''} CL:0000617 GABAergic neuron FALSE +Microglia CL:0000129 microglial cell DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Microglia', 'full_name': 'microglia', 'paper_synonyms': None, 'tissue_context': ''} CL:0000129 microglial cell TRUE +OPCs CL:0002453 oligodendrocyte precursor cell DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'OPCs', 'full_name': 'oligodendrocyte progenitor cells', 'paper_synonyms': 'OPCs', 'tissue_context': ''} CL:0002453 oligodendrocyte precursor cell TRUE +Oligodendrocytes CL:0000128 oligodendrocyte DOI:10.1007/s00401-023-02599-5 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique {'name': 'Oligodendrocytes', 'full_name': 'oligodendrocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000128 oligodendrocyte TRUE diff --git a/output/raw_output/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..aa56852 --- /dev/null +++ b/output/raw_output/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,17 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Activated fibroblasts CCL19 ADAMADEC1 CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Activated fibroblasts CCL19 ADAMADEC1', 'full_name': 'Fibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Endothelial cells CA4 CD36 CL:0000115 endothelial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Endothelial cells CA4 CD36', 'full_name': 'Endothelial cells CA4+ CD36+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +Endothelial cells CD36 CL:0000115 endothelial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Endothelial cells CD36', 'full_name': 'CD36+ endothelial cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000115 endothelial cell +Endothelial cells DARC CL:0000115 endothelial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Endothelial cells DARC', 'full_name': 'DARC/ACKR1+ endothelial cells', 'paper_synonyms': 'ACKR1; DARC/ACKR1', 'tissue_context': ''} CL:0000115 endothelial cell +Endothelial cells LTC4S SEMA3G CL:0000115 endothelial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Endothelial cells LTC4S SEMA3G', 'full_name': 'Endothelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +Fibroblasts ADAMDEC1 CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts ADAMDEC1', 'full_name': 'ADAMDEC1+ fibroblasts', 'paper_synonyms': 'ADAMDEC+ Fibroblast clusters', 'tissue_context': ''} CL:0000057 fibroblast +Fibroblasts KCNN3 LY6H CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts KCNN3 LY6H', 'full_name': 'Fibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Fibroblasts NPY SLITRK6 CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts NPY SLITRK6', 'full_name': 'Fibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Fibroblasts SFRP2 SLPI CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts SFRP2 SLPI', 'full_name': 'Fibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Fibroblasts SMOC2 PTGIS CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts SMOC2 PTGIS', 'full_name': 'SMOC2+ PTGIS+ fibroblasts', 'paper_synonyms': 'SMOC2+ PTGIS+ Fibroblast clusters', 'tissue_context': ''} CL:0000057 fibroblast +Glial cells CL:0000125 glial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Glial cells', 'full_name': 'Glial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000125 glial cell +Lymphatics CL:0000542 lymphocyte DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Lymphatics', 'full_name': 'Lymphatics', 'paper_synonyms': 'lymphatic endothelial cells', 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel +Myofibroblasts GREM1 GREM2 CL:0000186 myofibroblast cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Myofibroblasts GREM1 GREM2', 'full_name': 'GREM1+ GREM2+ myofibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000186 myofibroblast cell +Myofibroblasts HHIP NPNT CL:0000186 myofibroblast cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Myofibroblasts HHIP NPNT', 'full_name': 'HHIP+ NPNT+ myofibroblasts', 'paper_synonyms': 'Myofibroblasts HHIP+ NPNT+', 'tissue_context': ''} CL:0000186 myofibroblast cell +Pericytes HIGD1B STEAP4 CL:0000669 pericyte DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Pericytes HIGD1B STEAP4', 'full_name': 'Pericytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte +Pericytes RERGL NTRK2 CL:0000669 pericyte DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Pericytes RERGL NTRK2', 'full_name': 'Pericytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000669 pericyte diff --git a/output/raw_output/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique/groundings.tsv b/output/raw_output/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..1787e6d --- /dev/null +++ b/output/raw_output/0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,17 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Activated fibroblasts CCL19 ADAMADEC1 CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Activated fibroblasts CCL19 ADAMADEC1', 'full_name': 'Fibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +Endothelial cells CA4 CD36 CL:0000115 endothelial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Endothelial cells CA4 CD36', 'full_name': 'Endothelial cells CA4+ CD36+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Endothelial cells CD36 CL:0000115 endothelial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Endothelial cells CD36', 'full_name': 'CD36+ endothelial cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Endothelial cells DARC CL:0000115 endothelial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Endothelial cells DARC', 'full_name': 'DARC/ACKR1+ endothelial cells', 'paper_synonyms': 'ACKR1; DARC/ACKR1', 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Endothelial cells LTC4S SEMA3G CL:0000115 endothelial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Endothelial cells LTC4S SEMA3G', 'full_name': 'Endothelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Fibroblasts ADAMDEC1 CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts ADAMDEC1', 'full_name': 'ADAMDEC1+ fibroblasts', 'paper_synonyms': 'ADAMDEC+ Fibroblast clusters', 'tissue_context': ''} CL:0000057 fibroblast TRUE +Fibroblasts KCNN3 LY6H CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts KCNN3 LY6H', 'full_name': 'Fibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +Fibroblasts NPY SLITRK6 CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts NPY SLITRK6', 'full_name': 'Fibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +Fibroblasts SFRP2 SLPI CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts SFRP2 SLPI', 'full_name': 'Fibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +Fibroblasts SMOC2 PTGIS CL:0000057 fibroblast DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Fibroblasts SMOC2 PTGIS', 'full_name': 'SMOC2+ PTGIS+ fibroblasts', 'paper_synonyms': 'SMOC2+ PTGIS+ Fibroblast clusters', 'tissue_context': ''} CL:0000057 fibroblast TRUE +Glial cells CL:0000125 glial cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Glial cells', 'full_name': 'Glial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000125 glial cell TRUE +Lymphatics CL:0000542 lymphocyte DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Lymphatics', 'full_name': 'Lymphatics', 'paper_synonyms': 'lymphatic endothelial cells', 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel FALSE +Myofibroblasts GREM1 GREM2 CL:0000186 myofibroblast cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Myofibroblasts GREM1 GREM2', 'full_name': 'GREM1+ GREM2+ myofibroblasts', 'paper_synonyms': None, 'tissue_context': ''} CL:0000186 myofibroblast cell TRUE +Myofibroblasts HHIP NPNT CL:0000186 myofibroblast cell DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Myofibroblasts HHIP NPNT', 'full_name': 'HHIP+ NPNT+ myofibroblasts', 'paper_synonyms': 'Myofibroblasts HHIP+ NPNT+', 'tissue_context': ''} CL:0000186 myofibroblast cell TRUE +Pericytes HIGD1B STEAP4 CL:0000669 pericyte DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Pericytes HIGD1B STEAP4', 'full_name': 'Pericytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte TRUE +Pericytes RERGL NTRK2 CL:0000669 pericyte DOI:10.1016/j.immuni.2023.01.002 0f4865d5-8000-4f68-8ac7-f5efea9e5e70_cxg_dataset_unique {'name': 'Pericytes RERGL NTRK2', 'full_name': 'Pericytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000669 pericyte TRUE diff --git a/output/raw_output/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..72f85b5 --- /dev/null +++ b/output/raw_output/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,14 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Diff. Keratinocytes CL:0000312 keratinocyte DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Diff. Keratinocytes', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000312 keratinocyte +EpSC and undiff. progenitors CL:1000428 stem cell of epidermis DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'EpSC and undiff. progenitors', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0011026 progenitor cell +Erythrocytes CL:0000232 erythrocyte DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Erythrocytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte +Lymphatic EC CL:0002138 endothelial cell of lymphatic vessel DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Lymphatic EC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel +Macrophages+DC CL:0000235 macrophage DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Macrophages+DC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000113 mononuclear phagocyte +Melanocytes CL:0000148 melanocyte DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Melanocytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000148 melanocyte +Mesenchymal fibroblasts CL:0002620 skin fibroblast DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Mesenchymal fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Pericytes CL:0000669 pericyte DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Pericytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte +Pro-inflammatory fibroblasts CL:0002620 skin fibroblast DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Pro-inflammatory fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Secretory-papillary fibroblasts CL:0002620 skin fibroblast DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Secretory-papillary fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000302 fibroblast of papillary layer of dermis +Secretory-reticular fibroblasts CL:0002620 skin fibroblast DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Secretory-reticular fibroblasts', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:2000096 fibroblast of the reticular layer of dermis +T cells CL:0000084 T cell DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'T cells', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000084 T cell +Vascular EC CL:0002139 endothelial cell of vascular tree DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Vascular EC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000071 blood vessel endothelial cell diff --git a/output/raw_output/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique/groundings.tsv b/output/raw_output/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..78cc768 --- /dev/null +++ b/output/raw_output/124744b8-4681-474a-9894-683896122708_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,14 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Diff. Keratinocytes CL:0000312 keratinocyte DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Diff. Keratinocytes', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000312 keratinocyte TRUE +EpSC and undiff. progenitors CL:1000428 stem cell of epidermis DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'EpSC and undiff. progenitors', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0011026 progenitor cell FALSE +Erythrocytes CL:0000232 erythrocyte DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Erythrocytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte TRUE +Lymphatic EC CL:0002138 endothelial cell of lymphatic vessel DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Lymphatic EC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel TRUE +Macrophages+DC CL:0000235 macrophage DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Macrophages+DC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000113 mononuclear phagocyte FALSE +Melanocytes CL:0000148 melanocyte DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Melanocytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000148 melanocyte TRUE +Mesenchymal fibroblasts CL:0002620 skin fibroblast DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Mesenchymal fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast FALSE +Pericytes CL:0000669 pericyte DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Pericytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte TRUE +Pro-inflammatory fibroblasts CL:0002620 skin fibroblast DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Pro-inflammatory fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast FALSE +Secretory-papillary fibroblasts CL:0002620 skin fibroblast DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Secretory-papillary fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000302 fibroblast of papillary layer of dermis FALSE +Secretory-reticular fibroblasts CL:0002620 skin fibroblast DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Secretory-reticular fibroblasts', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:2000096 fibroblast of the reticular layer of dermis FALSE +T cells CL:0000084 T cell DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'T cells', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000084 T cell TRUE +Vascular EC CL:0002139 endothelial cell of vascular tree DOI:10.1038/s42003-020-0922-4 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique {'name': 'Vascular EC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000071 blood vessel endothelial cell FALSE diff --git a/output/raw_output/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..f287937 --- /dev/null +++ b/output/raw_output/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,31 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +AntiB CL:0000786 plasma cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'AntiB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000946 antibody secreting cell +C-Hepato CL:0019029 centrilobular region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'C-Hepato', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte +C-Hepato2 CL:0019029 centrilobular region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'C-Hepato2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte +CD4T CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'CD4T', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +Chol CL:0002538 intrahepatic cholangiocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Chol', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000488 cholangiocyte +Chol--Kupffer-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Chol--Kupffer-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000488 cholangiocyte +Chol--Stellate-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Chol--Stellate-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000488 cholangiocyte +Chol-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Chol-Doublet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1000488 cholangiocyte +CholMucus CL:0002538 intrahepatic cholangiocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'CholMucus', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000488 cholangiocyte +Fibroblast CL:0000057 fibroblast DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Fibroblast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Hepato-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Hepato-Doublet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +I-Hepato CL:0019028 midzonal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'I-Hepato', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte +Kupffer CL:0000091 Kupffer cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Kupffer', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000091 Kupffer cell +Kupffer-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Kupffer-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000091 Kupffer cell +Monocyte CL:0000576 monocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte +P-Hepato CL:0019026 periportal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'P-Hepato', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte +P-Hepato2 CL:0019026 periportal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'P-Hepato2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte +Prolif unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Prolif', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +Prolif-Mac CL:0000235 macrophage DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Prolif-Mac', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033076 cycling macrophage +Stellate CL:0000632 hepatic stellate cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Stellate', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000632 hepatic stellate cell +Stellate-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Stellate-Doublet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000632 hepatic stellate cell +Tcell-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Tcell-Doublet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000084 T cell +VSMC CL:0000359 vascular associated smooth muscle cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'VSMC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell +aStellate CL:0000632 hepatic stellate cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'aStellate', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000632 hepatic stellate cell +cvEndo CL:0002543 vein endothelial cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'cvEndo', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +cvLSEC CL:0019022 endothelial cell of pericentral hepatic sinusoid DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'cvLSEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000398 endothelial cell of hepatic sinusoid +cvLSEC--Mac unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'cvLSEC--Mac', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000235 macrophage +cvLSEC-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'cvLSEC-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000398 endothelial cell of hepatic sinusoid +lrNK CL:2000054 hepatic pit cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'lrNK', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:4047101 liver-resident natural killer cell +ppLSEC CL:0019021 endothelial cell of periportal hepatic sinusoid DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'ppLSEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0019021 endothelial cell of periportal hepatic sinusoid diff --git a/output/raw_output/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique/groundings.tsv b/output/raw_output/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..463a1f9 --- /dev/null +++ b/output/raw_output/1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,31 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +AntiB CL:0000786 plasma cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'AntiB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000946 antibody secreting cell FALSE +C-Hepato CL:0019029 centrilobular region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'C-Hepato', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte FALSE +C-Hepato2 CL:0019029 centrilobular region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'C-Hepato2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte FALSE +CD4T CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'CD4T', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell TRUE +Chol CL:0002538 intrahepatic cholangiocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Chol', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000488 cholangiocyte FALSE +Chol--Kupffer-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Chol--Kupffer-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000488 cholangiocyte FALSE +Chol--Stellate-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Chol--Stellate-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000488 cholangiocyte FALSE +Chol-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Chol-Doublet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:1000488 cholangiocyte FALSE +CholMucus CL:0002538 intrahepatic cholangiocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'CholMucus', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000488 cholangiocyte FALSE +Fibroblast CL:0000057 fibroblast DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Fibroblast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +Hepato-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Hepato-Doublet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +I-Hepato CL:0019028 midzonal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'I-Hepato', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte FALSE +Kupffer CL:0000091 Kupffer cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Kupffer', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000091 Kupffer cell TRUE +Kupffer-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Kupffer-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000091 Kupffer cell FALSE +Monocyte CL:0000576 monocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte TRUE +P-Hepato CL:0019026 periportal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'P-Hepato', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000182 hepatocyte FALSE +P-Hepato2 CL:0019026 periportal region hepatocyte DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'P-Hepato2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000182 hepatocyte FALSE +Prolif unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Prolif', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +Prolif-Mac CL:0000235 macrophage DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Prolif-Mac', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033076 cycling macrophage FALSE +Stellate CL:0000632 hepatic stellate cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Stellate', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000632 hepatic stellate cell TRUE +Stellate-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Stellate-Doublet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000632 hepatic stellate cell FALSE +Tcell-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'Tcell-Doublet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000084 T cell FALSE +VSMC CL:0000359 vascular associated smooth muscle cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'VSMC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell TRUE +aStellate CL:0000632 hepatic stellate cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'aStellate', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000632 hepatic stellate cell TRUE +cvEndo CL:0002543 vein endothelial cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'cvEndo', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell FALSE +cvLSEC CL:0019022 endothelial cell of pericentral hepatic sinusoid DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'cvLSEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000398 endothelial cell of hepatic sinusoid FALSE +cvLSEC--Mac unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'cvLSEC--Mac', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000235 macrophage FALSE +cvLSEC-Doublet unknown unknown DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'cvLSEC-Doublet', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000398 endothelial cell of hepatic sinusoid FALSE +lrNK CL:2000054 hepatic pit cell DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'lrNK', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:4047101 liver-resident natural killer cell FALSE +ppLSEC CL:0019021 endothelial cell of periportal hepatic sinusoid DOI:10.1016/j.jhep.2023.12.023 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique {'name': 'ppLSEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0019021 endothelial cell of periportal hepatic sinusoid TRUE diff --git a/output/raw_output/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..0192774 --- /dev/null +++ b/output/raw_output/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,15 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +CD4-positive, alpha-beta memory T cell CL:0000897 CD4-positive, alpha-beta memory T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'CD4-positive, alpha-beta memory T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000897 CD4-positive, alpha-beta memory T cell +CD8-positive, alpha-beta memory T cell CL:0000909 CD8-positive, alpha-beta memory T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'CD8-positive, alpha-beta memory T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000909 CD8-positive, alpha-beta memory T cell +TCRVbeta13.1pos CL:0000084 T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'TCRVbeta13.1pos', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +TissueResMemT CL:0000813 memory T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'TissueResMemT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000813 memory T cell +double negative T cell (DNT) CL:0002489 double negative thymocyte DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'double negative T cell (DNT)', 'full_name': 'double negative T cell', 'paper_synonyms': 'DNT', 'tissue_context': ''} CL:0002489 double negative thymocyte +double-positive T cell (DPT) CL:0000809 double-positive, alpha-beta thymocyte DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'double-positive T cell (DPT)', 'full_name': 'double-positive T cell', 'paper_synonyms': 'DPT', 'tissue_context': ''} CL:0000809 double-positive, alpha-beta thymocyte +gamma-delta T cell CL:0000798 gamma-delta T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'gamma-delta T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000798 gamma-delta T cell +memory B cell CL:0000787 memory B cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'memory B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000787 memory B cell +mucosal invariant T cell (MAIT) CL:0000940 mucosal invariant T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'mucosal invariant T cell (MAIT)', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000940 mucosal-associated invariant T cell +naive B cell CL:0000788 naive B cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'naive B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000788 naive B cell +naive CD4+ T cell CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'naive CD4+ T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell +naive CD8+ T cell CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'naive CD8+ T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell +plasmablast CL:0000980 plasmablast DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'plasmablast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000980 plasmablast +regulatory T cell CL:0000815 regulatory T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'regulatory T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000815 regulatory T cell diff --git a/output/raw_output/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique/groundings.tsv b/output/raw_output/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..aa1c0f4 --- /dev/null +++ b/output/raw_output/21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,15 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +CD4-positive, alpha-beta memory T cell CL:0000897 CD4-positive, alpha-beta memory T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'CD4-positive, alpha-beta memory T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000897 CD4-positive, alpha-beta memory T cell TRUE +CD8-positive, alpha-beta memory T cell CL:0000909 CD8-positive, alpha-beta memory T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'CD8-positive, alpha-beta memory T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000909 CD8-positive, alpha-beta memory T cell TRUE +TCRVbeta13.1pos CL:0000084 T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'TCRVbeta13.1pos', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +TissueResMemT CL:0000813 memory T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'TissueResMemT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000813 memory T cell TRUE +double negative T cell (DNT) CL:0002489 double negative thymocyte DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'double negative T cell (DNT)', 'full_name': 'double negative T cell', 'paper_synonyms': 'DNT', 'tissue_context': ''} CL:0002489 double negative thymocyte TRUE +double-positive T cell (DPT) CL:0000809 double-positive, alpha-beta thymocyte DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'double-positive T cell (DPT)', 'full_name': 'double-positive T cell', 'paper_synonyms': 'DPT', 'tissue_context': ''} CL:0000809 double-positive, alpha-beta thymocyte TRUE +gamma-delta T cell CL:0000798 gamma-delta T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'gamma-delta T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000798 gamma-delta T cell TRUE +memory B cell CL:0000787 memory B cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'memory B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000787 memory B cell TRUE +mucosal invariant T cell (MAIT) CL:0000940 mucosal invariant T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'mucosal invariant T cell (MAIT)', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000940 mucosal-associated invariant T cell TRUE +naive B cell CL:0000788 naive B cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'naive B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000788 naive B cell TRUE +naive CD4+ T cell CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'naive CD4+ T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell TRUE +naive CD8+ T cell CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'naive CD8+ T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell TRUE +plasmablast CL:0000980 plasmablast DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'plasmablast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000980 plasmablast TRUE +regulatory T cell CL:0000815 regulatory T cell DOI:10.1016/j.cell.2021.02.018 21d3e683-80a4-4d9b-bc89-ebb2df513dde_cxg_dataset_unique {'name': 'regulatory T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000815 regulatory T cell TRUE diff --git a/output/raw_output/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..821d3c7 --- /dev/null +++ b/output/raw_output/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,26 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Activated CD4 T CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Activated CD4 T', 'full_name': 'CD4+ T cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +B cell IgA Plasma CL:0000987 IgA plasma cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'B cell IgA Plasma', 'full_name': 'IgA+ plasma cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000987 IgA plasma cell +B cell IgG Plasma CL:0000236 B cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'B cell IgG Plasma', 'full_name': 'IgG+ plasma cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000985 IgG plasma cell +B cell cycling CL:0000236 B cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'B cell cycling', 'full_name': 'MKI67+ cycling B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:4033068 cycling B cell +B cell memory CL:0000787 memory B cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'B cell memory', 'full_name': 'memory B cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000787 memory B cell +CD8 T CL:0000625 CD8-positive, alpha-beta T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'CD8 T', 'full_name': 'CD8+ T cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell +Follicular B cell CL:0000843 follicular B cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Follicular B cell', 'full_name': 'follicular B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000843 follicular B cell +ILC CL:0001065 innate lymphoid cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'ILC', 'full_name': 'innate lymphoid cells', 'paper_synonyms': 'ILCs', 'tissue_context': ''} CL:0001065 innate lymphoid cell +LYVE1 Macrophage CL:0000235 macrophage DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'LYVE1 Macrophage', 'full_name': 'LYVE1+ macrophages', 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage +Lymphoid DC CL:0000451 dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Lymphoid DC', 'full_name': 'dendritic cells', 'paper_synonyms': 'DCs', 'tissue_context': ''} CL:0000451 dendritic cell +Macrophage CL:0009038 colon macrophage DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Macrophage', 'full_name': 'macrophage', 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage +Mast CL:0000097 mast cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Mast', 'full_name': 'mast cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000097 mast cell +Monocyte CL:0000576 monocyte DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Monocyte', 'full_name': 'monocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte +NK CL:0000623 natural killer cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'NK', 'full_name': 'natural killer cells', 'paper_synonyms': 'NK cells', 'tissue_context': ''} CL:0000623 natural killer cell +Tcm CL:0000813 memory T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Tcm', 'full_name': 'central memory T cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000813 memory T cell +Tfh CL:0002038 T follicular helper cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Tfh', 'full_name': 'follicular helper cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002038 T follicular helper cell +Th1 CL:0000545 T-helper 1 cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Th1', 'full_name': 'T helper 1 cells', 'paper_synonyms': 'TH1 cells', 'tissue_context': ''} CL:0000545 T-helper 1 cell +Th17 CL:0000899 T-helper 17 cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Th17', 'full_name': 'T helper 17 cell', 'paper_synonyms': 'TH17; T helper (TH) 17 cells', 'tissue_context': ''} CL:0000899 T-helper 17 cell +Treg CL:0000815 regulatory T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Treg', 'full_name': 'T regulatory cells', 'paper_synonyms': 'Treg cells; regulatory T cells', 'tissue_context': ''} CL:0000815 regulatory T cell +cDC1 CL:0000990 conventional dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'cDC1', 'full_name': 'conventional dendritic cell 1', 'paper_synonyms': None, 'tissue_context': ''} CL:0000990 conventional dendritic cell +cDC2 CL:0000990 conventional dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'cDC2', 'full_name': 'conventional dendritic cell 2', 'paper_synonyms': None, 'tissue_context': ''} CL:0000990 conventional dendritic cell +cycling DCs CL:0000451 dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'cycling DCs', 'full_name': 'cycling dendritic cells', 'paper_synonyms': None, 'tissue_context': ''} CL:4033070 cycling dendritic cell +cycling gd T CL:0000798 gamma-delta T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'cycling gd T', 'full_name': 'cycling gammadelta T cell', 'paper_synonyms': 'gammadelta T cells', 'tissue_context': ''} CL:4033072 cycling gamma-delta T cell +gd T CL:0000798 gamma-delta T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'gd T', 'full_name': 'gammadelta T cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000798 gamma-delta T cell +pDC CL:0000784 plasmacytoid dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'pDC', 'full_name': 'plasmacytoid DCs', 'paper_synonyms': 'pDCs', 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell diff --git a/output/raw_output/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique/groundings.tsv b/output/raw_output/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..55824c5 --- /dev/null +++ b/output/raw_output/2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,26 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Activated CD4 T CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Activated CD4 T', 'full_name': 'CD4+ T cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell TRUE +B cell IgA Plasma CL:0000987 IgA plasma cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'B cell IgA Plasma', 'full_name': 'IgA+ plasma cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000987 IgA plasma cell TRUE +B cell IgG Plasma CL:0000236 B cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'B cell IgG Plasma', 'full_name': 'IgG+ plasma cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000985 IgG plasma cell FALSE +B cell cycling CL:0000236 B cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'B cell cycling', 'full_name': 'MKI67+ cycling B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:4033068 cycling B cell FALSE +B cell memory CL:0000787 memory B cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'B cell memory', 'full_name': 'memory B cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000787 memory B cell TRUE +CD8 T CL:0000625 CD8-positive, alpha-beta T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'CD8 T', 'full_name': 'CD8+ T cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell TRUE +Follicular B cell CL:0000843 follicular B cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Follicular B cell', 'full_name': 'follicular B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000843 follicular B cell TRUE +ILC CL:0001065 innate lymphoid cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'ILC', 'full_name': 'innate lymphoid cells', 'paper_synonyms': 'ILCs', 'tissue_context': ''} CL:0001065 innate lymphoid cell TRUE +LYVE1 Macrophage CL:0000235 macrophage DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'LYVE1 Macrophage', 'full_name': 'LYVE1+ macrophages', 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage TRUE +Lymphoid DC CL:0000451 dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Lymphoid DC', 'full_name': 'dendritic cells', 'paper_synonyms': 'DCs', 'tissue_context': ''} CL:0000451 dendritic cell TRUE +Macrophage CL:0009038 colon macrophage DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Macrophage', 'full_name': 'macrophage', 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage FALSE +Mast CL:0000097 mast cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Mast', 'full_name': 'mast cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000097 mast cell TRUE +Monocyte CL:0000576 monocyte DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Monocyte', 'full_name': 'monocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte TRUE +NK CL:0000623 natural killer cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'NK', 'full_name': 'natural killer cells', 'paper_synonyms': 'NK cells', 'tissue_context': ''} CL:0000623 natural killer cell TRUE +Tcm CL:0000813 memory T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Tcm', 'full_name': 'central memory T cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000813 memory T cell TRUE +Tfh CL:0002038 T follicular helper cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Tfh', 'full_name': 'follicular helper cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002038 T follicular helper cell TRUE +Th1 CL:0000545 T-helper 1 cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Th1', 'full_name': 'T helper 1 cells', 'paper_synonyms': 'TH1 cells', 'tissue_context': ''} CL:0000545 T-helper 1 cell TRUE +Th17 CL:0000899 T-helper 17 cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Th17', 'full_name': 'T helper 17 cell', 'paper_synonyms': 'TH17; T helper (TH) 17 cells', 'tissue_context': ''} CL:0000899 T-helper 17 cell TRUE +Treg CL:0000815 regulatory T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'Treg', 'full_name': 'T regulatory cells', 'paper_synonyms': 'Treg cells; regulatory T cells', 'tissue_context': ''} CL:0000815 regulatory T cell TRUE +cDC1 CL:0000990 conventional dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'cDC1', 'full_name': 'conventional dendritic cell 1', 'paper_synonyms': None, 'tissue_context': ''} CL:0000990 conventional dendritic cell TRUE +cDC2 CL:0000990 conventional dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'cDC2', 'full_name': 'conventional dendritic cell 2', 'paper_synonyms': None, 'tissue_context': ''} CL:0000990 conventional dendritic cell TRUE +cycling DCs CL:0000451 dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'cycling DCs', 'full_name': 'cycling dendritic cells', 'paper_synonyms': None, 'tissue_context': ''} CL:4033070 cycling dendritic cell FALSE +cycling gd T CL:0000798 gamma-delta T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'cycling gd T', 'full_name': 'cycling gammadelta T cell', 'paper_synonyms': 'gammadelta T cells', 'tissue_context': ''} CL:4033072 cycling gamma-delta T cell FALSE +gd T CL:0000798 gamma-delta T cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'gd T', 'full_name': 'gammadelta T cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000798 gamma-delta T cell TRUE +pDC CL:0000784 plasmacytoid dendritic cell DOI:10.1038/s41590-020-0602-z 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique {'name': 'pDC', 'full_name': 'plasmacytoid DCs', 'paper_synonyms': 'pDCs', 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell TRUE diff --git a/output/raw_output/2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..ca18413 --- /dev/null +++ b/output/raw_output/2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,3 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +H1 CL:0000745 retina horizontal cell DOI:10.1038/s41598-020-66092-9 2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique {'name': 'H1', 'full_name': 'horizontal cell type H1', 'paper_synonyms': None, 'tissue_context': ''} CL:0004217 H1 horizontal cell +H2 CL:0000745 retina horizontal cell DOI:10.1038/s41598-020-66092-9 2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique {'name': 'H2', 'full_name': 'horizontal cell type H2', 'paper_synonyms': None, 'tissue_context': ''} CL:0004218 H2 horizontal cell diff --git a/output/raw_output/2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique/groundings.tsv b/output/raw_output/2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..e282b5e --- /dev/null +++ b/output/raw_output/2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,3 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +H1 CL:0000745 retina horizontal cell DOI:10.1038/s41598-020-66092-9 2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique {'name': 'H1', 'full_name': 'horizontal cell type H1', 'paper_synonyms': None, 'tissue_context': ''} CL:0004217 H1 horizontal cell FALSE +H2 CL:0000745 retina horizontal cell DOI:10.1038/s41598-020-66092-9 2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique {'name': 'H2', 'full_name': 'horizontal cell type H2', 'paper_synonyms': None, 'tissue_context': ''} CL:0004218 H2 horizontal cell FALSE diff --git a/output/raw_output/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..72d6f92 --- /dev/null +++ b/output/raw_output/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,11 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +NK_CD16hi CL:0000939 CD16-positive, CD56-dim natural killer cell, human DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'NK_CD16hi', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000939 CD16-positive, CD56-dim natural killer cell, human +NK_CD56hiCD16lo CL:0000938 CD16-negative, CD56-bright natural killer cell, human DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'NK_CD56hiCD16lo', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000938 CD16-negative, CD56-bright natural killer cell, human +NK_CD56loCD16lo CL:0000623 natural killer cell DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'NK_CD56loCD16lo', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell +classical monocyte CL:0000860 classical monocyte DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'classical monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000860 classical monocyte +conventional dendritic cell CL:0000990 conventional dendritic cell DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'conventional dendritic cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000990 conventional dendritic cell +granulocyte CL:0000094 granulocyte DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'granulocyte', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000094 granulocyte +intermediate monocyte CL:0002393 intermediate monocyte DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'intermediate monocyte', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0002393 intermediate monocyte +non-classical monocyte CL:0000875 non-classical monocyte DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'non-classical monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000875 non-classical monocyte +plasmacytoid dendritic cell CL:0000784 plasmacytoid dendritic cell DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'plasmacytoid dendritic cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell +platelet CL:0000233 platelet DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'platelet', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} diff --git a/output/raw_output/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique/groundings.tsv b/output/raw_output/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..8ca2e77 --- /dev/null +++ b/output/raw_output/30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,10 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +NK_CD16hi CL:0000939 CD16-positive, CD56-dim natural killer cell, human DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'NK_CD16hi', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000939 CD16-positive, CD56-dim natural killer cell, human TRUE +NK_CD56hiCD16lo CL:0000938 CD16-negative, CD56-bright natural killer cell, human DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'NK_CD56hiCD16lo', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000938 CD16-negative, CD56-bright natural killer cell, human TRUE +NK_CD56loCD16lo CL:0000623 natural killer cell DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'NK_CD56loCD16lo', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell TRUE +classical monocyte CL:0000860 classical monocyte DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'classical monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000860 classical monocyte TRUE +conventional dendritic cell CL:0000990 conventional dendritic cell DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'conventional dendritic cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000990 conventional dendritic cell TRUE +granulocyte CL:0000094 granulocyte DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'granulocyte', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000094 granulocyte TRUE +intermediate monocyte CL:0002393 intermediate monocyte DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'intermediate monocyte', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0002393 intermediate monocyte TRUE +non-classical monocyte CL:0000875 non-classical monocyte DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'non-classical monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000875 non-classical monocyte TRUE +plasmacytoid dendritic cell CL:0000784 plasmacytoid dendritic cell DOI:10.1016/j.cell.2021.02.018 30cd5311-6c09-46c9-94f1-71fe4b91813c_cxg_dataset_unique {'name': 'plasmacytoid dendritic cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell TRUE diff --git a/output/raw_output/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..632e360 --- /dev/null +++ b/output/raw_output/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,43 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +ACKR1+ endothelium CL:0000115 endothelial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'ACKR1+ endothelium', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +B cells CL:0000236 B cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'B cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +CD36+ endothelium CL:0000115 endothelial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'CD36+ endothelium', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +Cycling unknown unknown DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Cycling', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +Doublets unknown unknown DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Doublets', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +Endothelium CL:0000115 endothelial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Endothelium', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +Endothelium CL:0002138 endothelial cell of lymphatic vessel DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Endothelium', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +Enterocytes CL:1000342 enterocyte of epithelium proper of ileum DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Enterocytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte +Enteroendocrines CL:0009006 enteroendocrine cell of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Enteroendocrines', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell +Fibs CL:0000057 fibroblast DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Fibs', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +Glial cells CL:0000125 glial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Glial cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000125 glial cell +Goblets CL:1000326 ileal goblet cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Goblets', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell +ILC CL:0001065 innate lymphoid cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'ILC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0001065 innate lymphoid cell +Immune cells CL:0000786 plasma cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +Immune cells CL:0000789 alpha-beta T cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +Immune cells CL:0001065 innate lymphoid cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +Immune cells CL:0000236 B cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +Immune cells CL:0000113 mononuclear phagocyte DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +Immune cells CL:0000097 mast cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +Lymphatics CL:0002138 endothelial cell of lymphatic vessel DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Lymphatics', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel +MNP CL:0000113 mononuclear phagocyte DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'MNP', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000113 mononuclear phagocyte +Mast cells CL:0000097 mast cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Mast cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell +Paneth cells CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Paneth cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000510 paneth cell +Pericytes CL:0000669 pericyte DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Pericytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte +Plasma cells CL:0000786 plasma cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Plasma cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000786 plasma cell +Progenitors CL:0011026 progenitor cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Progenitors', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0011026 progenitor cell +SM CL:1000278 smooth muscle fiber of ileum DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'SM', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000192 smooth muscle cell +Stroma CL:0011026 progenitor cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:0000115 endothelial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma unknown unknown DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:1000342 enterocyte of epithelium proper of ileum DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:1000278 smooth muscle fiber of ileum DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:1000326 ileal goblet cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:0000057 fibroblast DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:0000669 pericyte DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:0009006 enteroendocrine cell of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:0000125 glial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +Stroma CL:0002138 endothelial cell of lymphatic vessel DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell +T cells CL:0000789 alpha-beta T cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'T cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000084 T cell +TA CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'TA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009010 transit amplifying cell diff --git a/output/raw_output/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique/groundings.tsv b/output/raw_output/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..518eda2 --- /dev/null +++ b/output/raw_output/36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,43 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +ACKR1+ endothelium CL:0000115 endothelial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'ACKR1+ endothelium', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +B cells CL:0000236 B cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'B cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell TRUE +CD36+ endothelium CL:0000115 endothelial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'CD36+ endothelium', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Cycling unknown unknown DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Cycling', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +Doublets unknown unknown DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Doublets', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +Endothelium CL:0000115 endothelial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Endothelium', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +Endothelium CL:0002138 endothelial cell of lymphatic vessel DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Endothelium', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell FALSE +Enterocytes CL:1000342 enterocyte of epithelium proper of ileum DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Enterocytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte FALSE +Enteroendocrines CL:0009006 enteroendocrine cell of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Enteroendocrines', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell FALSE +Fibs CL:0000057 fibroblast DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Fibs', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +Glial cells CL:0000125 glial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Glial cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000125 glial cell TRUE +Goblets CL:1000326 ileal goblet cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Goblets', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell FALSE +ILC CL:0001065 innate lymphoid cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'ILC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0001065 innate lymphoid cell TRUE +Immune cells CL:0000786 plasma cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte FALSE +Immune cells CL:0000789 alpha-beta T cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte FALSE +Immune cells CL:0001065 innate lymphoid cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte FALSE +Immune cells CL:0000236 B cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte FALSE +Immune cells CL:0000113 mononuclear phagocyte DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte FALSE +Immune cells CL:0000097 mast cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Immune cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte FALSE +Lymphatics CL:0002138 endothelial cell of lymphatic vessel DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Lymphatics', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel TRUE +MNP CL:0000113 mononuclear phagocyte DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'MNP', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000113 mononuclear phagocyte TRUE +Mast cells CL:0000097 mast cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Mast cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell TRUE +Paneth cells CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Paneth cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000510 paneth cell FALSE +Pericytes CL:0000669 pericyte DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Pericytes', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte TRUE +Plasma cells CL:0000786 plasma cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Plasma cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000786 plasma cell TRUE +Progenitors CL:0011026 progenitor cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Progenitors', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0011026 progenitor cell TRUE +SM CL:1000278 smooth muscle fiber of ileum DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'SM', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000192 smooth muscle cell FALSE +Stroma CL:0011026 progenitor cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:0000115 endothelial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma unknown unknown DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:1000342 enterocyte of epithelium proper of ileum DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:1000278 smooth muscle fiber of ileum DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:1000326 ileal goblet cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:0000057 fibroblast DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:0000669 pericyte DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:0009006 enteroendocrine cell of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:1000343 paneth cell of epithelium of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:0000125 glial cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +Stroma CL:0002138 endothelial cell of lymphatic vessel DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'Stroma', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000499 stromal cell FALSE +T cells CL:0000789 alpha-beta T cell DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'T cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000084 T cell FALSE +TA CL:0009012 transit amplifying cell of small intestine DOI:10.1016/j.cell.2019.08.008 36c867a7-be10-4e69-9b39-5de12b0af6da_cxg_dataset_unique {'name': 'TA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009010 transit amplifying cell FALSE diff --git a/output/raw_output/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..a59be2d --- /dev/null +++ b/output/raw_output/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,15 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +acinar CL:0002064 pancreatic acinar cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'acinar', 'full_name': 'acinar cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000622 acinar cell +acinar_minor_mhcclassII CL:0002064 pancreatic acinar cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'acinar_minor_mhcclassII', 'full_name': 'MHC Class II acinar cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000622 acinar cell +alpha CL:0000171 pancreatic A cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'alpha', 'full_name': 'alpha cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000171 pancreatic A cell +beta_major CL:0000169 type B pancreatic cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'beta_major', 'full_name': 'beta cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000169 type B pancreatic cell +beta_minor CL:0000169 type B pancreatic cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'beta_minor', 'full_name': 'beta cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000169 type B pancreatic cell +delta CL:0000173 pancreatic D cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'delta', 'full_name': 'delta cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000173 pancreatic D cell +duct_acinar_related CL:0002079 pancreatic ductal cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'duct_acinar_related', 'full_name': 'ductal-acinar related cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002080 pancreatic centro-acinar cell +duct_major CL:0002079 pancreatic ductal cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'duct_major', 'full_name': 'ductal cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002079 pancreatic ductal cell +endothelial CL:0000115 endothelial cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'endothelial', 'full_name': 'endothelial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +epsilon CL:0005019 pancreatic epsilon cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'epsilon', 'full_name': 'epsilon cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0005019 pancreatic epsilon cell +hybrid unknown unknown DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'hybrid', 'full_name': 'Hybrid cells', 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +immune_stellates unknown unknown DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'immune_stellates', 'full_name': 'immune and stellate cells', 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +pp CL:0000696 PP cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'pp', 'full_name': 'PP cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000696 PP cell +stellates CL:0002410 pancreatic stellate cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'stellates', 'full_name': 'stellate cell', 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found diff --git a/output/raw_output/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique/groundings.tsv b/output/raw_output/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..43c77bd --- /dev/null +++ b/output/raw_output/37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,15 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +acinar CL:0002064 pancreatic acinar cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'acinar', 'full_name': 'acinar cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000622 acinar cell FALSE +acinar_minor_mhcclassII CL:0002064 pancreatic acinar cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'acinar_minor_mhcclassII', 'full_name': 'MHC Class II acinar cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000622 acinar cell FALSE +alpha CL:0000171 pancreatic A cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'alpha', 'full_name': 'alpha cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000171 pancreatic A cell TRUE +beta_major CL:0000169 type B pancreatic cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'beta_major', 'full_name': 'beta cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000169 type B pancreatic cell TRUE +beta_minor CL:0000169 type B pancreatic cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'beta_minor', 'full_name': 'beta cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000169 type B pancreatic cell TRUE +delta CL:0000173 pancreatic D cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'delta', 'full_name': 'delta cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000173 pancreatic D cell TRUE +duct_acinar_related CL:0002079 pancreatic ductal cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'duct_acinar_related', 'full_name': 'ductal-acinar related cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002080 pancreatic centro-acinar cell FALSE +duct_major CL:0002079 pancreatic ductal cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'duct_major', 'full_name': 'ductal cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002079 pancreatic ductal cell TRUE +endothelial CL:0000115 endothelial cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'endothelial', 'full_name': 'endothelial cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +epsilon CL:0005019 pancreatic epsilon cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'epsilon', 'full_name': 'epsilon cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0005019 pancreatic epsilon cell TRUE +hybrid unknown unknown DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'hybrid', 'full_name': 'Hybrid cells', 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +immune_stellates unknown unknown DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'immune_stellates', 'full_name': 'immune and stellate cells', 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +pp CL:0000696 PP cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'pp', 'full_name': 'PP cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000696 PP cell TRUE +stellates CL:0002410 pancreatic stellate cell DOI:10.1038/s42255-022-00531-x 37b21763-7f0f-41ae-9001-60bad6e2841d_cxg_dataset_unique {'name': 'stellates', 'full_name': 'stellate cell', 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE diff --git a/output/raw_output/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..651e1bc --- /dev/null +++ b/output/raw_output/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,18 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Astrocytes CL:0000127 astrocyte DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Astrocytes', 'full_name': 'Astrocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000127 astrocyte +Endothelial CL:0000115 endothelial cell DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Endothelial', 'full_name': 'endothelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +L2-L3 Intratelencephalic CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L2-L3 Intratelencephalic', 'full_name': 'L2-L3 intratelencephalic', 'paper_synonyms': '', 'tissue_context': ''} CL:4030059 L2/3 intratelencephalic projecting glutamatergic neuron +L3-L5 Intratelencephalic Type 1 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L3-L5 Intratelencephalic Type 1', 'full_name': 'L3-L5 intratelencephalic type 1', 'paper_synonyms': '', 'tissue_context': ''} CL:4023008 intratelencephalic-projecting glutamatergic cortical neuron +L3-L5 Intratelencephalic Type 2 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L3-L5 Intratelencephalic Type 2', 'full_name': 'L3-L5 intratelencephalic type 2', 'paper_synonyms': '', 'tissue_context': ''} CL:4023008 intratelencephalic-projecting glutamatergic cortical neuron +L5 Extratelencephalic CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L5 Extratelencephalic', 'full_name': 'L5 extratelencephalic neurons', 'paper_synonyms': None, 'tissue_context': ''} CL:4023041 L5 extratelencephalic projecting glutamatergic cortical neuron +L5-L6 Near Projecting CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L5-L6 Near Projecting', 'full_name': 'L5-L6 near projecting neuronal cluster', 'paper_synonyms': None, 'tissue_context': ''} CL:4030067 L5/6 near-projecting glutamatergic neuron +L6 Corticothalamic / L6B CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L6 Corticothalamic / L6B', 'full_name': 'L6 corticothalamic / L6B', 'paper_synonyms': 'L6 corticothalamic; L6B', 'tissue_context': ''} CL:4023042 L6 corticothalamic-projecting glutamatergic cortical neuron +L6 Intratelencephalic - Type 1 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L6 Intratelencephalic - Type 1', 'full_name': 'L6 intratelencephalic type 1', 'paper_synonyms': '', 'tissue_context': ''} CL:4030065 L6 intratelencephalic projecting glutamatergic neuron +L6 Intratelencephalic - Type 2 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L6 Intratelencephalic - Type 2', 'full_name': 'L6 intratelencephalic type 2', 'paper_synonyms': '', 'tissue_context': ''} CL:4030065 L6 intratelencephalic projecting glutamatergic neuron +Microglia CL:0000129 microglial cell DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Microglia', 'full_name': 'microglia', 'paper_synonyms': None, 'tissue_context': ''} CL:0000129 microglial cell +OPCs CL:0002453 oligodendrocyte precursor cell DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'OPCs', 'full_name': 'oligodendrocyte progenitor cells', 'paper_synonyms': 'oligodendrocyte progenitor cells', 'tissue_context': ''} CL:0002453 oligodendrocyte precursor cell +Oligodendrocytes CL:0000128 oligodendrocyte DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Oligodendrocytes', 'full_name': 'Oligodendrocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000128 oligodendrocyte +Parvalbumin interneurons CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Parvalbumin interneurons', 'full_name': 'Parvalbumin interneurons', 'paper_synonyms': None, 'tissue_context': ''} CL:4023018 pvalb GABAergic interneuron +SV2C LAMP5 Interneurons CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'SV2C LAMP5 Interneurons', 'full_name': 'SV2C LAMP5 interneurons', 'paper_synonyms': '', 'tissue_context': ''} CL:4023011 lamp5 GABAergic interneuron +Somatostatin Interneurons CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Somatostatin Interneurons', 'full_name': 'somatostatin interneurons', 'paper_synonyms': None, 'tissue_context': ''} CL:4023017 sst GABAergic interneuron +VIP Interneurons CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'VIP Interneurons', 'full_name': 'VIP interneurons', 'paper_synonyms': None, 'tissue_context': ''} CL:4023016 VIP GABAergic interneuron diff --git a/output/raw_output/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique/groundings.tsv b/output/raw_output/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..59dbd00 --- /dev/null +++ b/output/raw_output/3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,18 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Astrocytes CL:0000127 astrocyte DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Astrocytes', 'full_name': 'Astrocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000127 astrocyte TRUE +Endothelial CL:0000115 endothelial cell DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Endothelial', 'full_name': 'endothelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +L2-L3 Intratelencephalic CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L2-L3 Intratelencephalic', 'full_name': 'L2-L3 intratelencephalic', 'paper_synonyms': '', 'tissue_context': ''} CL:4030059 L2/3 intratelencephalic projecting glutamatergic neuron FALSE +L3-L5 Intratelencephalic Type 1 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L3-L5 Intratelencephalic Type 1', 'full_name': 'L3-L5 intratelencephalic type 1', 'paper_synonyms': '', 'tissue_context': ''} CL:4023008 intratelencephalic-projecting glutamatergic cortical neuron FALSE +L3-L5 Intratelencephalic Type 2 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L3-L5 Intratelencephalic Type 2', 'full_name': 'L3-L5 intratelencephalic type 2', 'paper_synonyms': '', 'tissue_context': ''} CL:4023008 intratelencephalic-projecting glutamatergic cortical neuron FALSE +L5 Extratelencephalic CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L5 Extratelencephalic', 'full_name': 'L5 extratelencephalic neurons', 'paper_synonyms': None, 'tissue_context': ''} CL:4023041 L5 extratelencephalic projecting glutamatergic cortical neuron FALSE +L5-L6 Near Projecting CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L5-L6 Near Projecting', 'full_name': 'L5-L6 near projecting neuronal cluster', 'paper_synonyms': None, 'tissue_context': ''} CL:4030067 L5/6 near-projecting glutamatergic neuron FALSE +L6 Corticothalamic / L6B CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L6 Corticothalamic / L6B', 'full_name': 'L6 corticothalamic / L6B', 'paper_synonyms': 'L6 corticothalamic; L6B', 'tissue_context': ''} CL:4023042 L6 corticothalamic-projecting glutamatergic cortical neuron FALSE +L6 Intratelencephalic - Type 1 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L6 Intratelencephalic - Type 1', 'full_name': 'L6 intratelencephalic type 1', 'paper_synonyms': '', 'tissue_context': ''} CL:4030065 L6 intratelencephalic projecting glutamatergic neuron FALSE +L6 Intratelencephalic - Type 2 CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'L6 Intratelencephalic - Type 2', 'full_name': 'L6 intratelencephalic type 2', 'paper_synonyms': '', 'tissue_context': ''} CL:4030065 L6 intratelencephalic projecting glutamatergic neuron FALSE +Microglia CL:0000129 microglial cell DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Microglia', 'full_name': 'microglia', 'paper_synonyms': None, 'tissue_context': ''} CL:0000129 microglial cell TRUE +OPCs CL:0002453 oligodendrocyte precursor cell DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'OPCs', 'full_name': 'oligodendrocyte progenitor cells', 'paper_synonyms': 'oligodendrocyte progenitor cells', 'tissue_context': ''} CL:0002453 oligodendrocyte precursor cell TRUE +Oligodendrocytes CL:0000128 oligodendrocyte DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Oligodendrocytes', 'full_name': 'Oligodendrocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000128 oligodendrocyte TRUE +Parvalbumin interneurons CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Parvalbumin interneurons', 'full_name': 'Parvalbumin interneurons', 'paper_synonyms': None, 'tissue_context': ''} CL:4023018 pvalb GABAergic interneuron FALSE +SV2C LAMP5 Interneurons CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'SV2C LAMP5 Interneurons', 'full_name': 'SV2C LAMP5 interneurons', 'paper_synonyms': '', 'tissue_context': ''} CL:4023011 lamp5 GABAergic interneuron FALSE +Somatostatin Interneurons CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'Somatostatin Interneurons', 'full_name': 'somatostatin interneurons', 'paper_synonyms': None, 'tissue_context': ''} CL:4023017 sst GABAergic interneuron FALSE +VIP Interneurons CL:0000540 neuron DOI:10.1007/s00401-023-02599-5 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique {'name': 'VIP Interneurons', 'full_name': 'VIP interneurons', 'paper_synonyms': None, 'tissue_context': ''} CL:4023016 VIP GABAergic interneuron FALSE diff --git a/output/raw_output/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..7e9d19e --- /dev/null +++ b/output/raw_output/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,70 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +B cell CL:0000787 memory B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B cell', 'full_name': 'B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +B cell CL:0000788 naive B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B cell', 'full_name': 'B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +B cell CL:0000818 transitional stage B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B cell', 'full_name': 'B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +B intermediate CL:0000818 transitional stage B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B intermediate', 'full_name': 'intermediate B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000818 transitional stage B cell +B memory CL:0000787 memory B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B memory', 'full_name': 'memory B cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000787 memory B cell +B naive CL:0000788 naive B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B naive', 'full_name': 'naive B cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000788 naive B cell +CD14+ Monocyte CL:0000860 classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD14+ Monocyte', 'full_name': 'CD14+ monocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0001054 CD14-positive monocyte +CD16+ Monocyte CL:0000875 non-classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD16+ Monocyte', 'full_name': 'monocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000576 monocyte +CD4+ CTL CL:0000934 CD4-positive, alpha-beta cytotoxic T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ CTL', 'full_name': 'CD4+ Cytotoxic T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000934 CD4-positive, alpha-beta cytotoxic T cell +CD4+ T activated CL:0001043 activated CD4-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T activated', 'full_name': 'CD4+ activated T cell', 'paper_synonyms': 'activated T cells', 'tissue_context': ''} CL:0000896 activated CD4-positive, alpha-beta T cell +CD4+ T cell CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD4+ T cell CL:0000934 CD4-positive, alpha-beta cytotoxic T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD4+ T cell CL:0000904 central memory CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD4+ T cell CL:0000815 regulatory T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD4+ T cell CL:0001043 activated CD4-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD4+ T naive CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T naive', 'full_name': 'CD4+ Naive T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell +CD4+ Tcm CL:0000904 central memory CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ Tcm', 'full_name': 'CD4+ Central Memory T cell', 'paper_synonyms': 'CD4+ TCM; CD4+ Central Memory T cell', 'tissue_context': ''} CL:0000904 central memory CD4-positive, alpha-beta T cell +CD8+ T activated CL:0001049 activated CD8-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T activated', 'full_name': 'Activated CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000906 activated CD8-positive, alpha-beta T cell +CD8+ T cell CL:0000913 effector memory CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T cell', 'full_name': 'CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell +CD8+ T cell CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T cell', 'full_name': 'CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell +CD8+ T cell CL:0001049 activated CD8-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T cell', 'full_name': 'CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell +CD8+ T cell CL:0000940 mucosal invariant T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T cell', 'full_name': 'CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell +CD8+ T naive CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T naive', 'full_name': 'CD8+ Naive T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell +CD8+ Tem CL:0000913 effector memory CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ Tem', 'full_name': 'CD8+ Effector Memory cell', 'paper_synonyms': 'CD8+ TEM', 'tissue_context': ''} CL:0000913 effector memory CD8-positive, alpha-beta T cell +Classical Monocyte CL:0000860 classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Classical Monocyte', 'full_name': 'classical monocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000860 classical monocyte +HSPC CL:0000037 hematopoietic stem cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'HSPC', 'full_name': 'Hematopoietic stem and progenitor cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0008001 hematopoietic precursor cell +Hematopoietic_Mega CL:0000233 platelet DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Hematopoietic_Mega', 'full_name': 'hematopoietic megakaryocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000556 megakaryocyte +Hematopoietic_R CL:0000232 erythrocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Hematopoietic_R', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000988 hematopoietic cell +Hematopoietic_SC CL:0000037 hematopoietic stem cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Hematopoietic_SC', 'full_name': 'hematopoietic stem and progenitor cells', 'paper_synonyms': 'HSPC', 'tissue_context': ''} CL:0008001 hematopoietic precursor cell +Lymphoid_B CL:0000787 memory B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_B', 'full_name': 'B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +Lymphoid_B CL:0000788 naive B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_B', 'full_name': 'B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +Lymphoid_B CL:0000818 transitional stage B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_B', 'full_name': 'B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +Lymphoid_P CL:0000980 plasmablast DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_P', 'full_name': 'lymphoid', 'paper_synonyms': None, 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000623 natural killer cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000913 effector memory CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000934 CD4-positive, alpha-beta cytotoxic T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000542 lymphocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000938 CD16-negative, CD56-bright natural killer cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000904 central memory CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000815 regulatory T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0001043 activated CD4-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0001049 activated CD8-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +Lymphoid_T/NK CL:0000940 mucosal invariant T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte +MAIT CL:0000940 mucosal invariant T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'MAIT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000940 mucosal-associated invariant T cell +Myeloid CL:0000990 conventional dendritic cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid', 'full_name': 'myeloid cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000763 myeloid cell +Myeloid CL:0000860 classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid', 'full_name': 'myeloid cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000763 myeloid cell +Myeloid CL:0001058 plasmacytoid dendritic cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid', 'full_name': 'myeloid cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000763 myeloid cell +Myeloid CL:0000875 non-classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid', 'full_name': 'myeloid cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000763 myeloid cell +Myeloid_G CL:0000775 neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid_G', 'full_name': 'myeloid cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000763 myeloid cell +Myeloid_G CL:0000776 immature neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid_G', 'full_name': 'myeloid cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000763 myeloid cell +NK CL:0000623 natural killer cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK', 'full_name': 'NK cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000623 natural killer cell +NK CD56bright CL:0000938 CD16-negative, CD56-bright natural killer cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK CD56bright', 'full_name': 'CD56-bright NK cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000938 CD16-negative, CD56-bright natural killer cell, human +NK activated CL:0000623 natural killer cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK activated', 'full_name': 'Activated NK cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell +NK cell CL:0000623 natural killer cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK cell', 'full_name': 'NK cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell +NK cell CL:0000938 CD16-negative, CD56-bright natural killer cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK cell', 'full_name': 'NK cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell +Neutrophil CL:0000775 neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': 'Neutrophil', 'paper_synonyms': None, 'tissue_context': ''} CL:0000775 neutrophil +Neutrophil CL:0000776 immature neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': 'Neutrophil', 'paper_synonyms': None, 'tissue_context': ''} CL:0000775 neutrophil +Non-classical Monocyte CL:0000875 non-classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Non-classical Monocyte', 'full_name': 'non-classical monocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000875 non-classical monocyte +Other T CL:0000542 lymphocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Other T', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000084 T cell +Plasmablast CL:0000980 plasmablast DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Plasmablast', 'full_name': 'plasmablast', 'paper_synonyms': '', 'tissue_context': ''} CL:0000980 plasmablast +Platelet CL:0000233 platelet DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Platelet', 'full_name': 'platelet', 'paper_synonyms': None, 'tissue_context': ''} CL:0000233 platelet +RBC CL:0000232 erythrocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'RBC', 'full_name': 'red blood cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte +T/NK proliferative CL:0000542 lymphocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'T/NK proliferative', 'full_name': 'proliferative T and NK cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000542 lymphocyte +Treg CL:0000815 regulatory T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Treg', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000815 regulatory T cell +cDC CL:0000990 conventional dendritic cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'cDC', 'full_name': 'conventional dendritic cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000990 conventional dendritic cell +immature Neutrophil CL:0000776 immature neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'immature Neutrophil', 'full_name': 'immature neutrophil', 'paper_synonyms': None, 'tissue_context': ''} CL:0000776 immature neutrophil +pDC CL:0001058 plasmacytoid dendritic cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'pDC', 'full_name': 'plasmacytoid dendritic cell', 'paper_synonyms': 'plasmacytoid dendritic cells', 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell diff --git a/output/raw_output/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique/groundings.tsv b/output/raw_output/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..5dd63da --- /dev/null +++ b/output/raw_output/59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,70 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +B cell CL:0000787 memory B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B cell', 'full_name': 'B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell FALSE +B cell CL:0000788 naive B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B cell', 'full_name': 'B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell FALSE +B cell CL:0000818 transitional stage B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B cell', 'full_name': 'B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell FALSE +B intermediate CL:0000818 transitional stage B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B intermediate', 'full_name': 'intermediate B cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000818 transitional stage B cell TRUE +B memory CL:0000787 memory B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B memory', 'full_name': 'memory B cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000787 memory B cell TRUE +B naive CL:0000788 naive B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'B naive', 'full_name': 'naive B cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000788 naive B cell TRUE +CD14+ Monocyte CL:0000860 classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD14+ Monocyte', 'full_name': 'CD14+ monocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0001054 CD14-positive monocyte FALSE +CD16+ Monocyte CL:0000875 non-classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD16+ Monocyte', 'full_name': 'monocytes', 'paper_synonyms': '', 'tissue_context': ''} CL:0000576 monocyte FALSE +CD4+ CTL CL:0000934 CD4-positive, alpha-beta cytotoxic T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ CTL', 'full_name': 'CD4+ Cytotoxic T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000934 CD4-positive, alpha-beta cytotoxic T cell TRUE +CD4+ T activated CL:0001043 activated CD4-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T activated', 'full_name': 'CD4+ activated T cell', 'paper_synonyms': 'activated T cells', 'tissue_context': ''} CL:0000896 activated CD4-positive, alpha-beta T cell FALSE +CD4+ T cell CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell FALSE +CD4+ T cell CL:0000934 CD4-positive, alpha-beta cytotoxic T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell FALSE +CD4+ T cell CL:0000904 central memory CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell FALSE +CD4+ T cell CL:0000815 regulatory T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell FALSE +CD4+ T cell CL:0001043 activated CD4-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T cell', 'full_name': 'CD4+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell FALSE +CD4+ T naive CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ T naive', 'full_name': 'CD4+ Naive T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell TRUE +CD4+ Tcm CL:0000904 central memory CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD4+ Tcm', 'full_name': 'CD4+ Central Memory T cell', 'paper_synonyms': 'CD4+ TCM; CD4+ Central Memory T cell', 'tissue_context': ''} CL:0000904 central memory CD4-positive, alpha-beta T cell TRUE +CD8+ T activated CL:0001049 activated CD8-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T activated', 'full_name': 'Activated CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000906 activated CD8-positive, alpha-beta T cell FALSE +CD8+ T cell CL:0000913 effector memory CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T cell', 'full_name': 'CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell FALSE +CD8+ T cell CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T cell', 'full_name': 'CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell FALSE +CD8+ T cell CL:0001049 activated CD8-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T cell', 'full_name': 'CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell FALSE +CD8+ T cell CL:0000940 mucosal invariant T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T cell', 'full_name': 'CD8+ T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell FALSE +CD8+ T naive CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ T naive', 'full_name': 'CD8+ Naive T cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell TRUE +CD8+ Tem CL:0000913 effector memory CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'CD8+ Tem', 'full_name': 'CD8+ Effector Memory cell', 'paper_synonyms': 'CD8+ TEM', 'tissue_context': ''} CL:0000913 effector memory CD8-positive, alpha-beta T cell TRUE +Classical Monocyte CL:0000860 classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Classical Monocyte', 'full_name': 'classical monocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000860 classical monocyte TRUE +HSPC CL:0000037 hematopoietic stem cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'HSPC', 'full_name': 'Hematopoietic stem and progenitor cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0008001 hematopoietic precursor cell FALSE +Hematopoietic_Mega CL:0000233 platelet DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Hematopoietic_Mega', 'full_name': 'hematopoietic megakaryocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000556 megakaryocyte FALSE +Hematopoietic_R CL:0000232 erythrocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Hematopoietic_R', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000988 hematopoietic cell FALSE +Hematopoietic_SC CL:0000037 hematopoietic stem cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Hematopoietic_SC', 'full_name': 'hematopoietic stem and progenitor cells', 'paper_synonyms': 'HSPC', 'tissue_context': ''} CL:0008001 hematopoietic precursor cell FALSE +Lymphoid_B CL:0000787 memory B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_B', 'full_name': 'B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell FALSE +Lymphoid_B CL:0000788 naive B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_B', 'full_name': 'B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell FALSE +Lymphoid_B CL:0000818 transitional stage B cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_B', 'full_name': 'B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell FALSE +Lymphoid_P CL:0000980 plasmablast DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_P', 'full_name': 'lymphoid', 'paper_synonyms': None, 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000623 natural killer cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000913 effector memory CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000934 CD4-positive, alpha-beta cytotoxic T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000542 lymphocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte TRUE +Lymphoid_T/NK CL:0000938 CD16-negative, CD56-bright natural killer cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000904 central memory CD4-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000815 regulatory T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0001043 activated CD4-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0001049 activated CD8-positive, alpha-beta T cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +Lymphoid_T/NK CL:0000940 mucosal invariant T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Lymphoid_T/NK', 'full_name': 'Lymphoid T and NK cells', 'paper_synonyms': 'T cell; NK cell', 'tissue_context': ''} CL:0000542 lymphocyte FALSE +MAIT CL:0000940 mucosal invariant T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'MAIT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000940 mucosal-associated invariant T cell TRUE +Myeloid CL:0000990 conventional dendritic cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid', 'full_name': 'myeloid cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000763 myeloid cell FALSE +Myeloid CL:0000860 classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid', 'full_name': 'myeloid cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000763 myeloid cell FALSE +Myeloid CL:0001058 plasmacytoid dendritic cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid', 'full_name': 'myeloid cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000763 myeloid cell FALSE +Myeloid CL:0000875 non-classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid', 'full_name': 'myeloid cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000763 myeloid cell FALSE +Myeloid_G CL:0000775 neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid_G', 'full_name': 'myeloid cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000763 myeloid cell FALSE +Myeloid_G CL:0000776 immature neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Myeloid_G', 'full_name': 'myeloid cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000763 myeloid cell FALSE +NK CL:0000623 natural killer cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK', 'full_name': 'NK cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000623 natural killer cell TRUE +NK CD56bright CL:0000938 CD16-negative, CD56-bright natural killer cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK CD56bright', 'full_name': 'CD56-bright NK cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000938 CD16-negative, CD56-bright natural killer cell, human TRUE +NK activated CL:0000623 natural killer cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK activated', 'full_name': 'Activated NK cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell TRUE +NK cell CL:0000623 natural killer cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK cell', 'full_name': 'NK cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell TRUE +NK cell CL:0000938 CD16-negative, CD56-bright natural killer cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'NK cell', 'full_name': 'NK cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000623 natural killer cell FALSE +Neutrophil CL:0000775 neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': 'Neutrophil', 'paper_synonyms': None, 'tissue_context': ''} CL:0000775 neutrophil TRUE +Neutrophil CL:0000776 immature neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': 'Neutrophil', 'paper_synonyms': None, 'tissue_context': ''} CL:0000775 neutrophil FALSE +Non-classical Monocyte CL:0000875 non-classical monocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Non-classical Monocyte', 'full_name': 'non-classical monocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000875 non-classical monocyte TRUE +Other T CL:0000542 lymphocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Other T', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000084 T cell FALSE +Plasmablast CL:0000980 plasmablast DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Plasmablast', 'full_name': 'plasmablast', 'paper_synonyms': '', 'tissue_context': ''} CL:0000980 plasmablast TRUE +Platelet CL:0000233 platelet DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Platelet', 'full_name': 'platelet', 'paper_synonyms': None, 'tissue_context': ''} CL:0000233 platelet TRUE +RBC CL:0000232 erythrocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'RBC', 'full_name': 'red blood cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte TRUE +T/NK proliferative CL:0000542 lymphocyte DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'T/NK proliferative', 'full_name': 'proliferative T and NK cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000542 lymphocyte TRUE +Treg CL:0000815 regulatory T cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'Treg', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000815 regulatory T cell TRUE +cDC CL:0000990 conventional dendritic cell DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'cDC', 'full_name': 'conventional dendritic cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000990 conventional dendritic cell TRUE +immature Neutrophil CL:0000776 immature neutrophil DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'immature Neutrophil', 'full_name': 'immature neutrophil', 'paper_synonyms': None, 'tissue_context': ''} CL:0000776 immature neutrophil TRUE +pDC CL:0001058 plasmacytoid dendritic cell, human DOI:10.1016/j.isci.2021.103115 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique {'name': 'pDC', 'full_name': 'plasmacytoid dendritic cell', 'paper_synonyms': 'plasmacytoid dendritic cells', 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell FALSE diff --git a/output/raw_output/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..c68c033 --- /dev/null +++ b/output/raw_output/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,52 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +37- unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': '37-', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +38- unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': '38-', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +5- unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': '5-', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_01 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_01', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +AC_B_02 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_02', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_04 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_04', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +AC_B_05 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_05', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_06 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_06', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_07 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_07', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_08 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_08', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_09 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_09', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +AC_B_10 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_10', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_11 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_11', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +AC_B_12 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_12', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_13 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_13', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_15 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_15', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +AC_B_16 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_16', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_B_17 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_17', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +AC_B_18 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_18', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_Y_01 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_Y_01', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +AC_Y_03 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_Y_03', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000561 amacrine cell +Ast CL:0000127 astrocyte DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'Ast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000127 astrocyte +CdBC_01 CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_01', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron +CdBC_02 CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_02', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron +CdBC_03 CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_03', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +CdBC_04 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_04', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +CdBC_05 CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_05', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +ChBC_01 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'ChBC_01', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +ChBC_02 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'ChBC_02', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +ChBC_03 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'ChBC_03', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +ChBC_04 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'ChBC_04', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found +HC_02 CL:0000745 retina horizontal cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'HC_02', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000745 retina horizontal cell +L/M cone CL:0000573 retinal cone cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'L/M cone', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000573 retinal cone cell +MC_01 CL:0000636 Mueller cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'MC_01', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +MC_02 CL:0000636 Mueller cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'MC_02', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +MC_03 CL:0000636 Mueller cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'MC_03', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +RBC CL:0000751 rod bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'RBC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte +RPE CL:0002586 retinal pigment epithelial cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'RPE', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0002586 retinal pigment epithelial cell +S cone CL:0000573 retinal cone cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'S cone', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0003050 S cone cell +amacrine CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'amacrine', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000561 amacrine cell +amacrine unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'amacrine', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000561 amacrine cell +bipolar CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'bipolar', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000103 bipolar neuron +bipolar CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'bipolar', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000103 bipolar neuron +bipolar CL:0000751 rod bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'bipolar', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000103 bipolar neuron +cone CL:0000573 retinal cone cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'cone', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000573 retinal cone cell +horizontal CL:0000745 retina horizontal cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'horizontal', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000745 retina horizontal cell +horizontal unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'horizontal', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000745 retina horizontal cell +macroglia CL:0000636 Mueller cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'macroglia', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000126 macroglial cell +macroglia CL:0000127 astrocyte DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'macroglia', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000126 macroglial cell +pigmented CL:0002586 retinal pigment epithelial cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'pigmented', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000147 pigment cell +rod CL:0000604 retinal rod cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'rod', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell diff --git a/output/raw_output/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique/groundings.tsv b/output/raw_output/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..54ebcac --- /dev/null +++ b/output/raw_output/7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,52 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +37- unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': '37-', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +38- unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': '38-', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +5- unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': '5-', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_01 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_01', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +AC_B_02 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_02', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_04 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_04', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +AC_B_05 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_05', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_06 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_06', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_07 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_07', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_08 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_08', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_09 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_09', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +AC_B_10 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_10', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_11 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_11', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +AC_B_12 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_12', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_13 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_13', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_15 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_15', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +AC_B_16 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_16', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_B_17 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_17', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +AC_B_18 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_B_18', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_Y_01 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_Y_01', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +AC_Y_03 CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'AC_Y_03', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000561 amacrine cell TRUE +Ast CL:0000127 astrocyte DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'Ast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000127 astrocyte TRUE +CdBC_01 CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_01', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron FALSE +CdBC_02 CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_02', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron FALSE +CdBC_03 CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_03', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +CdBC_04 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_04', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +CdBC_05 CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'CdBC_05', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +ChBC_01 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'ChBC_01', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +ChBC_02 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'ChBC_02', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +ChBC_03 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'ChBC_03', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +ChBC_04 CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'ChBC_04', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} NO MATCH found FALSE +HC_02 CL:0000745 retina horizontal cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'HC_02', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000745 retina horizontal cell TRUE +L/M cone CL:0000573 retinal cone cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'L/M cone', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000573 retinal cone cell TRUE +MC_01 CL:0000636 Mueller cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'MC_01', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +MC_02 CL:0000636 Mueller cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'MC_02', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +MC_03 CL:0000636 Mueller cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'MC_03', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +RBC CL:0000751 rod bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'RBC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000232 erythrocyte FALSE +RPE CL:0002586 retinal pigment epithelial cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'RPE', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0002586 retinal pigment epithelial cell TRUE +S cone CL:0000573 retinal cone cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'S cone', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0003050 S cone cell FALSE +amacrine CL:0000561 amacrine cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'amacrine', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000561 amacrine cell TRUE +amacrine unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'amacrine', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000561 amacrine cell FALSE +bipolar CL:0000749 ON-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'bipolar', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000103 bipolar neuron FALSE +bipolar CL:0000750 OFF-bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'bipolar', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000103 bipolar neuron FALSE +bipolar CL:0000751 rod bipolar cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'bipolar', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000103 bipolar neuron FALSE +cone CL:0000573 retinal cone cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'cone', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000573 retinal cone cell TRUE +horizontal CL:0000745 retina horizontal cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'horizontal', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000745 retina horizontal cell TRUE +horizontal unknown unknown DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'horizontal', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000745 retina horizontal cell FALSE +macroglia CL:0000636 Mueller cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'macroglia', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000126 macroglial cell FALSE +macroglia CL:0000127 astrocyte DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'macroglia', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000126 macroglial cell FALSE +pigmented CL:0002586 retinal pigment epithelial cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'pigmented', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000147 pigment cell FALSE +rod CL:0000604 retinal rod cell DOI:10.1016/j.cell.2020.08.013 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique {'name': 'rod', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell TRUE diff --git a/output/raw_output/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..c296f4b --- /dev/null +++ b/output/raw_output/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,13 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +BB+GB* CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'BB+GB*', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +DB1 CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB1', 'full_name': 'bipolar type DB1', 'paper_synonyms': None, 'tissue_context': ''} CL:4033027 diffuse bipolar 1 cell +DB2 CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB2', 'full_name': 'bipolar type DB2', 'paper_synonyms': None, 'tissue_context': ''} CL:4033028 diffuse bipolar 2 cell +DB3a CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB3a', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033029 diffuse bipolar 3a cell +DB3b CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB3b', 'full_name': 'bipolar type DB3b', 'paper_synonyms': None, 'tissue_context': ''} CL:4033030 diffuse bipolar 3b cell +DB4 CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB4', 'full_name': 'bipolar type DB4', 'paper_synonyms': None, 'tissue_context': ''} CL:4033031 diffuse bipolar 4 cell +DB5* CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB5*', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033085 diffuse bipolar 5 cell +DB6 CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB6', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033032 diffuse bipolar 6 cell +FMB CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'FMB', 'full_name': 'bipolar type FMB', 'paper_synonyms': None, 'tissue_context': ''} CL:4033033 flat midget bipolar cell +IMB CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'IMB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033034 invaginating midget bipolar cell +OFFx CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'OFFx', 'full_name': 'OFFx type', 'paper_synonyms': None, 'tissue_context': ''} CL:4033036 OFFx cell +RB1 CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'RB1', 'full_name': None, 'paper_synonyms': 'rod bipolar cells; rod BCs', 'tissue_context': ''} CL:0000751 rod bipolar cell diff --git a/output/raw_output/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique/groundings.tsv b/output/raw_output/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..e0f03a1 --- /dev/null +++ b/output/raw_output/8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,13 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +BB+GB* CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'BB+GB*', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +DB1 CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB1', 'full_name': 'bipolar type DB1', 'paper_synonyms': None, 'tissue_context': ''} CL:4033027 diffuse bipolar 1 cell FALSE +DB2 CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB2', 'full_name': 'bipolar type DB2', 'paper_synonyms': None, 'tissue_context': ''} CL:4033028 diffuse bipolar 2 cell FALSE +DB3a CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB3a', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033029 diffuse bipolar 3a cell FALSE +DB3b CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB3b', 'full_name': 'bipolar type DB3b', 'paper_synonyms': None, 'tissue_context': ''} CL:4033030 diffuse bipolar 3b cell FALSE +DB4 CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB4', 'full_name': 'bipolar type DB4', 'paper_synonyms': None, 'tissue_context': ''} CL:4033031 diffuse bipolar 4 cell FALSE +DB5* CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB5*', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033085 diffuse bipolar 5 cell FALSE +DB6 CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'DB6', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033032 diffuse bipolar 6 cell FALSE +FMB CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'FMB', 'full_name': 'bipolar type FMB', 'paper_synonyms': None, 'tissue_context': ''} CL:4033033 flat midget bipolar cell FALSE +IMB CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'IMB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033034 invaginating midget bipolar cell FALSE +OFFx CL:0000750 OFF-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'OFFx', 'full_name': 'OFFx type', 'paper_synonyms': None, 'tissue_context': ''} CL:4033036 OFFx cell FALSE +RB1 CL:0000749 ON-bipolar cell DOI:10.1038/s41598-020-66092-9 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique {'name': 'RB1', 'full_name': None, 'paper_synonyms': 'rod bipolar cells; rod BCs', 'tissue_context': ''} CL:0000751 rod bipolar cell FALSE diff --git a/output/raw_output/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..e040730 --- /dev/null +++ b/output/raw_output/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,42 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Activated B cell CL:0000236 B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Activated B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +Activated T CL:0001043 activated CD4-positive, alpha-beta T cell, human DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Activated T', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000084 T cell +Arterial endothelial cell CL:1000413 endothelial cell of artery DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Arterial endothelial cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000413 endothelial cell of artery +B cell CL:0000236 B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +BEST4 enterocyte CL:0000584 enterocyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'BEST4 enterocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030026 BEST4+ enterocyte +CD4 T cell CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'CD4 T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD8 T cell CL:0000625 CD8-positive, alpha-beta T cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'CD8 T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell +Cycling B cell CL:0000236 B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Cycling B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033068 cycling B cell +Cycling myeloid cells CL:0000763 myeloid cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Cycling myeloid cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033081 cycling myeloid cell +Cycling plasma cell CL:0000786 plasma cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Cycling plasma cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047003 cycling plasma cell +FCER2 B cell CL:0000236 B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'FCER2 B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +Glial cell CL:0000125 glial cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Glial cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000125 glial cell +Goblet cell CL:0019031 intestine goblet cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Goblet cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell +IL2RG+ enterocyte (M cell) CL:0000682 M cell of gut DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'IL2RG+ enterocyte (M cell)', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000682 M cell of gut +IgA plasma cell CL:0000987 IgA plasma cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'IgA plasma cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000987 IgA plasma cell +IgG plasma cell CL:0000985 IgG plasma cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'IgG plasma cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000985 IgG plasma cell +Lymphatic endothelial cell CL:0002138 endothelial cell of lymphatic vessel DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Lymphatic endothelial cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel +Macrophage CL:0000125 glial cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Macrophage', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage +Memory B cell CL:0000787 memory B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Memory B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000787 memory B cell +Monocyte CL:0000576 monocyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte +Paneth cell CL:0000125 glial cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Paneth cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000510 paneth cell +S1 fibroblasts CL:0000057 fibroblast DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'S1 fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +S2 fibroblasts CL:0000057 fibroblast DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'S2 fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +S4 fibroblasts CL:0000057 fibroblast DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'S4 fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +TA CL:0009010 transit amplifying cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'TA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009010 transit amplifying cell +Tfh CL:0002038 T follicular helper cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Tfh', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002038 T follicular helper cell +Treg CL:0000815 regulatory T cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Treg', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000815 regulatory T cell +Tuft CL:0019032 intestinal tuft cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell +Venous endothelial cell CL:0002543 vein endothelial cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Venous endothelial cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002543 vein endothelial cell +activated DC CL:0001056 dendritic cell, human DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'activated DC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000451 dendritic cell +cDC1 CL:0000990 conventional dendritic cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'cDC1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002394 CD141-positive myeloid dendritic cell +cDC2 CL:0000990 conventional dendritic cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'cDC2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002399 CD1c-positive myeloid dendritic cell +crypt CL:0002250 intestinal crypt stem cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'crypt', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002250 intestinal crypt stem cell +early enterocyte CL:0000584 enterocyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'early enterocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047019 early enterocyte +enterocyte CL:0000584 enterocyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'enterocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte +enteroendocrine CL:0000164 enteroendocrine cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'enteroendocrine', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell +gd T/NK cell CL:0000798 gamma-delta T cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'gd T/NK cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000798 gamma-delta T cell +mast cells CL:0000097 mast cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'mast cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell +myofibroblast CL:0000186 myofibroblast cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'myofibroblast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000186 myofibroblast cell +pDC CL:0000784 plasmacytoid dendritic cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'pDC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell +pericyte CL:0000669 pericyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'pericyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte diff --git a/output/raw_output/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique/groundings.tsv b/output/raw_output/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..22502d9 --- /dev/null +++ b/output/raw_output/8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,42 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Activated B cell CL:0000236 B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Activated B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell TRUE +Activated T CL:0001043 activated CD4-positive, alpha-beta T cell, human DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Activated T', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000084 T cell FALSE +Arterial endothelial cell CL:1000413 endothelial cell of artery DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Arterial endothelial cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000413 endothelial cell of artery TRUE +B cell CL:0000236 B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell TRUE +BEST4 enterocyte CL:0000584 enterocyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'BEST4 enterocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030026 BEST4+ enterocyte FALSE +CD4 T cell CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'CD4 T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell TRUE +CD8 T cell CL:0000625 CD8-positive, alpha-beta T cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'CD8 T cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell TRUE +Cycling B cell CL:0000236 B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Cycling B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033068 cycling B cell FALSE +Cycling myeloid cells CL:0000763 myeloid cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Cycling myeloid cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4033081 cycling myeloid cell FALSE +Cycling plasma cell CL:0000786 plasma cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Cycling plasma cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047003 cycling plasma cell FALSE +FCER2 B cell CL:0000236 B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'FCER2 B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell TRUE +Glial cell CL:0000125 glial cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Glial cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000125 glial cell TRUE +Goblet cell CL:0019031 intestine goblet cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Goblet cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell FALSE +IL2RG+ enterocyte (M cell) CL:0000682 M cell of gut DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'IL2RG+ enterocyte (M cell)', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000682 M cell of gut TRUE +IgA plasma cell CL:0000987 IgA plasma cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'IgA plasma cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000987 IgA plasma cell TRUE +IgG plasma cell CL:0000985 IgG plasma cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'IgG plasma cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000985 IgG plasma cell TRUE +Lymphatic endothelial cell CL:0002138 endothelial cell of lymphatic vessel DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Lymphatic endothelial cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel TRUE +Macrophage CL:0000125 glial cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Macrophage', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage FALSE +Memory B cell CL:0000787 memory B cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Memory B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000787 memory B cell TRUE +Monocyte CL:0000576 monocyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Monocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte TRUE +Paneth cell CL:0000125 glial cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Paneth cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000510 paneth cell FALSE +S1 fibroblasts CL:0000057 fibroblast DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'S1 fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +S2 fibroblasts CL:0000057 fibroblast DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'S2 fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +S4 fibroblasts CL:0000057 fibroblast DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'S4 fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +TA CL:0009010 transit amplifying cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'TA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0009010 transit amplifying cell TRUE +Tfh CL:0002038 T follicular helper cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Tfh', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002038 T follicular helper cell TRUE +Treg CL:0000815 regulatory T cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Treg', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000815 regulatory T cell TRUE +Tuft CL:0019032 intestinal tuft cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell FALSE +Venous endothelial cell CL:0002543 vein endothelial cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'Venous endothelial cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002543 vein endothelial cell TRUE +activated DC CL:0001056 dendritic cell, human DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'activated DC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000451 dendritic cell FALSE +cDC1 CL:0000990 conventional dendritic cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'cDC1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002394 CD141-positive myeloid dendritic cell FALSE +cDC2 CL:0000990 conventional dendritic cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'cDC2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002399 CD1c-positive myeloid dendritic cell FALSE +crypt CL:0002250 intestinal crypt stem cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'crypt', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002250 intestinal crypt stem cell TRUE +early enterocyte CL:0000584 enterocyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'early enterocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4047019 early enterocyte FALSE +enterocyte CL:0000584 enterocyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'enterocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte TRUE +enteroendocrine CL:0000164 enteroendocrine cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'enteroendocrine', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000164 enteroendocrine cell TRUE +gd T/NK cell CL:0000798 gamma-delta T cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'gd T/NK cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000798 gamma-delta T cell TRUE +mast cells CL:0000097 mast cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'mast cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000097 mast cell TRUE +myofibroblast CL:0000186 myofibroblast cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'myofibroblast', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000186 myofibroblast cell TRUE +pDC CL:0000784 plasmacytoid dendritic cell DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'pDC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell TRUE +pericyte CL:0000669 pericyte DOI:10.1016/j.devcel.2020.11.010 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique {'name': 'pericyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte TRUE diff --git a/output/raw_output/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..2a18afe --- /dev/null +++ b/output/raw_output/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,10 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Iris_APE CL:0000529 pigmented epithelial cell DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Iris_APE', 'full_name': 'iris anterior pigmented epithelium', 'paper_synonyms': 'anterior pigmented epithelium; APE; iris dilator muscle', 'tissue_context': ''} CL:0002565 iris pigment epithelial cell +Iris_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Iris_Fibro', 'full_name': 'iris stromal fibroblast', 'paper_synonyms': 'iris fibroblasts', 'tissue_context': ''} CL:0000057 fibroblast +Iris_PPE CL:0000529 pigmented epithelial cell DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Iris_PPE', 'full_name': 'iris posterior pigmented epithelium', 'paper_synonyms': 'posterior pigmented epithelium; PPE', 'tissue_context': ''} CL:0002565 iris pigment epithelial cell +Iris_Sphincter CL:0002243 smooth muscle cell of sphincter of pupil DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Iris_Sphincter', 'full_name': 'iris sphincter muscle cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0002243 smooth muscle cell of sphincter of pupil +Lymphocyte CL:0000542 lymphocyte DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Lymphocyte', 'full_name': 'lymphocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000542 lymphocyte +Macrophage CL:0000235 macrophage DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Macrophage', 'full_name': 'macrophage', 'paper_synonyms': 'clump cells', 'tissue_context': ''} CL:0000235 macrophage +Schwann CL:0002573 Schwann cell DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Schwann', 'full_name': 'Schwann cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0002573 Schwann cell +Uveal_Melanocyte CL:0000148 melanocyte DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Uveal_Melanocyte', 'full_name': 'uveal melanocyte', 'paper_synonyms': '', 'tissue_context': ''} CL:0000148 melanocyte +Vasc_Endo CL:0000071 blood vessel endothelial cell DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Vasc_Endo', 'full_name': 'vascular endothelium', 'paper_synonyms': None, 'tissue_context': ''} CL:0000071 blood vessel endothelial cell diff --git a/output/raw_output/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique/groundings.tsv b/output/raw_output/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..fa8e0b3 --- /dev/null +++ b/output/raw_output/9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,10 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Iris_APE CL:0000529 pigmented epithelial cell DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Iris_APE', 'full_name': 'iris anterior pigmented epithelium', 'paper_synonyms': 'anterior pigmented epithelium; APE; iris dilator muscle', 'tissue_context': ''} CL:0002565 iris pigment epithelial cell FALSE +Iris_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Iris_Fibro', 'full_name': 'iris stromal fibroblast', 'paper_synonyms': 'iris fibroblasts', 'tissue_context': ''} CL:0000057 fibroblast TRUE +Iris_PPE CL:0000529 pigmented epithelial cell DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Iris_PPE', 'full_name': 'iris posterior pigmented epithelium', 'paper_synonyms': 'posterior pigmented epithelium; PPE', 'tissue_context': ''} CL:0002565 iris pigment epithelial cell FALSE +Iris_Sphincter CL:0002243 smooth muscle cell of sphincter of pupil DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Iris_Sphincter', 'full_name': 'iris sphincter muscle cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0002243 smooth muscle cell of sphincter of pupil TRUE +Lymphocyte CL:0000542 lymphocyte DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Lymphocyte', 'full_name': 'lymphocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000542 lymphocyte TRUE +Macrophage CL:0000235 macrophage DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Macrophage', 'full_name': 'macrophage', 'paper_synonyms': 'clump cells', 'tissue_context': ''} CL:0000235 macrophage TRUE +Schwann CL:0002573 Schwann cell DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Schwann', 'full_name': 'Schwann cell', 'paper_synonyms': None, 'tissue_context': ''} CL:0002573 Schwann cell TRUE +Uveal_Melanocyte CL:0000148 melanocyte DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Uveal_Melanocyte', 'full_name': 'uveal melanocyte', 'paper_synonyms': '', 'tissue_context': ''} CL:0000148 melanocyte TRUE +Vasc_Endo CL:0000071 blood vessel endothelial cell DOI:10.1073/pnas.2200914119 9a281de7-cee5-4e80-8584-1929f46f152f_cxg_dataset_unique {'name': 'Vasc_Endo', 'full_name': 'vascular endothelium', 'paper_synonyms': None, 'tissue_context': ''} CL:0000071 blood vessel endothelial cell TRUE diff --git a/output/raw_output/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..96e52ff --- /dev/null +++ b/output/raw_output/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,16 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +CNT CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'CNT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +DCT1 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'DCT1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030016 epithelial cell of early distal convoluted tubule +DCT2 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'DCT2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030017 epithelial cell of late distal convoluted tubule +ENDO CL:1000892 kidney capillary endothelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'ENDO', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +FIB CL:0000057 fibroblast DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'FIB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +ICA CL:0005011 renal alpha-intercalated cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'ICA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell +ICB CL:0002201 renal beta-intercalated cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'ICB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002201 renal beta-intercalated cell +LEUK CL:0000738 leukocyte DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'LEUK', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +MES CL:0000650 mesangial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'MES', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000650 mesangial cell +PC CL:0005009 renal principal cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0005009 renal principal cell +PEC CL:1000452 parietal epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000452 parietal epithelial cell +PODO CL:0000653 podocyte DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PODO', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000653 podocyte +PT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +PT_VCAM1 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PT_VCAM1', 'full_name': 'VCAM1', 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'TAL', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell diff --git a/output/raw_output/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique/groundings.tsv b/output/raw_output/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..233b46b --- /dev/null +++ b/output/raw_output/9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,16 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +CNT CL:1000768 kidney connecting tubule epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'CNT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell TRUE +DCT1 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'DCT1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030016 epithelial cell of early distal convoluted tubule FALSE +DCT2 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'DCT2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030017 epithelial cell of late distal convoluted tubule FALSE +ENDO CL:1000892 kidney capillary endothelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'ENDO', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell FALSE +FIB CL:0000057 fibroblast DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'FIB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +ICA CL:0005011 renal alpha-intercalated cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'ICA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell TRUE +ICB CL:0002201 renal beta-intercalated cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'ICB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002201 renal beta-intercalated cell TRUE +LEUK CL:0000738 leukocyte DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'LEUK', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte TRUE +MES CL:0000650 mesangial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'MES', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000650 mesangial cell TRUE +PC CL:0005009 renal principal cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0005009 renal principal cell TRUE +PEC CL:1000452 parietal epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000452 parietal epithelial cell TRUE +PODO CL:0000653 podocyte DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PODO', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000653 podocyte TRUE +PT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +PT_VCAM1 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'PT_VCAM1', 'full_name': 'VCAM1', 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41467-021-22368-w 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique {'name': 'TAL', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell TRUE diff --git a/output/raw_output/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..bf2c0dd --- /dev/null +++ b/output/raw_output/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,38 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Ascending vasa recta endothelium CL:1001131 vasa recta ascending limb cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Ascending vasa recta endothelium', 'full_name': 'ascending vasa recta endothelium', 'paper_synonyms': 'AVRE', 'tissue_context': ''} CL:1001131 vasa recta ascending limb cell +B cell CL:0000236 B cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'B cell', 'full_name': 'B cell', 'paper_synonyms': 'B', 'tissue_context': ''} CL:0000236 B cell +CD4 T cell CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'CD4 T cell', 'full_name': 'CD4 T cell', 'paper_synonyms': 'CD4 T', 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell +CD8 T cell CL:0000625 CD8-positive, alpha-beta T cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'CD8 T cell', 'full_name': 'CD8 T cell', 'paper_synonyms': 'CD8 T', 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell +Connecting tubule CL:1000768 kidney connecting tubule epithelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Connecting tubule', 'full_name': 'connecting nephron tubule', 'paper_synonyms': 'CNT', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +Descending vasa recta endothelium CL:1001285 vasa recta descending limb cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Descending vasa recta endothelium', 'full_name': 'descending vasa recta endothelium', 'paper_synonyms': 'DVRE', 'tissue_context': ''} CL:1000892 kidney capillary endothelial cell +Distinct proximal tubule 1 CL:0002306 epithelial cell of proximal tubule DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Distinct proximal tubule 1', 'full_name': 'distinct proximal tubule 1', 'paper_synonyms': 'dPT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +Distinct proximal tubule 2 CL:0002306 epithelial cell of proximal tubule DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Distinct proximal tubule 2', 'full_name': 'distinct proximal tubule 2', 'paper_synonyms': 'dPT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +Epithelial progenitor cell CL:0011026 progenitor cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Epithelial progenitor cell', 'full_name': 'epithelial progenitor cell', 'paper_synonyms': 'EPC', 'tissue_context': ''} CL:0011026 progenitor cell +Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Fibroblast', 'full_name': 'fibroblast', 'paper_synonyms': 'Fib', 'tissue_context': ''} CL:0000057 fibroblast +Glomerular endothelium CL:0002188 glomerular endothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Glomerular endothelium', 'full_name': 'glomerular endothelium', 'paper_synonyms': 'GE; glomerular endothelial cells (GE)', 'tissue_context': ''} CL:0002188 glomerular endothelial cell +Indistinct intercalated cell CL:0005010 renal intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Indistinct intercalated cell', 'full_name': 'intercalated cell', 'paper_synonyms': 'intercalated cells (IC); IC', 'tissue_context': ''} CL:0005010 renal intercalated cell +Intercalated cell CL:0005011 renal alpha-intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Intercalated cell', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:0005010 renal intercalated cell +Intercalated cell CL:0005010 renal intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Intercalated cell', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:0005010 renal intercalated cell +Intercalated cell CL:0002201 renal beta-intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Intercalated cell', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:0005010 renal intercalated cell +MNP-a/classical monocyte derived CL:0000860 classical monocyte DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'MNP-a/classical monocyte derived', 'full_name': 'mononuclear phagocyte a/classical monocyte-derived', 'paper_synonyms': 'MNPa', 'tissue_context': ''} CL:0000113 mononuclear phagocyte +MNP-b/non-classical monocyte derived CL:0000875 non-classical monocyte DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'MNP-b/non-classical monocyte derived', 'full_name': 'mononuclear phagocyte b/non-classical monocyte derived', 'paper_synonyms': 'MNPb', 'tissue_context': ''} CL:0000875 non-classical monocyte +MNP-c/dendritic cell CL:0000451 dendritic cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'MNP-c/dendritic cell', 'full_name': 'mononuclear phagocyte c (dendritic cell)', 'paper_synonyms': 'MNPc; classical myeloid DC; cDC', 'tissue_context': ''} CL:0000451 dendritic cell +MNP-d/Tissue macrophage CL:1000698 kidney resident macrophage DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'MNP-d/Tissue macrophage', 'full_name': 'mononuclear phagocyte d/Tissue macrophage', 'paper_synonyms': 'MNPd', 'tissue_context': ''} CL:0000864 tissue-resident macrophage +Mast cell CL:0000097 mast cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Mast cell', 'full_name': 'mast cell', 'paper_synonyms': 'Mast', 'tissue_context': ''} CL:0000097 mast cell +Myofibroblast CL:0000186 myofibroblast cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Myofibroblast', 'full_name': 'myofibroblast', 'paper_synonyms': 'MFib', 'tissue_context': ''} CL:0000186 myofibroblast cell +NK cell CL:0000623 natural killer cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'NK cell', 'full_name': 'natural killer cell', 'paper_synonyms': 'NK', 'tissue_context': ''} CL:0000623 natural killer cell +NKT cell CL:0000814 mature NK T cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'NKT cell', 'full_name': 'natural killer T cell', 'paper_synonyms': 'NKT', 'tissue_context': ''} CL:0000814 mature NK T cell +Neutrophil CL:0000775 neutrophil DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': 'neutrophil', 'paper_synonyms': 'NO', 'tissue_context': ''} CL:0000775 neutrophil +Pelvic epithelium CL:0002518 kidney epithelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Pelvic epithelium', 'full_name': 'pelvic epithelium', 'paper_synonyms': 'PE', 'tissue_context': ''} CL:0000731 urothelial cell +Peritubular capillary endothelium CL:0002144 capillary endothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Peritubular capillary endothelium', 'full_name': 'peritubular capillary endothelium', 'paper_synonyms': 'PCE', 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell +Peritubular capillary endothelium 1 CL:0002144 capillary endothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Peritubular capillary endothelium 1', 'full_name': 'peritubular capillary endothelium', 'paper_synonyms': 'peritubular capillaries (PCap); PCE', 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell +Peritubular capillary endothelium 2 CL:0002144 capillary endothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Peritubular capillary endothelium 2', 'full_name': 'peritubular capillary endothelium 2', 'paper_synonyms': 'PCE; peritubular capillaries; PCap', 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell +Plasmacytoid dendritic cell CL:0000784 plasmacytoid dendritic cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Plasmacytoid dendritic cell', 'full_name': 'plasmacytoid dendritic cell', 'paper_synonyms': 'pDC', 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell +Podocyte CL:0000653 podocyte DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Podocyte', 'full_name': 'podocyte', 'paper_synonyms': 'Podo', 'tissue_context': ''} CL:0000653 podocyte +Principal cell CL:0005009 renal principal cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Principal cell', 'full_name': 'principal cell', 'paper_synonyms': 'PC', 'tissue_context': ''} CL:0005009 renal principal cell +Proliferating Proximal Tubule CL:0002306 epithelial cell of proximal tubule DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Proliferating Proximal Tubule', 'full_name': 'proximal tubule', 'paper_synonyms': 'PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +Proximal tubule CL:0002306 epithelial cell of proximal tubule DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Proximal tubule', 'full_name': 'proximal tubule', 'paper_synonyms': 'PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +Thick ascending limb of Loop of Henle CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Thick ascending limb of Loop of Henle', 'full_name': 'loop of Henle', 'paper_synonyms': 'LOH; loop of Henle', 'tissue_context': ''} CL:1000909 kidney loop of Henle epithelial cell +Transitional urothelium CL:0000731 urothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Transitional urothelium', 'full_name': 'transitional epithelium of ureter', 'paper_synonyms': 'TE; transitional epithelium; transitional epithelium of ureter', 'tissue_context': ''} CL:1000706 ureter urothelial cell +Type A intercalated cell CL:0005011 renal alpha-intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Type A intercalated cell', 'full_name': 'type A intercalated cell', 'paper_synonyms': 'intercalated cells (IC); IC (A+B); IC', 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell +Type B intercalated cell CL:0002201 renal beta-intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Type B intercalated cell', 'full_name': 'type B intercalated cell', 'paper_synonyms': 'IC; intercalated cells; IC (A+B)', 'tissue_context': ''} CL:0002201 renal beta-intercalated cell diff --git a/output/raw_output/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique/groundings.tsv b/output/raw_output/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..58edacb --- /dev/null +++ b/output/raw_output/9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,38 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Ascending vasa recta endothelium CL:1001131 vasa recta ascending limb cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Ascending vasa recta endothelium', 'full_name': 'ascending vasa recta endothelium', 'paper_synonyms': 'AVRE', 'tissue_context': ''} CL:1001131 vasa recta ascending limb cell TRUE +B cell CL:0000236 B cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'B cell', 'full_name': 'B cell', 'paper_synonyms': 'B', 'tissue_context': ''} CL:0000236 B cell TRUE +CD4 T cell CL:0000624 CD4-positive, alpha-beta T cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'CD4 T cell', 'full_name': 'CD4 T cell', 'paper_synonyms': 'CD4 T', 'tissue_context': ''} CL:0000624 CD4-positive, alpha-beta T cell TRUE +CD8 T cell CL:0000625 CD8-positive, alpha-beta T cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'CD8 T cell', 'full_name': 'CD8 T cell', 'paper_synonyms': 'CD8 T', 'tissue_context': ''} CL:0000625 CD8-positive, alpha-beta T cell TRUE +Connecting tubule CL:1000768 kidney connecting tubule epithelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Connecting tubule', 'full_name': 'connecting nephron tubule', 'paper_synonyms': 'CNT', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell TRUE +Descending vasa recta endothelium CL:1001285 vasa recta descending limb cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Descending vasa recta endothelium', 'full_name': 'descending vasa recta endothelium', 'paper_synonyms': 'DVRE', 'tissue_context': ''} CL:1000892 kidney capillary endothelial cell FALSE +Distinct proximal tubule 1 CL:0002306 epithelial cell of proximal tubule DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Distinct proximal tubule 1', 'full_name': 'distinct proximal tubule 1', 'paper_synonyms': 'dPT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +Distinct proximal tubule 2 CL:0002306 epithelial cell of proximal tubule DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Distinct proximal tubule 2', 'full_name': 'distinct proximal tubule 2', 'paper_synonyms': 'dPT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +Epithelial progenitor cell CL:0011026 progenitor cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Epithelial progenitor cell', 'full_name': 'epithelial progenitor cell', 'paper_synonyms': 'EPC', 'tissue_context': ''} CL:0011026 progenitor cell TRUE +Fibroblast CL:1000692 kidney interstitial fibroblast DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Fibroblast', 'full_name': 'fibroblast', 'paper_synonyms': 'Fib', 'tissue_context': ''} CL:0000057 fibroblast FALSE +Glomerular endothelium CL:0002188 glomerular endothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Glomerular endothelium', 'full_name': 'glomerular endothelium', 'paper_synonyms': 'GE; glomerular endothelial cells (GE)', 'tissue_context': ''} CL:0002188 glomerular endothelial cell TRUE +Indistinct intercalated cell CL:0005010 renal intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Indistinct intercalated cell', 'full_name': 'intercalated cell', 'paper_synonyms': 'intercalated cells (IC); IC', 'tissue_context': ''} CL:0005010 renal intercalated cell TRUE +Intercalated cell CL:0005011 renal alpha-intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Intercalated cell', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:0005010 renal intercalated cell FALSE +Intercalated cell CL:0005010 renal intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Intercalated cell', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:0005010 renal intercalated cell TRUE +Intercalated cell CL:0002201 renal beta-intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Intercalated cell', 'full_name': 'intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''} CL:0005010 renal intercalated cell FALSE +MNP-a/classical monocyte derived CL:0000860 classical monocyte DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'MNP-a/classical monocyte derived', 'full_name': 'mononuclear phagocyte a/classical monocyte-derived', 'paper_synonyms': 'MNPa', 'tissue_context': ''} CL:0000113 mononuclear phagocyte FALSE +MNP-b/non-classical monocyte derived CL:0000875 non-classical monocyte DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'MNP-b/non-classical monocyte derived', 'full_name': 'mononuclear phagocyte b/non-classical monocyte derived', 'paper_synonyms': 'MNPb', 'tissue_context': ''} CL:0000875 non-classical monocyte TRUE +MNP-c/dendritic cell CL:0000451 dendritic cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'MNP-c/dendritic cell', 'full_name': 'mononuclear phagocyte c (dendritic cell)', 'paper_synonyms': 'MNPc; classical myeloid DC; cDC', 'tissue_context': ''} CL:0000451 dendritic cell TRUE +MNP-d/Tissue macrophage CL:1000698 kidney resident macrophage DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'MNP-d/Tissue macrophage', 'full_name': 'mononuclear phagocyte d/Tissue macrophage', 'paper_synonyms': 'MNPd', 'tissue_context': ''} CL:0000864 tissue-resident macrophage FALSE +Mast cell CL:0000097 mast cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Mast cell', 'full_name': 'mast cell', 'paper_synonyms': 'Mast', 'tissue_context': ''} CL:0000097 mast cell TRUE +Myofibroblast CL:0000186 myofibroblast cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Myofibroblast', 'full_name': 'myofibroblast', 'paper_synonyms': 'MFib', 'tissue_context': ''} CL:0000186 myofibroblast cell TRUE +NK cell CL:0000623 natural killer cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'NK cell', 'full_name': 'natural killer cell', 'paper_synonyms': 'NK', 'tissue_context': ''} CL:0000623 natural killer cell TRUE +NKT cell CL:0000814 mature NK T cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'NKT cell', 'full_name': 'natural killer T cell', 'paper_synonyms': 'NKT', 'tissue_context': ''} CL:0000814 mature NK T cell TRUE +Neutrophil CL:0000775 neutrophil DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Neutrophil', 'full_name': 'neutrophil', 'paper_synonyms': 'NO', 'tissue_context': ''} CL:0000775 neutrophil TRUE +Pelvic epithelium CL:0002518 kidney epithelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Pelvic epithelium', 'full_name': 'pelvic epithelium', 'paper_synonyms': 'PE', 'tissue_context': ''} CL:0000731 urothelial cell FALSE +Peritubular capillary endothelium CL:0002144 capillary endothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Peritubular capillary endothelium', 'full_name': 'peritubular capillary endothelium', 'paper_synonyms': 'PCE', 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell FALSE +Peritubular capillary endothelium 1 CL:0002144 capillary endothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Peritubular capillary endothelium 1', 'full_name': 'peritubular capillary endothelium', 'paper_synonyms': 'peritubular capillaries (PCap); PCE', 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell FALSE +Peritubular capillary endothelium 2 CL:0002144 capillary endothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Peritubular capillary endothelium 2', 'full_name': 'peritubular capillary endothelium 2', 'paper_synonyms': 'PCE; peritubular capillaries; PCap', 'tissue_context': ''} CL:1001033 peritubular capillary endothelial cell FALSE +Plasmacytoid dendritic cell CL:0000784 plasmacytoid dendritic cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Plasmacytoid dendritic cell', 'full_name': 'plasmacytoid dendritic cell', 'paper_synonyms': 'pDC', 'tissue_context': ''} CL:0000784 plasmacytoid dendritic cell TRUE +Podocyte CL:0000653 podocyte DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Podocyte', 'full_name': 'podocyte', 'paper_synonyms': 'Podo', 'tissue_context': ''} CL:0000653 podocyte TRUE +Principal cell CL:0005009 renal principal cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Principal cell', 'full_name': 'principal cell', 'paper_synonyms': 'PC', 'tissue_context': ''} CL:0005009 renal principal cell TRUE +Proliferating Proximal Tubule CL:0002306 epithelial cell of proximal tubule DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Proliferating Proximal Tubule', 'full_name': 'proximal tubule', 'paper_synonyms': 'PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +Proximal tubule CL:0002306 epithelial cell of proximal tubule DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Proximal tubule', 'full_name': 'proximal tubule', 'paper_synonyms': 'PT', 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +Thick ascending limb of Loop of Henle CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Thick ascending limb of Loop of Henle', 'full_name': 'loop of Henle', 'paper_synonyms': 'LOH; loop of Henle', 'tissue_context': ''} CL:1000909 kidney loop of Henle epithelial cell FALSE +Transitional urothelium CL:0000731 urothelial cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Transitional urothelium', 'full_name': 'transitional epithelium of ureter', 'paper_synonyms': 'TE; transitional epithelium; transitional epithelium of ureter', 'tissue_context': ''} CL:1000706 ureter urothelial cell FALSE +Type A intercalated cell CL:0005011 renal alpha-intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Type A intercalated cell', 'full_name': 'type A intercalated cell', 'paper_synonyms': 'intercalated cells (IC); IC (A+B); IC', 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell TRUE +Type B intercalated cell CL:0002201 renal beta-intercalated cell DOI:10.1126/science.aat5031 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique {'name': 'Type B intercalated cell', 'full_name': 'type B intercalated cell', 'paper_synonyms': 'IC; intercalated cells; IC (A+B)', 'tissue_context': ''} CL:0002201 renal beta-intercalated cell TRUE diff --git a/output/raw_output/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..4814ddc --- /dev/null +++ b/output/raw_output/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,8 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Immune CL:0000738 leukocyte DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'Immune', 'full_name': 'immune cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000738 leukocyte +K_Endo CL:0000132 corneal endothelial cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Endo', 'full_name': 'corneal endothelium', 'paper_synonyms': 'corneal endothelial cells', 'tissue_context': ''} CL:0000132 corneal endothelial cell +K_Epi-Basal CL:0000646 basal cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Epi-Basal', 'full_name': 'corneal basal epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000575 corneal epithelial cell +K_Epi-Superficial CL:0000575 corneal epithelial cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Epi-Superficial', 'full_name': 'corneal epithelium superficial cells', 'paper_synonyms': 'superficial-most squamous epithelial cells', 'tissue_context': ''} CL:0000575 corneal epithelial cell +K_Epi-TA CL:0009010 transit amplifying cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Epi-TA', 'full_name': 'corneal epithelium transit amplifying cell', 'paper_synonyms': 'TA; transit amplifying cells', 'tissue_context': ''} CL:0009010 transit amplifying cell +K_Epi-Wing CL:0000575 corneal epithelial cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Epi-Wing', 'full_name': 'corneal epithelium wing cells', 'paper_synonyms': 'polygonal suprabasal cells', 'tissue_context': ''} CL:0000575 corneal epithelial cell +K_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Fibro', 'full_name': 'corneal fibroblasts', 'paper_synonyms': 'stromal keratocytes; corneal stromal keratocytes', 'tissue_context': ''} CL:0002363 keratocyte diff --git a/output/raw_output/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique/groundings.tsv b/output/raw_output/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..4c03789 --- /dev/null +++ b/output/raw_output/a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,8 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Immune CL:0000738 leukocyte DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'Immune', 'full_name': 'immune cells', 'paper_synonyms': '', 'tissue_context': ''} CL:0000738 leukocyte TRUE +K_Endo CL:0000132 corneal endothelial cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Endo', 'full_name': 'corneal endothelium', 'paper_synonyms': 'corneal endothelial cells', 'tissue_context': ''} CL:0000132 corneal endothelial cell TRUE +K_Epi-Basal CL:0000646 basal cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Epi-Basal', 'full_name': 'corneal basal epithelial cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000575 corneal epithelial cell FALSE +K_Epi-Superficial CL:0000575 corneal epithelial cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Epi-Superficial', 'full_name': 'corneal epithelium superficial cells', 'paper_synonyms': 'superficial-most squamous epithelial cells', 'tissue_context': ''} CL:0000575 corneal epithelial cell TRUE +K_Epi-TA CL:0009010 transit amplifying cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Epi-TA', 'full_name': 'corneal epithelium transit amplifying cell', 'paper_synonyms': 'TA; transit amplifying cells', 'tissue_context': ''} CL:0009010 transit amplifying cell TRUE +K_Epi-Wing CL:0000575 corneal epithelial cell DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Epi-Wing', 'full_name': 'corneal epithelium wing cells', 'paper_synonyms': 'polygonal suprabasal cells', 'tissue_context': ''} CL:0000575 corneal epithelial cell TRUE +K_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique {'name': 'K_Fibro', 'full_name': 'corneal fibroblasts', 'paper_synonyms': 'stromal keratocytes; corneal stromal keratocytes', 'tissue_context': ''} CL:0002363 keratocyte FALSE diff --git a/output/raw_output/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..ca1246c --- /dev/null +++ b/output/raw_output/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,15 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Muller cell CL:0000636 Mueller cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'Muller cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000636 Mueller cell +amacrine cell CL:0000561 amacrine cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'amacrine cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000561 amacrine cell +microglial cell CL:0000129 microglial cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'microglial cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000129 microglial cell +retinal bipolar neuron type A CL:0000749 ON-bipolar cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal bipolar neuron type A', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron +retinal bipolar neuron type B CL:0000750 OFF-bipolar cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal bipolar neuron type B', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000748 retinal bipolar neuron +retinal bipolar neuron type C CL:0000749 ON-bipolar cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal bipolar neuron type C', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron +retinal bipolar neuron type D CL:0000749 ON-bipolar cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal bipolar neuron type D', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron +retinal cone cell CL:0000573 retinal cone cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal cone cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000573 retinal cone cell +retinal ganglion cell CL:0000740 retinal ganglion cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal ganglion cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000740 retinal ganglion cell +retinal rod cell type A CL:0000604 retinal rod cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal rod cell type A', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell +retinal rod cell type B CL:0000604 retinal rod cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal rod cell type B', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell +retinal rod cell type C CL:0000604 retinal rod cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal rod cell type C', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell +unannotated unknown unknown DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'unannotated', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +unspecified unknown unknown DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'unspecified', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000000 cell diff --git a/output/raw_output/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique/groundings.tsv b/output/raw_output/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..b6553cb --- /dev/null +++ b/output/raw_output/d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,15 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Muller cell CL:0000636 Mueller cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'Muller cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000636 Mueller cell TRUE +amacrine cell CL:0000561 amacrine cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'amacrine cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000561 amacrine cell TRUE +microglial cell CL:0000129 microglial cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'microglial cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000129 microglial cell TRUE +retinal bipolar neuron type A CL:0000749 ON-bipolar cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal bipolar neuron type A', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron FALSE +retinal bipolar neuron type B CL:0000750 OFF-bipolar cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal bipolar neuron type B', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000748 retinal bipolar neuron FALSE +retinal bipolar neuron type C CL:0000749 ON-bipolar cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal bipolar neuron type C', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron FALSE +retinal bipolar neuron type D CL:0000749 ON-bipolar cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal bipolar neuron type D', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000748 retinal bipolar neuron FALSE +retinal cone cell CL:0000573 retinal cone cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal cone cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000573 retinal cone cell TRUE +retinal ganglion cell CL:0000740 retinal ganglion cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal ganglion cell', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000740 retinal ganglion cell TRUE +retinal rod cell type A CL:0000604 retinal rod cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal rod cell type A', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell TRUE +retinal rod cell type B CL:0000604 retinal rod cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal rod cell type B', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell TRUE +retinal rod cell type C CL:0000604 retinal rod cell DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'retinal rod cell type C', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell TRUE +unannotated unknown unknown DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'unannotated', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +unspecified unknown unknown DOI:10.15252/embj.2018100811 d5c67a4e-a8d9-456d-a273-fa01adb1b308_cxg_dataset_unique {'name': 'unspecified', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000000 cell FALSE diff --git a/output/raw_output/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..7d6ec41 --- /dev/null +++ b/output/raw_output/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,29 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +CC_VenEndo CL:0000115 endothelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'CC_VenEndo', 'full_name': 'Collector Channel/Venous Endothelium', 'paper_synonyms': None, 'tissue_context': ''} CL:0002543 vein endothelial cell +Ciliary_Muscle CL:1000443 ciliary muscle cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Ciliary_Muscle', 'full_name': 'ciliary muscle cells', 'paper_synonyms': 'CM', 'tissue_context': ''} CL:1000443 ciliary muscle cell +Conj_Epi-Basal CL:1000432 conjunctival epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Conj_Epi-Basal', 'full_name': 'conjunctival basal epithelial cell', 'paper_synonyms': '', 'tissue_context': ''} CL:1000432 conjunctival epithelial cell +Conj_Epi-Superficial CL:1000432 conjunctival epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Conj_Epi-Superficial', 'full_name': 'conjunctival superficial epithelial cell', 'paper_synonyms': '', 'tissue_context': ''} CL:1000432 conjunctival epithelial cell +Conj_Epi-Wing CL:1000432 conjunctival epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Conj_Epi-Wing', 'full_name': 'conjunctival epithelial wing cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1000432 conjunctival epithelial cell +Conj_Melanocyte CL:0000148 melanocyte DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Conj_Melanocyte', 'full_name': 'conjunctival melanocyte', 'paper_synonyms': '', 'tissue_context': ''} CL:0000148 melanocyte +FibroX CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'FibroX', 'full_name': 'FibroX', 'paper_synonyms': '', 'tissue_context': ''} CL:0000057 fibroblast +Goblet CL:0000160 goblet cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Goblet', 'full_name': 'goblet cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell +K_Endo CL:0000132 corneal endothelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Endo', 'full_name': 'corneal endothelium', 'paper_synonyms': 'corneal endothelial cells', 'tissue_context': ''} CL:0000132 corneal endothelial cell +K_Epi-Basal CL:0000646 basal cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Epi-Basal', 'full_name': 'corneal epithelial basal cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000575 corneal epithelial cell +K_Epi-Superficial CL:0000575 corneal epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Epi-Superficial', 'full_name': 'corneal superficial epithelial cell', 'paper_synonyms': 'superficial-most squamous epithelial cells', 'tissue_context': ''} CL:0000575 corneal epithelial cell +K_Epi-Wing CL:0000575 corneal epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Epi-Wing', 'full_name': 'corneal epithelial wing cell', 'paper_synonyms': 'wing cells; polygonal suprabasal cells', 'tissue_context': ''} CL:0000575 corneal epithelial cell +K_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Fibro', 'full_name': 'corneal fibroblasts', 'paper_synonyms': 'K_Fibro; stromal keratocytes', 'tissue_context': ''} CL:0002363 keratocyte +Limbal_Epi-Basal CL:0000646 basal cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Limbal_Epi-Basal', 'full_name': 'limbal epithelial basal cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000575 corneal epithelial cell +Limbal_Epi-Superficial CL:0000646 basal cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Limbal_Epi-Superficial', 'full_name': 'limbal superficial epithelial cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000575 corneal epithelial cell +Limbal_Epi-Wing CL:0000646 basal cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Limbal_Epi-Wing', 'full_name': 'limbal epithelial wing cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000575 corneal epithelial cell +Lymphatic_Endo CL:0002138 endothelial cell of lymphatic vessel DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Lymphatic_Endo', 'full_name': 'lymphatic endothelium', 'paper_synonyms': 'conjunctival lymphatic endothelium', 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel +Lymphocyte CL:0000542 lymphocyte DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Lymphocyte', 'full_name': 'lymphocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000542 lymphocyte +Macrophage CL:0000235 macrophage DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Macrophage', 'full_name': 'macrophage', 'paper_synonyms': 'Mo; clump cells', 'tissue_context': ''} CL:0000235 macrophage +Mast CL:0000097 mast cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Mast', 'full_name': 'mast cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000097 mast cell +Pericyte CL:0000669 pericyte DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Pericyte', 'full_name': 'pericytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte +Schlemm_Endo CL:0000115 endothelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Schlemm_Endo', 'full_name': 'Schlemm canal endothelium', 'paper_synonyms': 'SC endothelium', 'tissue_context': ''} CL:4033097 Schlemm's canal endothelial cell +Schwann CL:0002573 Schwann cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Schwann', 'full_name': 'Schwann cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0002573 Schwann cell +Sclera_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Sclera_Fibro', 'full_name': 'scleral fibroblast', 'paper_synonyms': '', 'tissue_context': ''} CL:0000057 fibroblast +TM_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'TM_Fibro', 'full_name': 'trabecular meshwork fibroblasts', 'paper_synonyms': 'TM fibroblasts', 'tissue_context': ''} CL:0002367 trabecular meshwork cell +Uveal_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Uveal_Fibro', 'full_name': 'uveal fibroblast', 'paper_synonyms': 'ciliary fibroblasts', 'tissue_context': ''} CL:0000057 fibroblast +Uveal_Melanocyte CL:0000148 melanocyte DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Uveal_Melanocyte', 'full_name': 'uveal melanocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000148 melanocyte +VascEndo CL:0000071 blood vessel endothelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'VascEndo', 'full_name': 'vascular endothelium', 'paper_synonyms': 'Vasc_Endo', 'tissue_context': ''} CL:0000071 blood vessel endothelial cell diff --git a/output/raw_output/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique/groundings.tsv b/output/raw_output/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..69b9416 --- /dev/null +++ b/output/raw_output/d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,29 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +CC_VenEndo CL:0000115 endothelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'CC_VenEndo', 'full_name': 'Collector Channel/Venous Endothelium', 'paper_synonyms': None, 'tissue_context': ''} CL:0002543 vein endothelial cell FALSE +Ciliary_Muscle CL:1000443 ciliary muscle cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Ciliary_Muscle', 'full_name': 'ciliary muscle cells', 'paper_synonyms': 'CM', 'tissue_context': ''} CL:1000443 ciliary muscle cell TRUE +Conj_Epi-Basal CL:1000432 conjunctival epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Conj_Epi-Basal', 'full_name': 'conjunctival basal epithelial cell', 'paper_synonyms': '', 'tissue_context': ''} CL:1000432 conjunctival epithelial cell TRUE +Conj_Epi-Superficial CL:1000432 conjunctival epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Conj_Epi-Superficial', 'full_name': 'conjunctival superficial epithelial cell', 'paper_synonyms': '', 'tissue_context': ''} CL:1000432 conjunctival epithelial cell TRUE +Conj_Epi-Wing CL:1000432 conjunctival epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Conj_Epi-Wing', 'full_name': 'conjunctival epithelial wing cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1000432 conjunctival epithelial cell TRUE +Conj_Melanocyte CL:0000148 melanocyte DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Conj_Melanocyte', 'full_name': 'conjunctival melanocyte', 'paper_synonyms': '', 'tissue_context': ''} CL:0000148 melanocyte TRUE +FibroX CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'FibroX', 'full_name': 'FibroX', 'paper_synonyms': '', 'tissue_context': ''} CL:0000057 fibroblast TRUE +Goblet CL:0000160 goblet cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Goblet', 'full_name': 'goblet cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell TRUE +K_Endo CL:0000132 corneal endothelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Endo', 'full_name': 'corneal endothelium', 'paper_synonyms': 'corneal endothelial cells', 'tissue_context': ''} CL:0000132 corneal endothelial cell TRUE +K_Epi-Basal CL:0000646 basal cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Epi-Basal', 'full_name': 'corneal epithelial basal cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000575 corneal epithelial cell FALSE +K_Epi-Superficial CL:0000575 corneal epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Epi-Superficial', 'full_name': 'corneal superficial epithelial cell', 'paper_synonyms': 'superficial-most squamous epithelial cells', 'tissue_context': ''} CL:0000575 corneal epithelial cell TRUE +K_Epi-Wing CL:0000575 corneal epithelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Epi-Wing', 'full_name': 'corneal epithelial wing cell', 'paper_synonyms': 'wing cells; polygonal suprabasal cells', 'tissue_context': ''} CL:0000575 corneal epithelial cell TRUE +K_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'K_Fibro', 'full_name': 'corneal fibroblasts', 'paper_synonyms': 'K_Fibro; stromal keratocytes', 'tissue_context': ''} CL:0002363 keratocyte FALSE +Limbal_Epi-Basal CL:0000646 basal cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Limbal_Epi-Basal', 'full_name': 'limbal epithelial basal cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000575 corneal epithelial cell FALSE +Limbal_Epi-Superficial CL:0000646 basal cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Limbal_Epi-Superficial', 'full_name': 'limbal superficial epithelial cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000575 corneal epithelial cell FALSE +Limbal_Epi-Wing CL:0000646 basal cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Limbal_Epi-Wing', 'full_name': 'limbal epithelial wing cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000575 corneal epithelial cell FALSE +Lymphatic_Endo CL:0002138 endothelial cell of lymphatic vessel DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Lymphatic_Endo', 'full_name': 'lymphatic endothelium', 'paper_synonyms': 'conjunctival lymphatic endothelium', 'tissue_context': ''} CL:0002138 endothelial cell of lymphatic vessel TRUE +Lymphocyte CL:0000542 lymphocyte DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Lymphocyte', 'full_name': 'lymphocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000542 lymphocyte TRUE +Macrophage CL:0000235 macrophage DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Macrophage', 'full_name': 'macrophage', 'paper_synonyms': 'Mo; clump cells', 'tissue_context': ''} CL:0000235 macrophage TRUE +Mast CL:0000097 mast cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Mast', 'full_name': 'mast cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000097 mast cell TRUE +Pericyte CL:0000669 pericyte DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Pericyte', 'full_name': 'pericytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte TRUE +Schlemm_Endo CL:0000115 endothelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Schlemm_Endo', 'full_name': 'Schlemm canal endothelium', 'paper_synonyms': 'SC endothelium', 'tissue_context': ''} CL:4033097 Schlemm's canal endothelial cell FALSE +Schwann CL:0002573 Schwann cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Schwann', 'full_name': 'Schwann cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0002573 Schwann cell TRUE +Sclera_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Sclera_Fibro', 'full_name': 'scleral fibroblast', 'paper_synonyms': '', 'tissue_context': ''} CL:0000057 fibroblast TRUE +TM_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'TM_Fibro', 'full_name': 'trabecular meshwork fibroblasts', 'paper_synonyms': 'TM fibroblasts', 'tissue_context': ''} CL:0002367 trabecular meshwork cell FALSE +Uveal_Fibro CL:0000057 fibroblast DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Uveal_Fibro', 'full_name': 'uveal fibroblast', 'paper_synonyms': 'ciliary fibroblasts', 'tissue_context': ''} CL:0000057 fibroblast TRUE +Uveal_Melanocyte CL:0000148 melanocyte DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'Uveal_Melanocyte', 'full_name': 'uveal melanocyte', 'paper_synonyms': None, 'tissue_context': ''} CL:0000148 melanocyte TRUE +VascEndo CL:0000071 blood vessel endothelial cell DOI:10.1073/pnas.2200914119 d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique {'name': 'VascEndo', 'full_name': 'vascular endothelium', 'paper_synonyms': 'Vasc_Endo', 'tissue_context': ''} CL:0000071 blood vessel endothelial cell TRUE diff --git a/output/raw_output/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..0c4c6fa --- /dev/null +++ b/output/raw_output/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,17 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +ATL CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'ATL', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell +DCT1 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'DCT1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030016 epithelial cell of early distal convoluted tubule +DCT2 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'DCT2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030017 epithelial cell of late distal convoluted tubule +ENDO CL:0000115 endothelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'ENDO', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +FIB CL:0000057 fibroblast DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'FIB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast +ICA CL:0005011 renal alpha-intercalated cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'ICA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell +ICB CL:0002201 renal beta-intercalated cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'ICB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002201 renal beta-intercalated cell +LEUK CL:0000738 leukocyte DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'LEUK', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +MES CL:0000650 mesangial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'MES', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000650 mesangial cell +PC CL:0005009 renal principal cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0005009 renal principal cell +PEC CL:1000452 parietal epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000452 parietal epithelial cell +PODO CL:0000653 podocyte DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PODO', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000653 podocyte +PT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4023041 L5 extratelencephalic projecting glutamatergic cortical neuron +PTVCAM1 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PTVCAM1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +TAL1 CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'TAL1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell +TAL2 CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'TAL2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell diff --git a/output/raw_output/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique/groundings.tsv b/output/raw_output/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..3c60068 --- /dev/null +++ b/output/raw_output/e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,17 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +ATL CL:1001107 kidney loop of Henle thin ascending limb epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'ATL', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell TRUE +DCT1 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'DCT1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030016 epithelial cell of early distal convoluted tubule FALSE +DCT2 CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'DCT2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4030017 epithelial cell of late distal convoluted tubule FALSE +ENDO CL:0000115 endothelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'ENDO', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell TRUE +FIB CL:0000057 fibroblast DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'FIB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000057 fibroblast TRUE +ICA CL:0005011 renal alpha-intercalated cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'ICA', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell TRUE +ICB CL:0002201 renal beta-intercalated cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'ICB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002201 renal beta-intercalated cell TRUE +LEUK CL:0000738 leukocyte DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'LEUK', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte TRUE +MES CL:0000650 mesangial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'MES', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000650 mesangial cell TRUE +PC CL:0005009 renal principal cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0005009 renal principal cell TRUE +PEC CL:1000452 parietal epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PEC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1000452 parietal epithelial cell TRUE +PODO CL:0000653 podocyte DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PODO', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000653 podocyte TRUE +PT CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PT', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4023041 L5 extratelencephalic projecting glutamatergic cortical neuron FALSE +PTVCAM1 CL:0002306 epithelial cell of proximal tubule DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'PTVCAM1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +TAL1 CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'TAL1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell TRUE +TAL2 CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1038/s41467-022-32972-z e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique {'name': 'TAL2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell TRUE diff --git a/output/raw_output/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..e0363d6 --- /dev/null +++ b/output/raw_output/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,11 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +WNT1 CL:0000312 keratinocyte DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'WNT1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +basal1 CL:0002187 basal cell of epidermis DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'basal1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000646 basal cell +basal2 CL:0002187 basal cell of epidermis DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'basal2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000646 basal cell +channel CL:0000242 Merkel cell DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'channel', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +folicular CL:2000092 hair follicular keratinocyte DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'folicular', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000500 follicular epithelial cell +granular CL:0002189 granular cell of epidermis DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'granular', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000094 granulocyte +immune CL:0000988 hematopoietic cell DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'immune', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte +melanocyte CL:0000148 melanocyte DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'melanocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000148 melanocyte +mitotic CL:0000312 keratinocyte DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'mitotic', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +spinous CL:0000649 spinous cell of epidermis DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'spinous', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4052060 spinous cell diff --git a/output/raw_output/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique/groundings.tsv b/output/raw_output/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..8f91799 --- /dev/null +++ b/output/raw_output/f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,11 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +WNT1 CL:0000312 keratinocyte DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'WNT1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +basal1 CL:0002187 basal cell of epidermis DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'basal1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000646 basal cell FALSE +basal2 CL:0002187 basal cell of epidermis DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'basal2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000646 basal cell FALSE +channel CL:0000242 Merkel cell DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'channel', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +folicular CL:2000092 hair follicular keratinocyte DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'folicular', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000500 follicular epithelial cell FALSE +granular CL:0002189 granular cell of epidermis DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'granular', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000094 granulocyte FALSE +immune CL:0000988 hematopoietic cell DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'immune', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000738 leukocyte FALSE +melanocyte CL:0000148 melanocyte DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'melanocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000148 melanocyte TRUE +mitotic CL:0000312 keratinocyte DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'mitotic', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +spinous CL:0000649 spinous cell of epidermis DOI:10.1016/j.celrep.2018.09.006 f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique {'name': 'spinous', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:4052060 spinous cell FALSE diff --git a/output/raw_output/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..2e0f461 --- /dev/null +++ b/output/raw_output/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,15 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Muller CL:0000636 Mueller cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'Muller', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000636 Mueller cell +RGC CL:0000740 retinal ganglion cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'RGC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000740 retinal ganglion cell +amacrine CL:0000561 amacrine cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'amacrine', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000561 amacrine cell +astrocyte CL:4033015 retinal astrocyte DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'astrocyte', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000127 astrocyte +cone CL:0000573 retinal cone cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'cone', 'full_name': 'cone photoreceptor cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000573 retinal cone cell +cone-off-BC CL:0000752 cone retinal bipolar cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'cone-off-BC', 'full_name': 'cone photoreceptor cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000573 retinal cone cell +cone-off-BC-BC3A CL:0000752 cone retinal bipolar cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'cone-off-BC-BC3A', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0004213 type 3a cone bipolar cell +cone-on-BC CL:0000752 cone retinal bipolar cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'cone-on-BC', 'full_name': 'cone photoreceptor cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000573 retinal cone cell +endothelial CL:0002585 retinal blood vessel endothelial cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'endothelial', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell +horizontal CL:0000745 retina horizontal cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'horizontal', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000745 retina horizontal cell +microglia CL:0000129 microglial cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'microglia', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000129 microglial cell +pericyte CL:0000669 pericyte DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'pericyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte +rod CL:0000604 retinal rod cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'rod', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell +rod-BC CL:0000751 rod bipolar cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'rod-BC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000751 rod bipolar cell diff --git a/output/raw_output/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique/groundings.tsv b/output/raw_output/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..92ec7be --- /dev/null +++ b/output/raw_output/f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,15 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Muller CL:0000636 Mueller cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'Muller', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000636 Mueller cell TRUE +RGC CL:0000740 retinal ganglion cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'RGC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000740 retinal ganglion cell TRUE +amacrine CL:0000561 amacrine cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'amacrine', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000561 amacrine cell TRUE +astrocyte CL:4033015 retinal astrocyte DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'astrocyte', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000127 astrocyte FALSE +cone CL:0000573 retinal cone cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'cone', 'full_name': 'cone photoreceptor cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000573 retinal cone cell TRUE +cone-off-BC CL:0000752 cone retinal bipolar cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'cone-off-BC', 'full_name': 'cone photoreceptor cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000573 retinal cone cell FALSE +cone-off-BC-BC3A CL:0000752 cone retinal bipolar cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'cone-off-BC-BC3A', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0004213 type 3a cone bipolar cell FALSE +cone-on-BC CL:0000752 cone retinal bipolar cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'cone-on-BC', 'full_name': 'cone photoreceptor cell', 'paper_synonyms': '', 'tissue_context': ''} CL:0000573 retinal cone cell FALSE +endothelial CL:0002585 retinal blood vessel endothelial cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'endothelial', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000115 endothelial cell FALSE +horizontal CL:0000745 retina horizontal cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'horizontal', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000745 retina horizontal cell TRUE +microglia CL:0000129 microglial cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'microglia', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000129 microglial cell TRUE +pericyte CL:0000669 pericyte DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'pericyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte TRUE +rod CL:0000604 retinal rod cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'rod', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''} CL:0000604 retinal rod cell TRUE +rod-BC CL:0000751 rod bipolar cell DOI:10.1093/hmg/ddab140 f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique {'name': 'rod-BC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''} CL:0000751 rod bipolar cell TRUE diff --git a/output/raw_output/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..3b8d9fc --- /dev/null +++ b/output/raw_output/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,26 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +AEA-DVR CL:1001285 vasa recta descending limb cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'AEA-DVR', 'full_name': 'afferent/efferent arterioles/descending vasa recta', 'paper_synonyms': 'AEA/DVR', 'tissue_context': ''} CL:0000071 blood vessel endothelial cell +AVR CL:1001131 vasa recta ascending limb cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'AVR', 'full_name': 'ascending vasa recta', 'paper_synonyms': None, 'tissue_context': ''} CL:1001131 vasa recta ascending limb cell +Bcell CL:0000236 B cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Bcell', 'full_name': 'B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell +CNT CL:1001225 kidney collecting duct cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'CNT', 'full_name': 'connecting tubule', 'paper_synonyms': 'connecting duct', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell +DCT CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'DCT', 'full_name': 'distal convoluted tubule', 'paper_synonyms': None, 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell +DL CL:1001285 vasa recta descending limb cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'DL', 'full_name': 'descending limb', 'paper_synonyms': None, 'tissue_context': ''} CL:1001021 kidney loop of Henle descending limb epithelial cell +GC CL:1001005 glomerular capillary endothelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'GC', 'full_name': 'glomerular capillaries', 'paper_synonyms': None, 'tissue_context': ''} CL:1001005 glomerular capillary endothelial cell +IC-A CL:0005011 renal alpha-intercalated cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'IC-A', 'full_name': 'intercalated cell A', 'paper_synonyms': None, 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell +IC-B CL:0002201 renal beta-intercalated cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'IC-B', 'full_name': 'intercalated cell B', 'paper_synonyms': None, 'tissue_context': ''} CL:0002201 renal beta-intercalated cell +IC-PC CL:0000075 columnar/cuboidal epithelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'IC-PC', 'full_name': 'intercalated cell–principal cell', 'paper_synonyms': 'transitional cell type between PC and IC cells', 'tissue_context': ''} CL:0005010 renal intercalated cell +Macro CL:0000235 macrophage DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Macro', 'full_name': 'macrophages', 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage +Mesangial CL:0000650 mesangial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Mesangial', 'full_name': 'mesangial cells', 'paper_synonyms': 'Mesa', 'tissue_context': ''} CL:0000650 mesangial cell +Mono CL:0000576 monocyte DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Mono', 'full_name': 'monocytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte +NKcell CL:0000623 natural killer cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'NKcell', 'full_name': 'natural killer cells', 'paper_synonyms': 'NK', 'tissue_context': ''} CL:0000623 natural killer cell +PC CL:0005009 renal principal cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'PC', 'full_name': 'principal cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0005009 renal principal cell +PT-A CL:0002306 epithelial cell of proximal tubule DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'PT-A', 'full_name': 'proximal tubule cell A', 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +PT-B CL:0002306 epithelial cell of proximal tubule DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'PT-B', 'full_name': 'proximal tubule B', 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +PT-C CL:0002306 epithelial cell of proximal tubule DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'PT-C', 'full_name': 'proximal tubule C', 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule +Peri CL:0000669 pericyte DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Peri', 'full_name': 'pericytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte +Podo CL:0000653 podocyte DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Podo', 'full_name': 'podocytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000653 podocyte +TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'TAL', 'full_name': 'thick ascending limb', 'paper_synonyms': None, 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell +Tcell CL:0000084 T cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Tcell', 'full_name': 'T cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000084 T cell +UC unknown unknown DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'UC', 'full_name': 'uncharacterized', 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found +tAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'tAL', 'full_name': 'thin ascending limb cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell +vSMC CL:0000359 vascular associated smooth muscle cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'vSMC', 'full_name': 'vascular smooth muscle cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell diff --git a/output/raw_output/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique/groundings.tsv b/output/raw_output/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..c934d54 --- /dev/null +++ b/output/raw_output/f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,26 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +AEA-DVR CL:1001285 vasa recta descending limb cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'AEA-DVR', 'full_name': 'afferent/efferent arterioles/descending vasa recta', 'paper_synonyms': 'AEA/DVR', 'tissue_context': ''} CL:0000071 blood vessel endothelial cell FALSE +AVR CL:1001131 vasa recta ascending limb cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'AVR', 'full_name': 'ascending vasa recta', 'paper_synonyms': None, 'tissue_context': ''} CL:1001131 vasa recta ascending limb cell TRUE +Bcell CL:0000236 B cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Bcell', 'full_name': 'B cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000236 B cell TRUE +CNT CL:1001225 kidney collecting duct cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'CNT', 'full_name': 'connecting tubule', 'paper_synonyms': 'connecting duct', 'tissue_context': ''} CL:1000768 kidney connecting tubule epithelial cell FALSE +DCT CL:1000849 kidney distal convoluted tubule epithelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'DCT', 'full_name': 'distal convoluted tubule', 'paper_synonyms': None, 'tissue_context': ''} CL:1000849 kidney distal convoluted tubule epithelial cell TRUE +DL CL:1001285 vasa recta descending limb cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'DL', 'full_name': 'descending limb', 'paper_synonyms': None, 'tissue_context': ''} CL:1001021 kidney loop of Henle descending limb epithelial cell FALSE +GC CL:1001005 glomerular capillary endothelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'GC', 'full_name': 'glomerular capillaries', 'paper_synonyms': None, 'tissue_context': ''} CL:1001005 glomerular capillary endothelial cell TRUE +IC-A CL:0005011 renal alpha-intercalated cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'IC-A', 'full_name': 'intercalated cell A', 'paper_synonyms': None, 'tissue_context': ''} CL:0005011 renal alpha-intercalated cell TRUE +IC-B CL:0002201 renal beta-intercalated cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'IC-B', 'full_name': 'intercalated cell B', 'paper_synonyms': None, 'tissue_context': ''} CL:0002201 renal beta-intercalated cell TRUE +IC-PC CL:0000075 columnar/cuboidal epithelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'IC-PC', 'full_name': 'intercalated cell–principal cell', 'paper_synonyms': 'transitional cell type between PC and IC cells', 'tissue_context': ''} CL:0005010 renal intercalated cell FALSE +Macro CL:0000235 macrophage DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Macro', 'full_name': 'macrophages', 'paper_synonyms': None, 'tissue_context': ''} CL:0000235 macrophage TRUE +Mesangial CL:0000650 mesangial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Mesangial', 'full_name': 'mesangial cells', 'paper_synonyms': 'Mesa', 'tissue_context': ''} CL:0000650 mesangial cell TRUE +Mono CL:0000576 monocyte DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Mono', 'full_name': 'monocytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000576 monocyte TRUE +NKcell CL:0000623 natural killer cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'NKcell', 'full_name': 'natural killer cells', 'paper_synonyms': 'NK', 'tissue_context': ''} CL:0000623 natural killer cell TRUE +PC CL:0005009 renal principal cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'PC', 'full_name': 'principal cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0005009 renal principal cell TRUE +PT-A CL:0002306 epithelial cell of proximal tubule DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'PT-A', 'full_name': 'proximal tubule cell A', 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +PT-B CL:0002306 epithelial cell of proximal tubule DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'PT-B', 'full_name': 'proximal tubule B', 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +PT-C CL:0002306 epithelial cell of proximal tubule DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'PT-C', 'full_name': 'proximal tubule C', 'paper_synonyms': None, 'tissue_context': ''} CL:0002306 epithelial cell of proximal tubule TRUE +Peri CL:0000669 pericyte DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Peri', 'full_name': 'pericytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000669 pericyte TRUE +Podo CL:0000653 podocyte DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Podo', 'full_name': 'podocytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000653 podocyte TRUE +TAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'TAL', 'full_name': 'thick ascending limb', 'paper_synonyms': None, 'tissue_context': ''} CL:1001106 kidney loop of Henle thick ascending limb epithelial cell TRUE +Tcell CL:0000084 T cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'Tcell', 'full_name': 'T cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000084 T cell TRUE +UC unknown unknown DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'UC', 'full_name': 'uncharacterized', 'paper_synonyms': None, 'tissue_context': ''} NO MATCH found FALSE +tAL CL:1001106 kidney loop of Henle thick ascending limb epithelial cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'tAL', 'full_name': 'thin ascending limb cells', 'paper_synonyms': None, 'tissue_context': ''} CL:1001107 kidney loop of Henle thin ascending limb epithelial cell FALSE +vSMC CL:0000359 vascular associated smooth muscle cell DOI:10.1073/pnas.2103240118 f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique {'name': 'vSMC', 'full_name': 'vascular smooth muscle cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000359 vascular associated smooth muscle cell TRUE diff --git a/output/raw_output/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv b/output/raw_output/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv new file mode 100644 index 0000000..f526a98 --- /dev/null +++ b/output/raw_output/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique/cell_type_annotations_un_filtered.tsv @@ -0,0 +1,18 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label +Enterochromaffin cells CL:0000577 type EC enteroendocrine cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Enterochromaffin cells', 'full_name': 'Enterochromaffin cells', 'paper_synonyms': 'EC cells; EC', 'tissue_context': ''} CL:0000577 type EC enteroendocrine cell +Enterocytes BEST4 CL:0000584 enterocyte DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Enterocytes BEST4', 'full_name': 'Enterocytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte +Enterocytes TMIGD1 MEP1A CL:0000584 enterocyte DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Enterocytes TMIGD1 MEP1A', 'full_name': 'Enterocytes TMIGD1+ MEP1A+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte +Enterocytes TMIGD1 MEP1A GSTA1 CL:0000584 enterocyte DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Enterocytes TMIGD1 MEP1A GSTA1', 'full_name': 'Enterocytes TMIGD1+ MEP1A+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte +Epithelial Cycling cells CL:0000066 epithelial cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Epithelial Cycling cells', 'full_name': 'Cycling cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000000 cell +Epithelial HBB HBA CL:0000066 epithelial cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Epithelial HBB HBA', 'full_name': 'Epithelial cells HBB+ HBA+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +Epithelial cells METTL12 MAFB CL:0000066 epithelial cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Epithelial cells METTL12 MAFB', 'full_name': 'Epithelial cells METTL12+ MAFB+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell +Goblet cells MUC2 TFF1 CL:0000160 goblet cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Goblet cells MUC2 TFF1', 'full_name': 'Goblet cells', 'paper_synonyms': 'Goblets', 'tissue_context': ''} CL:0000160 goblet cell +Goblet cells MUC2 TFF1- CL:0000160 goblet cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Goblet cells MUC2 TFF1-', 'full_name': 'Goblet cells', 'paper_synonyms': 'Goblets', 'tissue_context': ''} CL:0000160 goblet cell +Goblet cells SPINK4 CL:0000160 goblet cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Goblet cells SPINK4', 'full_name': 'Goblet cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell +L cells CL:0002279 type L enteroendocrine cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'L cells', 'full_name': 'L-cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002279 type L enteroendocrine cell +Paneth cells CL:0000510 paneth cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Paneth cells', 'full_name': 'Paneth cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000510 paneth cell +Stem cells OLFM4 CL:0000034 stem cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Stem cells OLFM4', 'full_name': 'Stem cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000034 stem cell +Stem cells OLFM4 GSTA1 CL:0000034 stem cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Stem cells OLFM4 GSTA1', 'full_name': 'Stem cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000034 stem cell +Stem cells OLFM4 LGR5 CL:0000034 stem cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Stem cells OLFM4 LGR5', 'full_name': 'Stem cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000034 stem cell +Stem cells OLFM4 PCNA CL:0000034 stem cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Stem cells OLFM4 PCNA', 'full_name': 'Stem cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000034 stem cell +Tuft cells CL:0002204 tuft cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Tuft cells', 'full_name': 'Tuft cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell diff --git a/output/raw_output/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique/groundings.tsv b/output/raw_output/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique/groundings.tsv new file mode 100644 index 0000000..405ae62 --- /dev/null +++ b/output/raw_output/fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique/groundings.tsv @@ -0,0 +1,18 @@ +annotation_text cl_id cl_label article_id_doi dataset_name enrichment grounding_cl_id grounding_cl_label result +Enterochromaffin cells CL:0000577 type EC enteroendocrine cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Enterochromaffin cells', 'full_name': 'Enterochromaffin cells', 'paper_synonyms': 'EC cells; EC', 'tissue_context': ''} CL:0000577 type EC enteroendocrine cell TRUE +Enterocytes BEST4 CL:0000584 enterocyte DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Enterocytes BEST4', 'full_name': 'Enterocytes', 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte TRUE +Enterocytes TMIGD1 MEP1A CL:0000584 enterocyte DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Enterocytes TMIGD1 MEP1A', 'full_name': 'Enterocytes TMIGD1+ MEP1A+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte TRUE +Enterocytes TMIGD1 MEP1A GSTA1 CL:0000584 enterocyte DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Enterocytes TMIGD1 MEP1A GSTA1', 'full_name': 'Enterocytes TMIGD1+ MEP1A+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000584 enterocyte TRUE +Epithelial Cycling cells CL:0000066 epithelial cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Epithelial Cycling cells', 'full_name': 'Cycling cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000000 cell FALSE +Epithelial HBB HBA CL:0000066 epithelial cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Epithelial HBB HBA', 'full_name': 'Epithelial cells HBB+ HBA+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell TRUE +Epithelial cells METTL12 MAFB CL:0000066 epithelial cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Epithelial cells METTL12 MAFB', 'full_name': 'Epithelial cells METTL12+ MAFB+', 'paper_synonyms': None, 'tissue_context': ''} CL:0000066 epithelial cell TRUE +Goblet cells MUC2 TFF1 CL:0000160 goblet cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Goblet cells MUC2 TFF1', 'full_name': 'Goblet cells', 'paper_synonyms': 'Goblets', 'tissue_context': ''} CL:0000160 goblet cell TRUE +Goblet cells MUC2 TFF1- CL:0000160 goblet cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Goblet cells MUC2 TFF1-', 'full_name': 'Goblet cells', 'paper_synonyms': 'Goblets', 'tissue_context': ''} CL:0000160 goblet cell TRUE +Goblet cells SPINK4 CL:0000160 goblet cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Goblet cells SPINK4', 'full_name': 'Goblet cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000160 goblet cell TRUE +L cells CL:0002279 type L enteroendocrine cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'L cells', 'full_name': 'L-cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002279 type L enteroendocrine cell TRUE +Paneth cells CL:0000510 paneth cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Paneth cells', 'full_name': 'Paneth cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000510 paneth cell TRUE +Stem cells OLFM4 CL:0000034 stem cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Stem cells OLFM4', 'full_name': 'Stem cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000034 stem cell TRUE +Stem cells OLFM4 GSTA1 CL:0000034 stem cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Stem cells OLFM4 GSTA1', 'full_name': 'Stem cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000034 stem cell TRUE +Stem cells OLFM4 LGR5 CL:0000034 stem cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Stem cells OLFM4 LGR5', 'full_name': 'Stem cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000034 stem cell TRUE +Stem cells OLFM4 PCNA CL:0000034 stem cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Stem cells OLFM4 PCNA', 'full_name': 'Stem cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0000034 stem cell TRUE +Tuft cells CL:0002204 tuft cell DOI:10.1016/j.immuni.2023.01.002 fe4b89d5-461e-440c-a5a8-621b37b122c0_cxg_dataset_unique {'name': 'Tuft cells', 'full_name': 'Tuft cells', 'paper_synonyms': None, 'tissue_context': ''} CL:0002204 tuft cell TRUE diff --git a/output/reports/filtered_granularity_report.md b/output/reports/filtered_granularity_report.md new file mode 100644 index 0000000..cfce287 --- /dev/null +++ b/output/reports/filtered_granularity_report.md @@ -0,0 +1,14 @@ +# Annotation Granularity Report (Filtered) +> **Note:** This report excludes 'Broad term' and 'Overlaps' matches to reduce false regressions. + +## Aggregate Statistics +**Total Annotations Analyzed:** 740 +**Excluded (Noisy Data):** 115 + +| Category | Count | Percentage | Description | +| :--- | :--- | :--- | :--- | +| Improved Granularity | 128 | 17.30% | Agent provided a more specific or context-aware term. | +| Exact Match | 393 | 53.11% | Agent matched the author's term exactly. | +| Regression | 92 | 12.43% | Agent provided a less specific term (ancestor). | +| No Match Found | 56 | 7.57% | Agent could not find a CL term (potential new term). | +| Other | 71 | 9.59% | Agent term is unrelated to the author term. | diff --git a/output/reports/granularity_report.md b/output/reports/granularity_report.md new file mode 100644 index 0000000..1337919 --- /dev/null +++ b/output/reports/granularity_report.md @@ -0,0 +1,682 @@ +# Good Examples of Improved Granularity + +## Dataset: 1873a18a-66fd-4a4d-8277-a872c93f5b59_cxg_dataset_unique +- **Annotation Text:** Prolif-Mac +- **Author's Mapping:** macrophage (CL:0000235) +- **Agent's Mapping:** cycling macrophage (CL:4033076) +- **Enrichment Info:** `{'name': 'Prolif-Mac', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: f801b7a9-80a6-4d09-9161-71474deb58ae_cxg_dataset_unique +- **Annotation Text:** IC-PC +- **Author's Mapping:** columnar/cuboidal epithelial cell (CL:0000075) +- **Agent's Mapping:** renal intercalated cell (CL:0005010) +- **Enrichment Info:** `{'name': 'IC-PC', 'full_name': 'intercalated cell–principal cell', 'paper_synonyms': 'transitional cell type between PC and IC cells', 'tissue_context': ''}` + + +## Dataset: 0b75c598-0893-4216-afe8-5414cab7739d_cxg_dataset_unique +- **Annotation Text:** Afferent / Efferent Arteriole Endothelial Cell +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** endothelial cell of arteriole (CL:1000412) +- **Enrichment Info:** `{'name': 'Afferent / Efferent Arteriole Endothelial Cell', 'full_name': 'endothelial cell of the afferent/efferent arterioles (EC-AEA)', 'paper_synonyms': 'EC-AEA', 'tissue_context': ''}` + +- **Annotation Text:** Ascending Vasa Recta Endothelial Cell +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** vasa recta ascending limb cell (CL:1001131) +- **Enrichment Info:** `{'name': 'Ascending Vasa Recta Endothelial Cell', 'full_name': 'ascending vasa recta endothelial cell', 'paper_synonyms': 'EC-AVR', 'tissue_context': ''}` + +- **Annotation Text:** C-PC +- **Author's Mapping:** kidney collecting duct principal cell (CL:1001431) +- **Agent's Mapping:** kidney cortex collecting duct principal cell (CL:1000714) +- **Enrichment Info:** `{'name': 'C-PC', 'full_name': 'cortical principal cell', 'paper_synonyms': 'PC; principal cells', 'tissue_context': ''}` + +- **Annotation Text:** C-TAL +- **Author's Mapping:** kidney loop of Henle thick ascending limb epithelial cell (CL:1001106) +- **Agent's Mapping:** kidney loop of Henle cortical thick ascending limb epithelial cell (CL:1001109) +- **Enrichment Info:** `{'name': 'C-TAL', 'full_name': 'cortical thick ascending limb', 'paper_synonyms': 'thick ascending limb (TAL)', 'tissue_context': ''}` + +- **Annotation Text:** CCD-IC-A +- **Author's Mapping:** kidney collecting duct intercalated cell (CL:1001432) +- **Agent's Mapping:** kidney cortex collecting duct intercalated cell (CL:1000715) +- **Enrichment Info:** `{'name': 'CCD-IC-A', 'full_name': 'cortical collecting duct intercalated cells', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** CCD-PC +- **Author's Mapping:** kidney collecting duct principal cell (CL:1001431) +- **Agent's Mapping:** kidney cortex collecting duct principal cell (CL:1000714) +- **Enrichment Info:** `{'name': 'CCD-PC', 'full_name': 'cortical collecting duct principal cell', 'paper_synonyms': 'CCD; cortical collecting duct; PC; principal cells', 'tissue_context': ''}` + +- **Annotation Text:** CNT-PC +- **Author's Mapping:** kidney connecting tubule epithelial cell (CL:1000768) +- **Agent's Mapping:** kidney connecting tubule principal cell (CL:4030018) +- **Enrichment Info:** `{'name': 'CNT-PC', 'full_name': 'connecting tubule principal cell', 'paper_synonyms': 'CNT; connecting tubule; PC; principal cells', 'tissue_context': ''}` + +- **Annotation Text:** Connecting Tubule Principal Cell +- **Author's Mapping:** kidney connecting tubule epithelial cell (CL:1000768) +- **Agent's Mapping:** kidney connecting tubule principal cell (CL:4030018) +- **Enrichment Info:** `{'name': 'Connecting Tubule Principal Cell', 'full_name': 'Connecting tubule principal cell', 'paper_synonyms': 'CNT-PC; CNT; PC', 'tissue_context': ''}` + +- **Annotation Text:** Cortical Collecting Duct Intercalated Cell Type A +- **Author's Mapping:** kidney collecting duct intercalated cell (CL:1001432) +- **Agent's Mapping:** kidney collecting duct alpha-intercalated cell (CL:4030015) +- **Enrichment Info:** `{'name': 'Cortical Collecting Duct Intercalated Cell Type A', 'full_name': 'Cortical collecting duct intercalated cell type A', 'paper_synonyms': 'CCD; IC; collecting duct (CD)', 'tissue_context': ''}` + +- **Annotation Text:** Cortical Collecting Duct Principal Cell +- **Author's Mapping:** kidney collecting duct principal cell (CL:1001431) +- **Agent's Mapping:** kidney cortex collecting duct principal cell (CL:1000714) +- **Enrichment Info:** `{'name': 'Cortical Collecting Duct Principal Cell', 'full_name': 'cortical collecting duct principal cell', 'paper_synonyms': 'C-PC; PC', 'tissue_context': ''}` + +- **Annotation Text:** Cortical Thick Ascending Limb Cell +- **Author's Mapping:** kidney loop of Henle thick ascending limb epithelial cell (CL:1001106) +- **Agent's Mapping:** kidney loop of Henle cortical thick ascending limb epithelial cell (CL:1001109) +- **Enrichment Info:** `{'name': 'Cortical Thick Ascending Limb Cell', 'full_name': 'cortical thick ascending limb (C-TAL) cell', 'paper_synonyms': 'C-TAL; TAL', 'tissue_context': ''}` + +- **Annotation Text:** Cycling Mononuclear Phagocyte +- **Author's Mapping:** mononuclear phagocyte (CL:0000113) +- **Agent's Mapping:** cycling mononuclear phagocyte (CL:4033078) +- **Enrichment Info:** `{'name': 'Cycling Mononuclear Phagocyte', 'full_name': 'cycling mononuclear phagocyte', 'paper_synonyms': 'cycMNP', 'tissue_context': ''}` + +- **Annotation Text:** Cycling Natural Killer Cell / Natural Killer T Cell +- **Author's Mapping:** lymphocyte (CL:0000542) +- **Agent's Mapping:** cycling natural killer cell (CL:4033071) +- **Enrichment Info:** `{'name': 'Cycling Natural Killer Cell / Natural Killer T Cell', 'full_name': 'cycling natural killer cell / natural killer T cell', 'paper_synonyms': 'NKT', 'tissue_context': ''}` + +- **Annotation Text:** DCT1 +- **Author's Mapping:** kidney distal convoluted tubule epithelial cell (CL:1000849) +- **Agent's Mapping:** epithelial cell of early distal convoluted tubule (CL:4030016) +- **Enrichment Info:** `{'name': 'DCT1', 'full_name': 'distal convoluted tubule cell 1', 'paper_synonyms': 'DCT; distal convoluted tubule', 'tissue_context': ''}` + +- **Annotation Text:** DCT2 +- **Author's Mapping:** kidney distal convoluted tubule epithelial cell (CL:1000849) +- **Agent's Mapping:** epithelial cell of late distal convoluted tubule (CL:4030017) +- **Enrichment Info:** `{'name': 'DCT2', 'full_name': 'distal convoluted tubule cell 2', 'paper_synonyms': 'DCT', 'tissue_context': ''}` + +- **Annotation Text:** Degenerative Cortical Intercalated Cell Type A +- **Author's Mapping:** kidney collecting duct intercalated cell (CL:1001432) +- **Agent's Mapping:** kidney cortex collecting duct intercalated cell (CL:1000715) +- **Enrichment Info:** `{'name': 'Degenerative Cortical Intercalated Cell Type A', 'full_name': 'Degenerative cortical intercalated cell', 'paper_synonyms': 'IC', 'tissue_context': ''}` + +- **Annotation Text:** Degenerative Cortical Thick Ascending Limb Cell +- **Author's Mapping:** kidney loop of Henle thick ascending limb epithelial cell (CL:1001106) +- **Agent's Mapping:** kidney loop of Henle cortical thick ascending limb epithelial cell (CL:1001109) +- **Enrichment Info:** `{'name': 'Degenerative Cortical Thick Ascending Limb Cell', 'full_name': 'degenerative cortical thick ascending limb cell', 'paper_synonyms': 'C-TAL; cortical TAL', 'tissue_context': ''}` + +- **Annotation Text:** Degenerative Medullary Fibroblast +- **Author's Mapping:** kidney interstitial fibroblast (CL:1000692) +- **Agent's Mapping:** renal medullary fibroblast (CL:4030022) +- **Enrichment Info:** `{'name': 'Degenerative Medullary Fibroblast', 'full_name': 'Degenerative Medullary Fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''}` + +- **Annotation Text:** Degenerative Medullary Thick Ascending Limb Cell +- **Author's Mapping:** kidney loop of Henle thick ascending limb epithelial cell (CL:1001106) +- **Agent's Mapping:** kidney loop of Henle medullary thick ascending limb epithelial cell (CL:1001108) +- **Enrichment Info:** `{'name': 'Degenerative Medullary Thick Ascending Limb Cell', 'full_name': 'degenerative medullary thick ascending limb cell', 'paper_synonyms': 'TAL; M-TAL', 'tissue_context': ''}` + +- **Annotation Text:** Degenerative Outer Medullary Collecting Duct Principal Cell +- **Author's Mapping:** kidney collecting duct principal cell (CL:1001431) +- **Agent's Mapping:** kidney outer medulla collecting duct principal cell (CL:1000716) +- **Enrichment Info:** `{'name': 'Degenerative Outer Medullary Collecting Duct Principal Cell', 'full_name': 'Degenerative Outer Medullary Collecting Duct Principal Cell', 'paper_synonyms': 'OMCD; PC; degenerative medullary principal cells; dM-PCs', 'tissue_context': ''}` + +- **Annotation Text:** Degenerative Peritubular Capilary Endothelial Cell +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** peritubular capillary endothelial cell (CL:1001033) +- **Enrichment Info:** `{'name': 'Degenerative Peritubular Capilary Endothelial Cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Descending Vasa Recta Endothelial Cell +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** kidney capillary endothelial cell (CL:1000892) +- **Enrichment Info:** `{'name': 'Descending Vasa Recta Endothelial Cell', 'full_name': 'Descending vasa recta endothelial cell', 'paper_synonyms': 'EC-DVR', 'tissue_context': ''}` + +- **Annotation Text:** Distal Convoluted Tubule Cell Type 1 +- **Author's Mapping:** kidney distal convoluted tubule epithelial cell (CL:1000849) +- **Agent's Mapping:** epithelial cell of early distal convoluted tubule (CL:4030016) +- **Enrichment Info:** `{'name': 'Distal Convoluted Tubule Cell Type 1', 'full_name': 'Distal convoluted tubule cell type 1', 'paper_synonyms': 'DCT1', 'tissue_context': ''}` + +- **Annotation Text:** Distal Convoluted Tubule Cell Type 2 +- **Author's Mapping:** kidney distal convoluted tubule epithelial cell (CL:1000849) +- **Agent's Mapping:** epithelial cell of late distal convoluted tubule (CL:4030017) +- **Enrichment Info:** `{'name': 'Distal Convoluted Tubule Cell Type 2', 'full_name': 'distal convoluted tubule cell 2', 'paper_synonyms': 'DCT2', 'tissue_context': ''}` + +- **Annotation Text:** EC-AEA +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** endothelial cell of arteriole (CL:1000412) +- **Enrichment Info:** `{'name': 'EC-AEA', 'full_name': 'endothelial cells of the afferent/efferent arterioles', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** EC-AVR +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** kidney capillary endothelial cell (CL:1000892) +- **Enrichment Info:** `{'name': 'EC-AVR', 'full_name': 'endothelial cell of the vasa recta', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** EC-DVR +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** kidney capillary endothelial cell (CL:1000892) +- **Enrichment Info:** `{'name': 'EC-DVR', 'full_name': 'endothelial cells of the vasa recta', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** EC-GC +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** glomerular capillary endothelial cell (CL:1001005) +- **Enrichment Info:** `{'name': 'EC-GC', 'full_name': 'glomerular capillaries', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** EC-LYM +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** endothelial cell of lymphatic vessel (CL:0002138) +- **Enrichment Info:** `{'name': 'EC-LYM', 'full_name': 'endothelial cells of the lymphatics', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** EC-PTC +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** peritubular capillary endothelial cell (CL:1001033) +- **Enrichment Info:** `{'name': 'EC-PTC', 'full_name': 'endothelial cell PTC', 'paper_synonyms': 'EC; endothelial cells', 'tissue_context': ''}` + +- **Annotation Text:** Glomerular Capillary Endothelial Cell +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** glomerular capillary endothelial cell (CL:1001005) +- **Enrichment Info:** `{'name': 'Glomerular Capillary Endothelial Cell', 'full_name': 'glomerular capillary endothelial cell', 'paper_synonyms': 'EC-GC', 'tissue_context': ''}` + +- **Annotation Text:** Lymphatic Endothelial Cell +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** endothelial cell of lymphatic vessel (CL:0002138) +- **Enrichment Info:** `{'name': 'Lymphatic Endothelial Cell', 'full_name': 'endothelial cell of the lymphatics', 'paper_synonyms': 'EC-LYM', 'tissue_context': ''}` + +- **Annotation Text:** M-FIB +- **Author's Mapping:** kidney interstitial fibroblast (CL:1000692) +- **Agent's Mapping:** renal medullary fibroblast (CL:4030022) +- **Enrichment Info:** `{'name': 'M-FIB', 'full_name': 'medullary fibroblast', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** M-TAL +- **Author's Mapping:** kidney loop of Henle thick ascending limb epithelial cell (CL:1001106) +- **Agent's Mapping:** kidney loop of Henle medullary thick ascending limb epithelial cell (CL:1001108) +- **Enrichment Info:** `{'name': 'M-TAL', 'full_name': 'medullary thick ascending limb', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** MDC +- **Author's Mapping:** mononuclear phagocyte (CL:0000113) +- **Agent's Mapping:** myeloid dendritic cell (CL:0000782) +- **Enrichment Info:** `{'name': 'MDC', 'full_name': 'monocyte-derived cells', 'paper_synonyms': 'MDCs', 'tissue_context': ''}` + +- **Annotation Text:** Medullary Thick Ascending Limb Cell +- **Author's Mapping:** kidney loop of Henle thick ascending limb epithelial cell (CL:1001106) +- **Agent's Mapping:** kidney loop of Henle medullary thick ascending limb epithelial cell (CL:1001108) +- **Enrichment Info:** `{'name': 'Medullary Thick Ascending Limb Cell', 'full_name': 'Medullary thick ascending limb cell', 'paper_synonyms': 'M-TAL; thick ascending limb (TAL)', 'tissue_context': ''}` + +- **Annotation Text:** Mesangial Cell +- **Author's Mapping:** renal interstitial pericyte (CL:1001318) +- **Agent's Mapping:** mesangial cell (CL:0000650) +- **Enrichment Info:** `{'name': 'Mesangial Cell', 'full_name': 'mesangial cell', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** NEU +- **Author's Mapping:** neural cell (CL:0002319) +- **Agent's Mapping:** neuron (CL:0000540) +- **Enrichment Info:** `{'name': 'NEU', 'full_name': 'neuronal cell', 'paper_synonyms': 'SCI/NEU; Schwann/neuronal', 'tissue_context': ''}` + +- **Annotation Text:** NKC/T +- **Author's Mapping:** lymphocyte (CL:0000542) +- **Agent's Mapping:** T cell (CL:0000084) +- **Enrichment Info:** `{'name': 'NKC/T', 'full_name': 'T cells', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Natural Killer Cell / Natural Killer T Cell +- **Author's Mapping:** lymphocyte (CL:0000542) +- **Agent's Mapping:** natural killer cell (CL:0000623) +- **Enrichment Info:** `{'name': 'Natural Killer Cell / Natural Killer T Cell', 'full_name': 'Natural killer cell / natural killer T cell', 'paper_synonyms': 'NKT', 'tissue_context': ''}` + +- **Annotation Text:** OMCD-IC-A +- **Author's Mapping:** kidney collecting duct intercalated cell (CL:1001432) +- **Agent's Mapping:** kidney outer medulla collecting duct intercalated cell (CL:1000717) +- **Enrichment Info:** `{'name': 'OMCD-IC-A', 'full_name': 'outer medullary collecting duct intercalated cells', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** OMCD-PC +- **Author's Mapping:** kidney collecting duct principal cell (CL:1001431) +- **Agent's Mapping:** kidney outer medulla collecting duct principal cell (CL:1000716) +- **Enrichment Info:** `{'name': 'OMCD-PC', 'full_name': 'outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; outer medullary collecting duct; PC; principal cells', 'tissue_context': ''}` + +- **Annotation Text:** Outer Medullary Collecting Duct Intercalated Cell Type A +- **Author's Mapping:** kidney collecting duct intercalated cell (CL:1001432) +- **Agent's Mapping:** kidney outer medulla collecting duct intercalated cell (CL:1000717) +- **Enrichment Info:** `{'name': 'Outer Medullary Collecting Duct Intercalated Cell Type A', 'full_name': 'outer medullary collecting duct intercalated cell', 'paper_synonyms': 'OMCD; IC', 'tissue_context': ''}` + +- **Annotation Text:** Outer Medullary Collecting Duct Principal Cell +- **Author's Mapping:** kidney collecting duct principal cell (CL:1001431) +- **Agent's Mapping:** kidney outer medulla collecting duct principal cell (CL:1000716) +- **Enrichment Info:** `{'name': 'Outer Medullary Collecting Duct Principal Cell', 'full_name': 'outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; PC; M-PC', 'tissue_context': ''}` + +- **Annotation Text:** PT-S3 +- **Author's Mapping:** epithelial cell of proximal tubule (CL:0002306) +- **Agent's Mapping:** epithelial cell of proximal tubule segment 3 (CL:4030011) +- **Enrichment Info:** `{'name': 'PT-S3', 'full_name': 'proximal tubule S3', 'paper_synonyms': 'proximal tubule (PT)', 'tissue_context': ''}` + +- **Annotation Text:** Peritubular Capilary Endothelial Cell +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** peritubular capillary endothelial cell (CL:1001033) +- **Enrichment Info:** `{'name': 'Peritubular Capilary Endothelial Cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Proximal Tubule Epithelial Cell Segment 3 +- **Author's Mapping:** epithelial cell of proximal tubule (CL:0002306) +- **Agent's Mapping:** epithelial cell of proximal tubule segment 3 (CL:4030011) +- **Enrichment Info:** `{'name': 'Proximal Tubule Epithelial Cell Segment 3', 'full_name': 'proximal tubule (PT) epithelial cell, segment 3', 'paper_synonyms': 'PT-S3; PT', 'tissue_context': ''}` + +- **Annotation Text:** cycMNP +- **Author's Mapping:** mononuclear phagocyte (CL:0000113) +- **Agent's Mapping:** cycling mononuclear phagocyte (CL:4033078) +- **Enrichment Info:** `{'name': 'cycMNP', 'full_name': 'cycling MNP', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** cycNKC/T +- **Author's Mapping:** lymphocyte (CL:0000542) +- **Agent's Mapping:** cycling T cell (CL:4033069) +- **Enrichment Info:** `{'name': 'cycNKC/T', 'full_name': 'cycling T cells', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** dC-TAL +- **Author's Mapping:** kidney loop of Henle thick ascending limb epithelial cell (CL:1001106) +- **Agent's Mapping:** kidney loop of Henle cortical thick ascending limb epithelial cell (CL:1001109) +- **Enrichment Info:** `{'name': 'dC-TAL', 'full_name': 'degenerative cortical thick ascending limb cell', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** dM-FIB +- **Author's Mapping:** kidney interstitial fibroblast (CL:1000692) +- **Agent's Mapping:** renal medullary fibroblast (CL:4030022) +- **Enrichment Info:** `{'name': 'dM-FIB', 'full_name': 'degenerative medullary fibroblast', 'paper_synonyms': 'FIB', 'tissue_context': ''}` + +- **Annotation Text:** dM-TAL +- **Author's Mapping:** kidney loop of Henle thick ascending limb epithelial cell (CL:1001106) +- **Agent's Mapping:** kidney loop of Henle medullary thick ascending limb epithelial cell (CL:1001108) +- **Enrichment Info:** `{'name': 'dM-TAL', 'full_name': 'degenerative medullary thick ascending limb cell', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** dOMCD-PC +- **Author's Mapping:** kidney collecting duct principal cell (CL:1001431) +- **Agent's Mapping:** kidney outer medulla collecting duct principal cell (CL:1000716) +- **Enrichment Info:** `{'name': 'dOMCD-PC', 'full_name': 'degenerative outer medullary collecting duct principal cell', 'paper_synonyms': 'OMCD; outer medullary collecting duct; PC; principal cells', 'tissue_context': ''}` + + +## Dataset: 3b8b5de4-3aa1-4ac6-8890-8d03c8219981_cxg_dataset_unique +- **Annotation Text:** L2-L3 Intratelencephalic +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** L2/3 intratelencephalic projecting glutamatergic neuron (CL:4030059) +- **Enrichment Info:** `{'name': 'L2-L3 Intratelencephalic', 'full_name': 'L2-L3 intratelencephalic', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** L3-L5 Intratelencephalic Type 1 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** intratelencephalic-projecting glutamatergic cortical neuron (CL:4023008) +- **Enrichment Info:** `{'name': 'L3-L5 Intratelencephalic Type 1', 'full_name': 'L3-L5 intratelencephalic type 1', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** L3-L5 Intratelencephalic Type 2 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** intratelencephalic-projecting glutamatergic cortical neuron (CL:4023008) +- **Enrichment Info:** `{'name': 'L3-L5 Intratelencephalic Type 2', 'full_name': 'L3-L5 intratelencephalic type 2', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** L5 Extratelencephalic +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** L5 extratelencephalic projecting glutamatergic cortical neuron (CL:4023041) +- **Enrichment Info:** `{'name': 'L5 Extratelencephalic', 'full_name': 'L5 extratelencephalic neurons', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** L5-L6 Near Projecting +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** L5/6 near-projecting glutamatergic neuron (CL:4030067) +- **Enrichment Info:** `{'name': 'L5-L6 Near Projecting', 'full_name': 'L5-L6 near projecting neuronal cluster', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** L6 Corticothalamic / L6B +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** L6 corticothalamic-projecting glutamatergic cortical neuron (CL:4023042) +- **Enrichment Info:** `{'name': 'L6 Corticothalamic / L6B', 'full_name': 'L6 corticothalamic / L6B', 'paper_synonyms': 'L6 corticothalamic; L6B', 'tissue_context': ''}` + +- **Annotation Text:** L6 Intratelencephalic - Type 1 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** L6 intratelencephalic projecting glutamatergic neuron (CL:4030065) +- **Enrichment Info:** `{'name': 'L6 Intratelencephalic - Type 1', 'full_name': 'L6 intratelencephalic type 1', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** L6 Intratelencephalic - Type 2 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** L6 intratelencephalic projecting glutamatergic neuron (CL:4030065) +- **Enrichment Info:** `{'name': 'L6 Intratelencephalic - Type 2', 'full_name': 'L6 intratelencephalic type 2', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Parvalbumin interneurons +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** pvalb GABAergic interneuron (CL:4023018) +- **Enrichment Info:** `{'name': 'Parvalbumin interneurons', 'full_name': 'Parvalbumin interneurons', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** SV2C LAMP5 Interneurons +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** lamp5 GABAergic interneuron (CL:4023011) +- **Enrichment Info:** `{'name': 'SV2C LAMP5 Interneurons', 'full_name': 'SV2C LAMP5 interneurons', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Somatostatin Interneurons +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** sst GABAergic interneuron (CL:4023017) +- **Enrichment Info:** `{'name': 'Somatostatin Interneurons', 'full_name': 'somatostatin interneurons', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** VIP Interneurons +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** VIP GABAergic interneuron (CL:4023016) +- **Enrichment Info:** `{'name': 'VIP Interneurons', 'full_name': 'VIP interneurons', 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: d967b47c-a9e6-4337-b2f4-977f690cb67f_cxg_dataset_unique +- **Annotation Text:** CC_VenEndo +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** vein endothelial cell (CL:0002543) +- **Enrichment Info:** `{'name': 'CC_VenEndo', 'full_name': 'Collector Channel/Venous Endothelium', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** K_Fibro +- **Author's Mapping:** fibroblast (CL:0000057) +- **Agent's Mapping:** keratocyte (CL:0002363) +- **Enrichment Info:** `{'name': 'K_Fibro', 'full_name': 'corneal fibroblasts', 'paper_synonyms': 'K_Fibro; stromal keratocytes', 'tissue_context': ''}` + +- **Annotation Text:** Schlemm_Endo +- **Author's Mapping:** endothelial cell (CL:0000115) +- **Agent's Mapping:** Schlemm's canal endothelial cell (CL:4033097) +- **Enrichment Info:** `{'name': 'Schlemm_Endo', 'full_name': 'Schlemm canal endothelium', 'paper_synonyms': 'SC endothelium', 'tissue_context': ''}` + + +## Dataset: 9ea768a2-87ab-46b6-a73d-c4e915f25af3_cxg_dataset_unique +- **Annotation Text:** Peritubular capillary endothelium +- **Author's Mapping:** capillary endothelial cell (CL:0002144) +- **Agent's Mapping:** peritubular capillary endothelial cell (CL:1001033) +- **Enrichment Info:** `{'name': 'Peritubular capillary endothelium', 'full_name': 'peritubular capillary endothelium', 'paper_synonyms': 'PCE', 'tissue_context': ''}` + +- **Annotation Text:** Peritubular capillary endothelium 1 +- **Author's Mapping:** capillary endothelial cell (CL:0002144) +- **Agent's Mapping:** peritubular capillary endothelial cell (CL:1001033) +- **Enrichment Info:** `{'name': 'Peritubular capillary endothelium 1', 'full_name': 'peritubular capillary endothelium', 'paper_synonyms': 'peritubular capillaries (PCap); PCE', 'tissue_context': ''}` + +- **Annotation Text:** Peritubular capillary endothelium 2 +- **Author's Mapping:** capillary endothelial cell (CL:0002144) +- **Agent's Mapping:** peritubular capillary endothelial cell (CL:1001033) +- **Enrichment Info:** `{'name': 'Peritubular capillary endothelium 2', 'full_name': 'peritubular capillary endothelium 2', 'paper_synonyms': 'PCE; peritubular capillaries; PCap', 'tissue_context': ''}` + +- **Annotation Text:** Transitional urothelium +- **Author's Mapping:** urothelial cell (CL:0000731) +- **Agent's Mapping:** ureter urothelial cell (CL:1000706) +- **Enrichment Info:** `{'name': 'Transitional urothelium', 'full_name': 'transitional epithelium of ureter', 'paper_synonyms': 'TE; transitional epithelium; transitional epithelium of ureter', 'tissue_context': ''}` + + +## Dataset: 2f6a20f1-173d-4b8d-860b-c47ffea120fa_cxg_dataset_unique +- **Annotation Text:** H1 +- **Author's Mapping:** retina horizontal cell (CL:0000745) +- **Agent's Mapping:** H1 horizontal cell (CL:0004217) +- **Enrichment Info:** `{'name': 'H1', 'full_name': 'horizontal cell type H1', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** H2 +- **Author's Mapping:** retina horizontal cell (CL:0000745) +- **Agent's Mapping:** H2 horizontal cell (CL:0004218) +- **Enrichment Info:** `{'name': 'H2', 'full_name': 'horizontal cell type H2', 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: 7e7f63c5-d964-40be-83de-ecbcccafd233_cxg_dataset_unique +- **Annotation Text:** S cone +- **Author's Mapping:** retinal cone cell (CL:0000573) +- **Agent's Mapping:** S cone cell (CL:0003050) +- **Enrichment Info:** `{'name': 'S cone', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: 8e47ed12-c658-4252-b126-381df8d52a3d_cxg_dataset_unique +- **Annotation Text:** BEST4 enterocyte +- **Author's Mapping:** enterocyte (CL:0000584) +- **Agent's Mapping:** BEST4+ enterocyte (CL:4030026) +- **Enrichment Info:** `{'name': 'BEST4 enterocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Cycling B cell +- **Author's Mapping:** B cell (CL:0000236) +- **Agent's Mapping:** cycling B cell (CL:4033068) +- **Enrichment Info:** `{'name': 'Cycling B cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Cycling myeloid cells +- **Author's Mapping:** myeloid cell (CL:0000763) +- **Agent's Mapping:** cycling myeloid cell (CL:4033081) +- **Enrichment Info:** `{'name': 'Cycling myeloid cells', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Cycling plasma cell +- **Author's Mapping:** plasma cell (CL:0000786) +- **Agent's Mapping:** cycling plasma cell (CL:4047003) +- **Enrichment Info:** `{'name': 'Cycling plasma cell', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** cDC1 +- **Author's Mapping:** conventional dendritic cell (CL:0000990) +- **Agent's Mapping:** CD141-positive myeloid dendritic cell (CL:0002394) +- **Enrichment Info:** `{'name': 'cDC1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** cDC2 +- **Author's Mapping:** conventional dendritic cell (CL:0000990) +- **Agent's Mapping:** CD1c-positive myeloid dendritic cell (CL:0002399) +- **Enrichment Info:** `{'name': 'cDC2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** early enterocyte +- **Author's Mapping:** enterocyte (CL:0000584) +- **Agent's Mapping:** early enterocyte (CL:4047019) +- **Enrichment Info:** `{'name': 'early enterocyte', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: 124744b8-4681-474a-9894-683896122708_cxg_dataset_unique +- **Annotation Text:** Secretory-papillary fibroblasts +- **Author's Mapping:** skin fibroblast (CL:0002620) +- **Agent's Mapping:** fibroblast of papillary layer of dermis (CL:1000302) +- **Enrichment Info:** `{'name': 'Secretory-papillary fibroblasts', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Secretory-reticular fibroblasts +- **Author's Mapping:** skin fibroblast (CL:0002620) +- **Agent's Mapping:** fibroblast of the reticular layer of dermis (CL:2000096) +- **Enrichment Info:** `{'name': 'Secretory-reticular fibroblasts', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Vascular EC +- **Author's Mapping:** endothelial cell of vascular tree (CL:0002139) +- **Agent's Mapping:** blood vessel endothelial cell (CL:0000071) +- **Enrichment Info:** `{'name': 'Vascular EC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: f5be9ed2-5d41-4a52-91e4-4ff24ff84900_cxg_dataset_unique +- **Annotation Text:** cone-off-BC-BC3A +- **Author's Mapping:** cone retinal bipolar cell (CL:0000752) +- **Agent's Mapping:** type 3a cone bipolar cell (CL:0004213) +- **Enrichment Info:** `{'name': 'cone-off-BC-BC3A', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''}` + + +## Dataset: 02792605-4760-4023-82ad-40fc4458a5db_cxg_dataset_unique +- **Annotation Text:** LAM-like +- **Author's Mapping:** macrophage (CL:0000235) +- **Agent's Mapping:** lipid-associated macrophage (CL:4033086) +- **Enrichment Info:** `{'name': 'LAM-like', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''}` + + +## Dataset: a4157949-6f2a-40e2-b960-63f6e2bde918_cxg_dataset_unique +- **Annotation Text:** K_Fibro +- **Author's Mapping:** fibroblast (CL:0000057) +- **Agent's Mapping:** keratocyte (CL:0002363) +- **Enrichment Info:** `{'name': 'K_Fibro', 'full_name': 'corneal fibroblasts', 'paper_synonyms': 'stromal keratocytes; corneal stromal keratocytes', 'tissue_context': ''}` + + +## Dataset: 59b69042-47c2-47fd-ad03-d21beb99818f_cxg_dataset_unique +- **Annotation Text:** Other T +- **Author's Mapping:** lymphocyte (CL:0000542) +- **Agent's Mapping:** T cell (CL:0000084) +- **Enrichment Info:** `{'name': 'Other T', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''}` + + +## Dataset: 9df60c57-fdf3-4e93-828e-fe9303f20438_cxg_dataset_unique +- **Annotation Text:** DCT1 +- **Author's Mapping:** kidney distal convoluted tubule epithelial cell (CL:1000849) +- **Agent's Mapping:** epithelial cell of early distal convoluted tubule (CL:4030016) +- **Enrichment Info:** `{'name': 'DCT1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** DCT2 +- **Author's Mapping:** kidney distal convoluted tubule epithelial cell (CL:1000849) +- **Agent's Mapping:** epithelial cell of late distal convoluted tubule (CL:4030017) +- **Enrichment Info:** `{'name': 'DCT2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: e067e5ca-e53e-485f-aa8e-efd5435229c8_cxg_dataset_unique +- **Annotation Text:** DCT1 +- **Author's Mapping:** kidney distal convoluted tubule epithelial cell (CL:1000849) +- **Agent's Mapping:** epithelial cell of early distal convoluted tubule (CL:4030016) +- **Enrichment Info:** `{'name': 'DCT1', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** DCT2 +- **Author's Mapping:** kidney distal convoluted tubule epithelial cell (CL:1000849) +- **Agent's Mapping:** epithelial cell of late distal convoluted tubule (CL:4030017) +- **Enrichment Info:** `{'name': 'DCT2', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: 0bc7235a-ae5a-479d-a487-510435377e55_cxg_dataset_unique +- **Annotation Text:** Excitatory_1 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_1', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_10 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_10', 'full_name': 'excitatory neuron 10', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_2 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_2', 'full_name': 'excitatory neurons', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_3 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_3', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_4 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_4', 'full_name': 'excitatory neurons', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_5 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_5', 'full_name': 'excitatory neuron', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_6 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_6', 'full_name': 'excitatory neuron 6', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_7 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_7', 'full_name': 'excitatory neuron 7', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_8 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_8', 'full_name': 'excitatory neurons', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Excitatory_9 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** glutamatergic neuron (CL:0000679) +- **Enrichment Info:** `{'name': 'Excitatory_9', 'full_name': 'excitatory neuron 9', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Inhibitory_1 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** GABAergic neuron (CL:0000617) +- **Enrichment Info:** `{'name': 'Inhibitory_1', 'full_name': 'inhibitory neuron', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Inhibitory_2 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** GABAergic neuron (CL:0000617) +- **Enrichment Info:** `{'name': 'Inhibitory_2', 'full_name': 'inhibitory neurons', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** Inhibitory_3 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** GABAergic neuron (CL:0000617) +- **Enrichment Info:** `{'name': 'Inhibitory_3', 'full_name': 'inhibitory neurons', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** Inhibitory_4 +- **Author's Mapping:** neuron (CL:0000540) +- **Agent's Mapping:** GABAergic neuron (CL:0000617) +- **Enrichment Info:** `{'name': 'Inhibitory_4', 'full_name': 'inhibitory neurons', 'paper_synonyms': '', 'tissue_context': ''}` + + +## Dataset: 019c7af2-c827-4454-9970-44d5e39ce068_cxg_dataset_unique +- **Annotation Text:** C_earlyACC +- **Author's Mapping:** enterocyte of epithelium of large intestine (CL:0002071) +- **Agent's Mapping:** early colonocyte (CL:4047018) +- **Enrichment Info:** `{'name': 'C_earlyACC', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** C_earlyCC +- **Author's Mapping:** enterocyte of epithelium of large intestine (CL:0002071) +- **Agent's Mapping:** early colonocyte (CL:4047018) +- **Enrichment Info:** `{'name': 'C_earlyCC', 'full_name': '', 'paper_synonyms': '', 'tissue_context': ''}` + +- **Annotation Text:** SI_BEST4 +- **Author's Mapping:** epithelial cell of small intestine (CL:0002254) +- **Agent's Mapping:** small intestine BEST4+ enterocyte (CL:4047051) +- **Enrichment Info:** `{'name': 'SI_BEST4', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** SI_tuft +- **Author's Mapping:** intestinal tuft cell (CL:0019032) +- **Agent's Mapping:** tuft cell of small intestine (CL:0009080) +- **Enrichment Info:** `{'name': 'SI_tuft', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: f512b8b6-369d-4a85-a695-116e0806857f_cxg_dataset_unique +- **Annotation Text:** immune +- **Author's Mapping:** hematopoietic cell (CL:0000988) +- **Agent's Mapping:** leukocyte (CL:0000738) +- **Enrichment Info:** `{'name': 'immune', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + + +## Dataset: 8623d55f-d91c-41c2-ae68-ed2072fd268d_cxg_dataset_unique +- **Annotation Text:** DB1 +- **Author's Mapping:** OFF-bipolar cell (CL:0000750) +- **Agent's Mapping:** diffuse bipolar 1 cell (CL:4033027) +- **Enrichment Info:** `{'name': 'DB1', 'full_name': 'bipolar type DB1', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** DB2 +- **Author's Mapping:** OFF-bipolar cell (CL:0000750) +- **Agent's Mapping:** diffuse bipolar 2 cell (CL:4033028) +- **Enrichment Info:** `{'name': 'DB2', 'full_name': 'bipolar type DB2', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** DB3a +- **Author's Mapping:** OFF-bipolar cell (CL:0000750) +- **Agent's Mapping:** diffuse bipolar 3a cell (CL:4033029) +- **Enrichment Info:** `{'name': 'DB3a', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** DB3b +- **Author's Mapping:** OFF-bipolar cell (CL:0000750) +- **Agent's Mapping:** diffuse bipolar 3b cell (CL:4033030) +- **Enrichment Info:** `{'name': 'DB3b', 'full_name': 'bipolar type DB3b', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** DB4 +- **Author's Mapping:** ON-bipolar cell (CL:0000749) +- **Agent's Mapping:** diffuse bipolar 4 cell (CL:4033031) +- **Enrichment Info:** `{'name': 'DB4', 'full_name': 'bipolar type DB4', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** DB5* +- **Author's Mapping:** ON-bipolar cell (CL:0000749) +- **Agent's Mapping:** diffuse bipolar 5 cell (CL:4033085) +- **Enrichment Info:** `{'name': 'DB5*', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** DB6 +- **Author's Mapping:** ON-bipolar cell (CL:0000749) +- **Agent's Mapping:** diffuse bipolar 6 cell (CL:4033032) +- **Enrichment Info:** `{'name': 'DB6', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** FMB +- **Author's Mapping:** OFF-bipolar cell (CL:0000750) +- **Agent's Mapping:** flat midget bipolar cell (CL:4033033) +- **Enrichment Info:** `{'name': 'FMB', 'full_name': 'bipolar type FMB', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** IMB +- **Author's Mapping:** ON-bipolar cell (CL:0000749) +- **Agent's Mapping:** invaginating midget bipolar cell (CL:4033034) +- **Enrichment Info:** `{'name': 'IMB', 'full_name': None, 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** OFFx +- **Author's Mapping:** OFF-bipolar cell (CL:0000750) +- **Agent's Mapping:** OFFx cell (CL:4033036) +- **Enrichment Info:** `{'name': 'OFFx', 'full_name': 'OFFx type', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** RB1 +- **Author's Mapping:** ON-bipolar cell (CL:0000749) +- **Agent's Mapping:** rod bipolar cell (CL:0000751) +- **Enrichment Info:** `{'name': 'RB1', 'full_name': None, 'paper_synonyms': 'rod bipolar cells; rod BCs', 'tissue_context': ''}` + + +## Dataset: 2872f4b0-b171-46e2-abc6-befcf6de6306_cxg_dataset_unique +- **Annotation Text:** B cell cycling +- **Author's Mapping:** B cell (CL:0000236) +- **Agent's Mapping:** cycling B cell (CL:4033068) +- **Enrichment Info:** `{'name': 'B cell cycling', 'full_name': 'MKI67+ cycling B cells', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** cycling DCs +- **Author's Mapping:** dendritic cell (CL:0000451) +- **Agent's Mapping:** cycling dendritic cell (CL:4033070) +- **Enrichment Info:** `{'name': 'cycling DCs', 'full_name': 'cycling dendritic cells', 'paper_synonyms': None, 'tissue_context': ''}` + +- **Annotation Text:** cycling gd T +- **Author's Mapping:** gamma-delta T cell (CL:0000798) +- **Agent's Mapping:** cycling gamma-delta T cell (CL:4033072) +- **Enrichment Info:** `{'name': 'cycling gd T', 'full_name': 'cycling gammadelta T cell', 'paper_synonyms': 'gammadelta T cells', 'tissue_context': ''}` diff --git a/output/reports/raw_stats_report.md b/output/reports/raw_stats_report.md new file mode 100644 index 0000000..64ae6ab --- /dev/null +++ b/output/reports/raw_stats_report.md @@ -0,0 +1,9 @@ +# Raw Grounding Statistics +Total Annotations Analyzed: **855** +| Category | Count | Percentage | +| :--- | :--- | :--- | +| Improved Granularity | 128 | 14.97% | +| Identical Mapping | 401 | 46.90% | +| Less Specific Mapping | 177 | 20.70% | +| No Match Found | 56 | 6.55% | +| Other / Different Branch | 93 | 10.88% | diff --git a/scripts/generate_validation_reports.py b/scripts/generate_validation_reports.py new file mode 100644 index 0000000..e3c8264 --- /dev/null +++ b/scripts/generate_validation_reports.py @@ -0,0 +1,104 @@ +#!/usr/bin/env python +"""CLI entrypoint for CXG validation/report generation.""" + +from __future__ import annotations + +import argparse +import logging +import sys +from pathlib import Path +from typing import Optional + +from amica import bootstrap +from amica.validation_reporting import generate_reports + + +def parse_args(argv: Optional[list[str]] = None) -> argparse.Namespace: + parser = argparse.ArgumentParser( + description="Summarize CXG grounding outputs using validation reports." + ) + parser.add_argument( + "--output-root", + type=Path, + help="Base directory containing raw_output/, pandasaurus_cxg_outputs_30/, and reports/. Defaults to the CXG layout output directory.", + ) + parser.add_argument( + "--raw-output-dir", + type=Path, + help="Direct path to the raw_output directory (overrides --output-root).", + ) + parser.add_argument( + "--match-type-dir", + type=Path, + help="Direct path to the Pandasaurus match-type directory (overrides --output-root).", + ) + parser.add_argument( + "--reports-dir", + type=Path, + help="Directory to write markdown reports (defaults to /reports).", + ) + parser.add_argument( + "--skip-filtered", + action="store_true", + help="Skip generating the filtered granularity report.", + ) + parser.add_argument( + "--skip-examples", + action="store_true", + help="Skip generating the improved examples report.", + ) + parser.add_argument( + "--skip-raw-stats", + action="store_true", + help="Skip generating the raw aggregate stats report.", + ) + parser.add_argument( + "--skip-ontology", + action="store_true", + help="Disable ontology lookups (runs offline but degrades improved/regression counts).", + ) + parser.add_argument( + "--ontology-adapter", + help="Override the oaklib adapter spec (ex: 'ols:cl', 'pronto:/path/to/cl.owl').", + ) + parser.add_argument( + "--log-level", + default="INFO", + choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"], + help="Logging verbosity.", + ) + return parser.parse_args(argv) + + +def configure_logging(level: str) -> None: + logging.basicConfig( + level=getattr(logging, level.upper(), logging.INFO), + format="%(asctime)s [%(levelname)s] %(name)s: %(message)s", + ) + + +def main() -> None: + args = parse_args() + configure_logging(args.log_level) + bootstrap() + try: + written = generate_reports( + include_filtered=not args.skip_filtered, + include_examples=not args.skip_examples, + include_raw_stats=not args.skip_raw_stats, + output_root=args.output_root, + raw_output_dir=args.raw_output_dir, + match_type_dir=args.match_type_dir, + reports_dir=args.reports_dir, + skip_ontology=args.skip_ontology, + adapter_spec=args.ontology_adapter, + ) + if not written: + logging.warning("No reports were generated (all sections skipped).") + except Exception as exc: # pragma: no cover - CLI + logging.error("Validation reporting failed: %s", exc) + sys.exit(1) + + +if __name__ == "__main__": # pragma: no cover + main() diff --git a/src/amica/validation_reporting/__init__.py b/src/amica/validation_reporting/__init__.py new file mode 100644 index 0000000..247a400 --- /dev/null +++ b/src/amica/validation_reporting/__init__.py @@ -0,0 +1,5 @@ +"""Utilities for summarizing CXG grounding outputs.""" + +from .cli import generate_reports + +__all__ = ["generate_reports"] diff --git a/src/amica/validation_reporting/cli.py b/src/amica/validation_reporting/cli.py new file mode 100644 index 0000000..7b73834 --- /dev/null +++ b/src/amica/validation_reporting/cli.py @@ -0,0 +1,103 @@ +"""Public entrypoints for validation-report generation.""" + +from __future__ import annotations + +import logging +from pathlib import Path +from typing import Any + +from oaklib import get_adapter + +from amica.utils.cxg import CxgResourceLayout + +from .config import ValidationPaths +from .data_loader import MatchTypeResolver, load_grounding_datasets +from .reports import ( + build_examples_markdown, + build_filtered_markdown, + build_raw_stats_markdown, +) +from .stats import ( + collect_improved_examples, + compute_filtered_stats, + compute_raw_stats, + reset_ontology_tracker, +) + +LOGGER = logging.getLogger(__name__) + + +def _initialise_adapter(skip_ontology: bool, adapter_spec: str | None) -> Any | None: + if skip_ontology: + LOGGER.warning("Ontology lookups skipped per CLI flag.") + return None + spec = adapter_spec or "ols:cl" + try: + LOGGER.info("Initializing ontology adapter (%s) ...", spec) + adapter = get_adapter(spec) + LOGGER.info("Ontology adapter ready.") + return adapter + except Exception as exc: # pragma: no cover - network failures + LOGGER.warning("Could not initialize ontology adapter %s: %s", spec, exc) + return None + + +def generate_reports( + *, + include_filtered: bool = True, + include_examples: bool = True, + include_raw_stats: bool = True, + output_root: Path | None = None, + raw_output_dir: Path | None = None, + match_type_dir: Path | None = None, + reports_dir: Path | None = None, + skip_ontology: bool = False, + adapter_spec: str | None = None, +) -> dict[str, Path]: + """Generate requested validation reports using existing CXG outputs.""" + layout = CxgResourceLayout.from_env() + paths = ValidationPaths.from_layout( + layout, + output_root=output_root, + raw_output_dir=raw_output_dir, + match_type_dir=match_type_dir, + reports_dir=reports_dir, + ) + + datasets = load_grounding_datasets(paths.raw_output) + resolver = MatchTypeResolver(paths.match_type_inputs) + adapter = _initialise_adapter( + skip_ontology=skip_ontology, adapter_spec=adapter_spec + ) + + paths.ensure_report_dir() + written: dict[str, Path] = {} + + if include_filtered: + reset_ontology_tracker() + filtered_stats = compute_filtered_stats(datasets, resolver, adapter) + filtered_content = build_filtered_markdown(filtered_stats) + filtered_path = paths.reports_dir / "filtered_granularity_report.md" + filtered_path.write_text(filtered_content) + written["filtered"] = filtered_path + LOGGER.info("Filtered granularity report written to %s", filtered_path) + + if include_examples: + reset_ontology_tracker() + examples = collect_improved_examples(datasets, adapter) + examples_content = build_examples_markdown(examples) + examples_path = paths.reports_dir / "granularity_report.md" + examples_path.write_text(examples_content) + written["examples"] = examples_path + LOGGER.info("Improved examples report written to %s", examples_path) + + if include_raw_stats: + reset_ontology_tracker() + raw_stats = compute_raw_stats(datasets, adapter) + raw_content = build_raw_stats_markdown(raw_stats) + raw_path = paths.reports_dir / "raw_stats_report.md" + raw_path.write_text(raw_content) + written["raw_stats"] = raw_path + LOGGER.info("Raw stats report written to %s", raw_path) + + return written diff --git a/src/amica/validation_reporting/config.py b/src/amica/validation_reporting/config.py new file mode 100644 index 0000000..6e83061 --- /dev/null +++ b/src/amica/validation_reporting/config.py @@ -0,0 +1,50 @@ +"""Shared configuration helpers for validation report generation.""" + +from __future__ import annotations + +from dataclasses import dataclass +from pathlib import Path + +from amica.utils.cxg import CxgResourceLayout + + +def _resolve(path: Path | None) -> Path | None: + if path is None: + return None + return Path(path).expanduser().resolve() + + +@dataclass(slots=True) +class ValidationPaths: + """Filesystem locations that contain CXG outputs + validation reports.""" + + raw_output: Path + match_type_inputs: Path + reports_dir: Path + + @classmethod + def from_layout( + cls, + layout: CxgResourceLayout, + *, + output_root: Path | None = None, + raw_output_dir: Path | None = None, + match_type_dir: Path | None = None, + reports_dir: Path | None = None, + ) -> "ValidationPaths": + """Build directory references from the CXG resource layout.""" + + base_output_override = ( + _resolve(output_root) if output_root is not None else None + ) + base_output: Path = base_output_override or layout.output_dir + return cls( + raw_output=_resolve(raw_output_dir) or (base_output / "raw_output"), + match_type_inputs=_resolve(match_type_dir) + or (base_output / "pandasaurus_cxg_outputs_30"), + reports_dir=_resolve(reports_dir) or (base_output / "reports"), + ) + + def ensure_report_dir(self) -> None: + """Create the reports directory if it does not exist.""" + self.reports_dir.mkdir(parents=True, exist_ok=True) diff --git a/src/amica/validation_reporting/data_loader.py b/src/amica/validation_reporting/data_loader.py new file mode 100644 index 0000000..ab3fdee --- /dev/null +++ b/src/amica/validation_reporting/data_loader.py @@ -0,0 +1,80 @@ +"""Raw data ingestion helpers for validation reporting.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from pathlib import Path +from typing import Dict + +import pandas as pd + + +GROUNDINGS_FILENAME = "groundings.tsv" + + +def load_grounding_datasets(raw_output_dir: Path) -> dict[str, pd.DataFrame]: + """Return a mapping of dataset folder -> groundings DataFrame.""" + raw_output_dir = Path(raw_output_dir) + if not raw_output_dir.exists(): + raise FileNotFoundError(f"raw output directory not found: {raw_output_dir}") + + datasets: dict[str, pd.DataFrame] = {} + for groundings_file in raw_output_dir.glob(f"**/{GROUNDINGS_FILENAME}"): + dataset_name = groundings_file.parent.name + df = pd.read_csv(groundings_file, sep="\t") + datasets[dataset_name] = df + if not datasets: + raise FileNotFoundError( + f"No {GROUNDINGS_FILENAME} files found under {raw_output_dir}" + ) + return datasets + + +@dataclass(slots=True) +class MatchTypeResolver: + """Caches Pandasaurus match-type lookups for each dataset.""" + + match_type_dir: Path + _cache: Dict[str, dict[tuple[str, str], str]] = field(default_factory=dict) + + def get_map(self, dataset_name: str) -> dict[tuple[str, str], str]: + """Return the cached match type mapping for a dataset.""" + if dataset_name not in self._cache: + self._cache[dataset_name] = self._load_dataset_map(dataset_name) + return self._cache[dataset_name] + + def _load_dataset_map(self, dataset_name: str) -> dict[tuple[str, str], str]: + base = Path(self.match_type_dir) + if not base.exists(): + raise FileNotFoundError( + f"match type directory not found: {self.match_type_dir}" + ) + + for suffix in (".tsv", ".csv"): + candidate = base / f"{dataset_name}{suffix}" + if candidate.exists(): + return self._parse_match_types(candidate) + return {} + + @staticmethod + def _parse_match_types(path: Path) -> dict[tuple[str, str], str]: + if path.suffix == ".tsv": + df = pd.read_csv(path, sep="\t") + else: + df = pd.read_csv(path) + + if "author_cell_type" in df.columns: + df["annotation_text"] = df["author_cell_type"] + if "CL_ID" in df.columns: + df["cl_id"] = df["CL_ID"] + + if "match_type" not in df.columns or "cl_id" not in df.columns: + return {} + + df["annotation_text"] = df["annotation_text"].astype(str).str.strip() + df["cl_id"] = df["cl_id"].astype(str).str.strip() + df["match_type"] = ( + df["match_type"].astype(str).str.lower().str.replace(" ", "_") + ) + + return df.set_index(["annotation_text", "cl_id"])["match_type"].to_dict() diff --git a/src/amica/validation_reporting/reports.py b/src/amica/validation_reporting/reports.py new file mode 100644 index 0000000..1a8bfd2 --- /dev/null +++ b/src/amica/validation_reporting/reports.py @@ -0,0 +1,104 @@ +"""Markdown rendering helpers for validation reporting.""" + +from __future__ import annotations + + +from .stats import FilteredStats, ImprovedExample, RawStats + + +def build_filtered_markdown(stats: FilteredStats) -> str: + """Create the filtered granularity markdown report.""" + lines: list[str] = ["# Annotation Granularity Report (Filtered)"] + lines.append( + "> **Note:** This report excludes 'Broad term' and 'Overlaps' matches to reduce false regressions.\n" + ) + + if not stats.ontology_available: + lines.append( + "> Warning: Ontology lookups were unavailable, so improved/regression counts may be understated.\n" + ) + + lines.append("## Aggregate Statistics") + lines.append(f"**Total Annotations Analyzed:** {stats.total_filtered}") + lines.append(f"**Excluded (Noisy Data):** {stats.excluded_broad}\n") + + lines.append("| Category | Count | Percentage | Description |") + lines.append("| :--- | :--- | :--- | :--- |") + + descriptions = { + "improved_granularity": "Agent provided a more specific or context-aware term.", + "exact_match": "Agent matched the author's term exactly.", + "regression": "Agent provided a less specific term (ancestor).", + "no_match_found": "Agent could not find a CL term (potential new term).", + "other": "Agent term is unrelated to the author term.", + } + + categories = [ + ("improved_granularity", stats.improved_granularity), + ("exact_match", stats.exact_match), + ("regression", stats.regression), + ("no_match_found", stats.no_match_found), + ("other", stats.other), + ] + + total = max(stats.total_filtered, 1) + for key, count in categories: + percent = (count / total) * 100 + lines.append( + f"| {key.replace('_', ' ').title()} | {count} | {percent:.2f}% | {descriptions[key]} |" + ) + + return "\n".join(lines) + "\n" + + +def build_examples_markdown(examples: list[ImprovedExample]) -> str: + """Create the markdown report highlighting improved granularity examples.""" + lines = ["# Good Examples of Improved Granularity"] + if not examples: + lines.append( + "\n_No improved examples were detected (ontology lookups may have been unavailable)._" + ) + return "\n".join(lines) + "\n" + + current_dataset: str | None = None + for example in examples: + if example.dataset != current_dataset: + lines.append(f"\n## Dataset: {example.dataset}") + current_dataset = example.dataset + lines.append(f"- **Annotation Text:** {example.annotation_text}") + lines.append(f"- **Author's Mapping:** {example.author_mapping}") + lines.append(f"- **Agent's Mapping:** {example.agent_mapping}") + if example.enrichment: + lines.append(f"- **Enrichment Info:** `{example.enrichment}`") + lines.append("") + return "\n".join(lines).strip() + "\n" + + +def build_raw_stats_markdown(stats: RawStats) -> str: + """Render the raw aggregate statistics similar to the legacy script output.""" + if stats.total_annotations == 0: + return "# Raw Grounding Statistics\n\n_No annotations were found to analyze._\n" + + warning = "" + if not stats.ontology_available: + warning = "> Warning: Ontology lookups were unavailable; improved/regression counts may be understated.\n\n" + + lines = [ + "# Raw Grounding Statistics", + warning, + f"Total Annotations Analyzed: **{stats.total_annotations}**", + "", + "| Category | Count | Percentage |", + "| :--- | :--- | :--- |", + ] + total = max(stats.total_annotations, 1) + rows = [ + ("Improved Granularity", stats.improved), + ("Identical Mapping", stats.identical), + ("Less Specific Mapping", stats.less_specific), + ("No Match Found", stats.no_match), + ("Other / Different Branch", stats.other), + ] + for label, count in rows: + lines.append(f"| {label} | {count} | {(count / total) * 100:.2f}% |") + return "\n".join(filter(None, lines)) + "\n" diff --git a/src/amica/validation_reporting/stats.py b/src/amica/validation_reporting/stats.py new file mode 100644 index 0000000..9acd290 --- /dev/null +++ b/src/amica/validation_reporting/stats.py @@ -0,0 +1,231 @@ +"""Pure aggregation helpers for validation reporting.""" + +from __future__ import annotations + +import logging +from dataclasses import dataclass +from typing import Any, Iterable, Mapping, Sequence + +import pandas as pd + +from .data_loader import MatchTypeResolver + +LOGGER = logging.getLogger(__name__) +_ONTOLOGY_FAILURE = False + + +def _clean_str(value: Any) -> str: + if pd.isna(value): + return "" + return str(value).strip() + + +def _normalise_curie(entry: Any) -> str: + """Best-effort extraction of a CL-style identifier from oaklib responses.""" + if isinstance(entry, str): + return entry.strip() + if isinstance(entry, Iterable): + for part in entry: + if isinstance(part, str) and part.startswith("CL:"): + return part.strip() + return _clean_str(entry) + + +def _get_ancestors( + adapter: Any | None, cl_id: str, predicates: Sequence[str] +) -> set[str]: + global _ONTOLOGY_FAILURE + if adapter is None or not cl_id: + return set() + # Validate that cl_id is a proper CL identifier before attempting lookup + if not cl_id.startswith("CL:"): + return set() + try: + values = adapter.ancestors(cl_id, predicates=list(predicates)) + except Exception as exc: + if not _ONTOLOGY_FAILURE: + LOGGER.warning( + "Ontology ancestor lookup failed for %s (predicates=%s): %s", + cl_id, + predicates, + exc, + ) + _ONTOLOGY_FAILURE = True + return set() + return {_normalise_curie(entry) for entry in values} + + +def reset_ontology_tracker() -> None: + """Clear any cached ontology failure flags between report sections.""" + global _ONTOLOGY_FAILURE + _ONTOLOGY_FAILURE = False + + +@dataclass(slots=True) +class FilteredStats: + improved_granularity: int = 0 + exact_match: int = 0 + regression: int = 0 + no_match_found: int = 0 + other: int = 0 + total_filtered: int = 0 + excluded_broad: int = 0 + ontology_available: bool = True + + +@dataclass(slots=True) +class RawStats: + total_annotations: int = 0 + improved: int = 0 + identical: int = 0 + less_specific: int = 0 + no_match: int = 0 + other: int = 0 + ontology_available: bool = True + + +@dataclass(slots=True) +class ImprovedExample: + dataset: str + annotation_text: str + author_mapping: str + agent_mapping: str + enrichment: str + + +def compute_filtered_stats( + datasets: Mapping[str, pd.DataFrame], + match_types: MatchTypeResolver, + cl_adapter: Any | None, +) -> FilteredStats: + stats = FilteredStats(ontology_available=cl_adapter is not None) + for dataset_name, df in datasets.items(): + match_map = match_types.get_map(dataset_name) + for _, row in df.iterrows(): + author_cl_id = _clean_str(row.get("cl_id")) + agent_raw = _clean_str(row.get("grounding_cl_id")) + annotation = _clean_str(row.get("annotation_text")) + + if not author_cl_id: + continue + + match_type = match_map.get((annotation, author_cl_id), "unknown") + if match_type in {"broad_term", "overlaps"}: + stats.excluded_broad += 1 + continue + + stats.total_filtered += 1 + + if ( + not agent_raw + or agent_raw.lower() == "none" + or agent_raw.lower() == "nan" + or "NO MATCH" in agent_raw.upper() + ): + stats.no_match_found += 1 + continue + + if author_cl_id == agent_raw: + stats.exact_match += 1 + continue + + agent_ancestors = _get_ancestors( + cl_adapter, agent_raw, ["rdfs:subClassOf", "BFO:0000050"] + ) + if author_cl_id in agent_ancestors: + stats.improved_granularity += 1 + continue + + author_ancestors = _get_ancestors( + cl_adapter, author_cl_id, ["rdfs:subClassOf"] + ) + if agent_raw in author_ancestors: + stats.regression += 1 + continue + + stats.other += 1 + global _ONTOLOGY_FAILURE + if _ONTOLOGY_FAILURE: + stats.ontology_available = False + return stats + + +def compute_raw_stats( + datasets: Mapping[str, pd.DataFrame], + cl_adapter: Any | None, +) -> RawStats: + stats = RawStats(ontology_available=cl_adapter is not None) + for df in datasets.values(): + for _, row in df.iterrows(): + author_id = _clean_str(row.get("cl_id")) + agent_id = _clean_str(row.get("grounding_cl_id")) + stats.total_annotations += 1 + + if not author_id or not agent_id: + stats.other += 1 + continue + + if "NO MATCH" in agent_id.upper(): + stats.no_match += 1 + continue + + if author_id == agent_id: + stats.identical += 1 + continue + + if "CL:" in author_id and "CL:" in agent_id: + agent_ancestors = _get_ancestors( + cl_adapter, agent_id, ["rdfs:subClassOf", "BFO:0000050"] + ) + if author_id in agent_ancestors: + stats.improved += 1 + continue + + author_ancestors = _get_ancestors( + cl_adapter, author_id, ["rdfs:subClassOf"] + ) + if agent_id in author_ancestors: + stats.less_specific += 1 + continue + + stats.other += 1 + global _ONTOLOGY_FAILURE + if _ONTOLOGY_FAILURE: + stats.ontology_available = False + return stats + + +def collect_improved_examples( + datasets: Mapping[str, pd.DataFrame], + cl_adapter: Any | None, +) -> list[ImprovedExample]: + if cl_adapter is None: + return [] + + examples: list[ImprovedExample] = [] + for dataset_name, df in datasets.items(): + for _, row in df.iterrows(): + author_cl_id = _clean_str(row.get("cl_id")) + agent_cl_id = _clean_str(row.get("grounding_cl_id")) + if not author_cl_id or not agent_cl_id or author_cl_id == agent_cl_id: + continue + + agent_ancestors = _get_ancestors( + cl_adapter, agent_cl_id, ["rdfs:subClassOf", "BFO:0000050"] + ) + if author_cl_id in agent_ancestors: + author_label = _clean_str(row.get("cl_label")) or author_cl_id + agent_label = _clean_str(row.get("grounding_cl_label")) or agent_cl_id + enrichment = row.get("enrichment") + enrichment_str = "" if pd.isna(enrichment) else str(enrichment) + + examples.append( + ImprovedExample( + dataset=dataset_name, + annotation_text=_clean_str(row.get("annotation_text")), + author_mapping=f"{author_label} ({author_cl_id})", + agent_mapping=f"{agent_label} ({agent_cl_id})", + enrichment=enrichment_str, + ) + ) + return examples