obophenotype · JABelfiore · May 2, 2025 · May 2, 2025 · May 2, 2025 · May 2, 2025
diff --git a/.github/workflows/diff.yml b/.github/workflows/diff.yml
@@ -53,7 +53,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.6
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -87,7 +87,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.6
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -115,7 +115,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.6
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -140,7 +140,7 @@ jobs:
   diff_classification:
     needs:  [classify_branch, classify_main]
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.6
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout main
-        uses: actions/checkout@v4
+        uses: actions/checkout@v3
 
       - name: Deploy docs
         uses: mhausenblas/mkdocs-deploy-gh-pages@master

diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml
@@ -31,7 +31,7 @@ jobs:
     needs: check
     if: needs.check.outputs.phraseExists == 'true'
     runs-on: ${{ matrix.os }}
-    container: obolibrary/odkfull:v1.6
+    container: obolibrary/odkfull:v1.5
     strategy:
       matrix:
         python-version: ["3.9"]

diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -19,12 +19,12 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.6
+    container: obolibrary/odkfull:v1.5.3
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
 
       - name: Run ontology QC checks
         id: check

diff --git a/.gitignore b/.gitignore
@@ -1,87 +1,56 @@
-# ODK-managed rules, do not modify
-# If you need to add your own ignore rules, you may do so below
-# the "End ODK-managed rules" marker at the end of this file.
-.DS_Store
-semantic.cache
-bin/
 
+.DS_Store
 *.tmp
+*.tmp.json
 *.tmp.obo
 *.tmp.owl
-*.tmp.json
-*-relation-graph.tsv.gz
-.template.db
-
-.github/token.txt
-
-/cl.owl
-/cl.obo
-/cl.json
-/cl.db
-/cl-base.*
-/cl-basic.*
-/cl-full.*
-/cl-simple.*
-/cl-simple-non-classified.*
-/mappings/
-/patterns/
-/reports/
-/subsets/
-
-src/ontology/mirror
-src/ontology/mirror/*
-src/ontology/reports/*
-!src/ontology/reports/release-diff.md
-src/ontology/cl.owl
-src/ontology/cl.obo
-src/ontology/cl.json
-src/ontology/cl.db
+bin/
+semantic.cache
 src/ontology/cl-base.*
+src/ontology/cl-base.json
+src/ontology/cl-base.obo
 src/ontology/cl-basic.*
 src/ontology/cl-full.*
-src/ontology/cl-simple.*
+src/ontology/cl-non-classified.*
 src/ontology/cl-simple-non-classified.*
-
-src/ontology/seed.txt
+src/ontology/cl-simple.*
+src/ontology/cl.json
+src/ontology/cl.obo
+src/ontology/cl.owl
 src/ontology/dosdp-tools.log
 src/ontology/ed_definitions_merged.owl
+src/ontology/imports/*_terms_combined.txt
+src/ontology/merged-cl-edit.owl
+src/ontology/mirror
+src/ontology/mirror/*
 src/ontology/ontologyterms.txt
-src/ontology/simple_seed.txt
+src/ontology/oort
 src/ontology/patterns
-src/ontology/merged-cl-edit.owl
-src/ontology/cl-edit.properties
-
+src/ontology/patterns 
+src/ontology/seed.txt
+src/ontology/simple_seed.txt
 src/ontology/target/
+src/ontology/tmp
 src/ontology/tmp/*
-!src/ontology/tmp/.gitkeep
 !src/ontology/tmp/README.md
 
-src/ontology/run.sh.conf
-src/ontology/run.sh.env
-
-src/ontology/imports/*_terms_combined.txt
-
+src/patterns/all_pattern_terms.txt
 src/patterns/data/**/*.ofn
 src/patterns/data/**/*.txt
-src/patterns/pattern_owl_seed.txt
-src/patterns/all_pattern_terms.txt
-
-# End of ODK-managed rules
-
-src/ontology/cl-base.json
-src/ontology/cl-base.obo
-src/ontology/cl-non-classified.*
-src/ontology/oort
-src/ontology/tmp
-
 src/patterns/imports/seed_sorted.txt
+src/patterns/pattern_owl_seed.txt
 src/ontology/remove_template_classes_from_edit.txt
 src/ontology/tmp.txt
 .idea
+src/patterns/pattern_owl_seed.txt
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/reports/*
 !src/ontology/reports/cl-base-diff.md
 src/ontology/cl-hipc.owl
 site/
 src/ontology/cl-check.obo
+src/ontology/cl-edit.properties
 src/ontology/imports/*_import.owl
 subsets/BDS_subset.tsv
 subsets/BDS_subset.owl

diff --git a/docs/odk-workflows/ManageAutomatedTest.md b/docs/odk-workflows/ManageAutomatedTest.md
@@ -25,3 +25,4 @@ We can define custom checks using [SPARQL](https://www.w3.org/TR/rdf-sparql-quer
 ```shell
 sh run.sh make update_repo
 ```
+
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -16,14 +16,15 @@ These are the current imports in CL
 
 | Import | URL | Type |
 | ------ | --- | ---- |
-| pr | https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl | slme |
-| go | http://purl.obolibrary.org/obo/go.owl | slme |
-| uberon | http://purl.obolibrary.org/obo/uberon.owl | slme |
-| ro | http://purl.obolibrary.org/obo/ro.owl | slme |
-| pato | http://purl.obolibrary.org/obo/pato.owl | slme |
-| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | slme |
-| ncbitaxondisjoints | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl | slme |
+| pr | https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl | None |
+| go | http://purl.obolibrary.org/obo/go.owl | None |
+| uberon | http://purl.obolibrary.org/obo/uberon.owl | None |
+| ro | http://purl.obolibrary.org/obo/ro.owl | None |
+| pato | http://purl.obolibrary.org/obo/pato.owl | None |
+| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
+| ncbitaxondisjoints | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl | None |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
+
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:
 
@@ -35,11 +36,11 @@ These are the components in CL
 
 | Filename | URL |
 | -------- | --- |
-| hra_subset.owl | https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/CL_ASCTB_subset.owl |
+| hra_subset.owl | None |
 | mappings.owl | None |
 | blood_and_immune_upper_slim.owl | None |
 | eye_upper_slim.owl | None |
 | general_cell_types_upper_slim.owl | None |
 | kidney_upper_slim.owl | None |
 | cellxgene_subset.owl | None |
-| clm-cl.owl | https://raw.githubusercontent.com/Cellular-Semantics/CellMark/main/clm-cl.owl |
+| clm-cl.owl | None |
diff --git a/docs/odk-workflows/components.md b/docs/odk-workflows/components.md
@@ -14,46 +14,35 @@ components:
     - filename: your-component-name.owl
 ```
 
-3) Refresh your repo by running `sh run update_repo`. This will automatically (1) create a new file in `src/ontology/components/`, (2) update the `-edit` file so that it imports `http://purl.obolibrary.org/obo/cl/components/your-component-name.owl` (the IRI of your new component), and (3) update the XML catalog file (`src/ontology/catalog-v001.xml`) to redirect that IRI to the file in the `src/ontology/components` directory, so that the new component can be found by tools such as Protégé or ROBOT, when they load the `-edit` file.
-
-If your component is to be generated by some automated process, add a goal in your custom Makefile (`src/ontology/cl.Makefile`) and make it perform any task needed to generate the component:
+3) Add the component to your catalog file (src/ontology/catalog-v001.xml)
 
 ```
-$(COMPONENTSDIR)/your-component-name.owl: $(SRC)
-	<Insert here the code to produce the component>
+  <uri name="http://purl.obolibrary.org/obo/cl/components/your-component-name.owl" uri="components/your-component-name.owl"/>
 ```
 
-If the component is to be generated from a ROBOT template, the ODK can generate the appropriate code for you. For that, when adding the component fo the ODK configuration file (step 2 above), explicitly indicate that the component should be derived from template(s) and list the source templates:
+4) Add the component to the edit file (src/ontology/cl-edit.obo)
+for .obo formats: 
 
 ```
-components:
-  products:
-    - filename: your-component-name.owl
-      use_template: true
-      templates:
-        - template1.tsv
-        - template2.tsv
+import: http://purl.obolibrary.org/obo/cl/components/your-component-name.owl
 ```
 
-In this example, the component will be derived from the templates found in `src/templates/template1.tsv` and `src/templates/template2.tsv`. Initial empty templates will automatically be generated when the repository is refreshed (step 3).
-
-Likewise, the ODK can generate the required code for the case where the component is to be derived from SSSOM mappings:
+for .owl formats: 
 
 ```
-components:
-  products:
-    - filename: your-component-name.owl
-      use_mappings: true
-      mappings:
-        - my-mappings.sssom.tsv
+Import(<http://purl.obolibrary.org/obo/cl/components/your-component-name.owl>)
 ```
 
-and for the case where the component is to be fetched from a remote resource:
+5) Refresh your repo by running `sh run.sh make update_repo` - this should create a new file in src/ontology/components.
+6) In your custom makefile (src/ontology/cl.Makefile) add a goal for your custom make file. In this example, the goal is a ROBOT template.
 
 ```
-components:
-  products:
-    - filename: your-component-name.owl
-      source: https://example.org/component-source.owl
+$(COMPONENTSDIR)/your-component-name.owl: $(SRC) ../templates/your-component-template.tsv 
+	$(ROBOT) template --template ../templates/your-component-template.tsv \
+  annotate --ontology-iri $(ONTBASE)/$@ --output $(COMPONENTSDIR)/your-component-name.owl
 ```
 
+(If using a ROBOT template, do not forget to add your template tsv in src/templates/)
+
+7) Make the file by running `sh run.sh make components/your-component-name.owl`
+
Original file line number	Diff line number	Diff line change
Expand Up		@@ -25,3 +25,4 @@ We can define custom checks using [SPARQL](https://www.w3.org/TR/rdf-sparql-quer
		```shell
		sh run.sh make update_repo
		```