From 1c09142ad98dbf481002863f41268055499285b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=B6khan?= <81560784+gokhanturer@users.noreply.github.com> Date: Thu, 3 Oct 2024 21:56:43 +0300 Subject: [PATCH] pp update (#1514) * pp update * updated md cards * Update 2023-06-17-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md * Update 2023-03-14-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md * Update 2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md * Update 2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md * Update 2022-03-21-jsl_rd_ner_wip_greedy_clinical_pipeline_en_3_0.md * updated md cards * updated md * updated md * updated md --------- Co-authored-by: Akar <67700732+akrztrk@users.noreply.github.com> --- ...3-06-17-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md | 5 ++++- .../2023-06-17-ner_cellular_biobert_pipeline_en.md | 2 ++ ...06-17-ner_human_phenotype_gene_biobert_pipeline_en.md | 2 ++ .../2023-06-17-ner_living_species_biobert_pipeline_en.md | 2 ++ ...3-03-14-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md | 9 ++++++++- .../2023-03-20-ner_cellular_biobert_pipeline_en.md | 4 ++++ ...03-20-ner_human_phenotype_gene_biobert_pipeline_en.md | 4 ++++ .../2023-03-20-ner_living_species_biobert_pipeline_en.md | 4 ++++ ...3-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md | 5 ++++- .../2023-06-16-ner_cellular_biobert_pipeline_en.md | 2 ++ ...06-16-ner_human_phenotype_gene_biobert_pipeline_en.md | 2 ++ .../2023-06-17-ner_living_species_biobert_pipeline_en.md | 1 + .../2023-07-01-icd10gm_resolver_pipeline_de.md | 1 + .../2023-06-13-ner_living_species_biobert_pipeline_en.md | 2 ++ ...3-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md | 5 ++++- .../2023-06-16-ner_cellular_biobert_pipeline_en.md | 2 ++ ...06-16-ner_human_phenotype_gene_biobert_pipeline_en.md | 2 ++ .../2023-06-16-ner_living_species_biobert_pipeline_en.md | 2 ++ .../ahmet-mesut/2024-01-18-hpo_resolver_pipeline_en.md | 4 ++++ .../ahmet-mesut/2024-01-25-mesh_resolver_pipeline_en.md | 4 ++++ .../akrztrk/2024-01-18-hpo_resolver_pipeline_en.md | 5 +++++ .../akrztrk/2024-01-25-mesh_resolver_pipeline_en.md | 4 ++++ .../2024-01-17-hpo_resolver_pipeline_en.md | 4 ++++ .../2024-01-25-mesh_resolver_pipeline_en.md | 4 ++++ ...-21-jsl_rd_ner_wip_greedy_clinical_pipeline_en_3_0.md | 5 +++++ .../2022-03-21-ner_cellular_biobert_pipeline_en_3_0.md | 4 ++++ ...-ner_deid_subentity_augmented_i2b2_pipeline_en_3_0.md | 4 ++++ ...1-ner_human_phenotype_gene_biobert_pipeline_en_3_0.md | 4 ++++ 28 files changed, 94 insertions(+), 4 deletions(-) diff --git a/docs/_posts/C-K-Loan/2023-06-17-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md b/docs/_posts/C-K-Loan/2023-06-17-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md index 95df40eda5..a9760f97b5 100644 --- a/docs/_posts/C-K-Loan/2023-06-17-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md +++ b/docs/_posts/C-K-Loan/2023-06-17-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md @@ -22,6 +22,9 @@ This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical] ## Predicted Entities +`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL` + + {:.btn-box} @@ -116,4 +119,4 @@ nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""The patient is a 21 - TokenizerModel - WordEmbeddingsModel - MedicalNerModel -- NerConverterInternalModel \ No newline at end of file +- NerConverterInternalModel diff --git a/docs/_posts/C-K-Loan/2023-06-17-ner_cellular_biobert_pipeline_en.md b/docs/_posts/C-K-Loan/2023-06-17-ner_cellular_biobert_pipeline_en.md index 1d1e845674..4b17e03029 100644 --- a/docs/_posts/C-K-Loan/2023-06-17-ner_cellular_biobert_pipeline_en.md +++ b/docs/_posts/C-K-Loan/2023-06-17-ner_cellular_biobert_pipeline_en.md @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_cellular_biobert](https://n ## Predicted Entities +`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`. + {:.btn-box} diff --git a/docs/_posts/C-K-Loan/2023-06-17-ner_human_phenotype_gene_biobert_pipeline_en.md b/docs/_posts/C-K-Loan/2023-06-17-ner_human_phenotype_gene_biobert_pipeline_en.md index 3de9801b92..2ef5a682e1 100644 --- a/docs/_posts/C-K-Loan/2023-06-17-ner_human_phenotype_gene_biobert_pipeline_en.md +++ b/docs/_posts/C-K-Loan/2023-06-17-ner_human_phenotype_gene_biobert_pipeline_en.md @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biober ## Predicted Entities +`GENE`, `HP`. + {:.btn-box} diff --git a/docs/_posts/C-K-Loan/2023-06-17-ner_living_species_biobert_pipeline_en.md b/docs/_posts/C-K-Loan/2023-06-17-ner_living_species_biobert_pipeline_en.md index d59a3f3b64..6753eb69e6 100644 --- a/docs/_posts/C-K-Loan/2023-06-17-ner_living_species_biobert_pipeline_en.md +++ b/docs/_posts/C-K-Loan/2023-06-17-ner_living_species_biobert_pipeline_en.md @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_living_species_biobert](htt ## Predicted Entities +`SPECIES`, `HUMAN` + {:.btn-box} diff --git a/docs/_posts/Cabir40/2023-03-14-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md b/docs/_posts/Cabir40/2023-03-14-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md index 2ccf10c275..c5378e4dd3 100644 --- a/docs/_posts/Cabir40/2023-03-14-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md +++ b/docs/_posts/Cabir40/2023-03-14-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md @@ -20,6 +20,13 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical](https://nlp.johnsnowlabs.com/2021/04/01/jsl_rd_ner_wip_greedy_clinical_en.html) model. +## Predicted Entities + +`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL` + + + + {:.btn-box} @@ -113,4 +120,4 @@ nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""The patient is a 21 - TokenizerModel - WordEmbeddingsModel - MedicalNerModel -- NerConverterInternalModel \ No newline at end of file +- NerConverterInternalModel diff --git a/docs/_posts/Cabir40/2023-03-20-ner_cellular_biobert_pipeline_en.md b/docs/_posts/Cabir40/2023-03-20-ner_cellular_biobert_pipeline_en.md index 47dda0a494..b765708aca 100644 --- a/docs/_posts/Cabir40/2023-03-20-ner_cellular_biobert_pipeline_en.md +++ b/docs/_posts/Cabir40/2023-03-20-ner_cellular_biobert_pipeline_en.md @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [ner_cellular_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_cellular_biobert_en.html) model. +## Predicted Entities + +`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`. + {:.btn-box} diff --git a/docs/_posts/Cabir40/2023-03-20-ner_human_phenotype_gene_biobert_pipeline_en.md b/docs/_posts/Cabir40/2023-03-20-ner_human_phenotype_gene_biobert_pipeline_en.md index 6a8422333f..0f6c3f4e5a 100644 --- a/docs/_posts/Cabir40/2023-03-20-ner_human_phenotype_gene_biobert_pipeline_en.md +++ b/docs/_posts/Cabir40/2023-03-20-ner_human_phenotype_gene_biobert_pipeline_en.md @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_human_phenotype_gene_biobert_en.html) model. +## Predicted Entities + +`GENE`, `HP`. + {:.btn-box} diff --git a/docs/_posts/Cabir40/2023-03-20-ner_living_species_biobert_pipeline_en.md b/docs/_posts/Cabir40/2023-03-20-ner_living_species_biobert_pipeline_en.md index f1fe2f90ea..8ccc7e6ce8 100644 --- a/docs/_posts/Cabir40/2023-03-20-ner_living_species_biobert_pipeline_en.md +++ b/docs/_posts/Cabir40/2023-03-20-ner_living_species_biobert_pipeline_en.md @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [ner_living_species_biobert](https://nlp.johnsnowlabs.com/2022/06/22/ner_living_species_biobert_en_3_0.html) model. +## Predicted Entities + +`SPECIES`, `HUMAN` + {:.btn-box} diff --git a/docs/_posts/Cabir40/2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md b/docs/_posts/Cabir40/2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md index db36b8b962..67e3bb4a55 100644 --- a/docs/_posts/Cabir40/2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md +++ b/docs/_posts/Cabir40/2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md @@ -22,6 +22,9 @@ This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical] ## Predicted Entities +`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL` + + {:.btn-box} @@ -116,4 +119,4 @@ nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""The patient is a 21 - TokenizerModel - WordEmbeddingsModel - MedicalNerModel -- NerConverterInternalModel \ No newline at end of file +- NerConverterInternalModel diff --git a/docs/_posts/Cabir40/2023-06-16-ner_cellular_biobert_pipeline_en.md b/docs/_posts/Cabir40/2023-06-16-ner_cellular_biobert_pipeline_en.md index 52f131c71a..8996e1d214 100644 --- a/docs/_posts/Cabir40/2023-06-16-ner_cellular_biobert_pipeline_en.md +++ b/docs/_posts/Cabir40/2023-06-16-ner_cellular_biobert_pipeline_en.md @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_cellular_biobert](https://n ## Predicted Entities +`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`. + {:.btn-box} diff --git a/docs/_posts/Cabir40/2023-06-16-ner_human_phenotype_gene_biobert_pipeline_en.md b/docs/_posts/Cabir40/2023-06-16-ner_human_phenotype_gene_biobert_pipeline_en.md index 8f92c00c19..36b26907ef 100644 --- a/docs/_posts/Cabir40/2023-06-16-ner_human_phenotype_gene_biobert_pipeline_en.md +++ b/docs/_posts/Cabir40/2023-06-16-ner_human_phenotype_gene_biobert_pipeline_en.md @@ -20,8 +20,10 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_human_phenotype_gene_biobert_en.html) model. + ## Predicted Entities +`GENE`, `HP`. {:.btn-box} diff --git a/docs/_posts/Cabir40/2023-06-17-ner_living_species_biobert_pipeline_en.md b/docs/_posts/Cabir40/2023-06-17-ner_living_species_biobert_pipeline_en.md index 58bfc7ccc5..08d1adf921 100644 --- a/docs/_posts/Cabir40/2023-06-17-ner_living_species_biobert_pipeline_en.md +++ b/docs/_posts/Cabir40/2023-06-17-ner_living_species_biobert_pipeline_en.md @@ -22,6 +22,7 @@ This pretrained pipeline is built on the top of [ner_living_species_biobert](htt ## Predicted Entities +`SPECIES`, `HUMAN` {:.btn-box} diff --git a/docs/_posts/Damla-Gurbaz/2023-07-01-icd10gm_resolver_pipeline_de.md b/docs/_posts/Damla-Gurbaz/2023-07-01-icd10gm_resolver_pipeline_de.md index 5ad26bd8a7..a4840e765e 100644 --- a/docs/_posts/Damla-Gurbaz/2023-07-01-icd10gm_resolver_pipeline_de.md +++ b/docs/_posts/Damla-Gurbaz/2023-07-01-icd10gm_resolver_pipeline_de.md @@ -32,6 +32,7 @@ This pretrained pipeline maps extracted entities in the German language to ICD-1
{% include programmingLanguageSelectScalaPythonNLU.html %} + ```python from sparknlp.pretrained import PretrainedPipeline diff --git a/docs/_posts/ahmedlone127/2023-06-13-ner_living_species_biobert_pipeline_en.md b/docs/_posts/ahmedlone127/2023-06-13-ner_living_species_biobert_pipeline_en.md index 69e48bbc35..cef9e3c9a7 100644 --- a/docs/_posts/ahmedlone127/2023-06-13-ner_living_species_biobert_pipeline_en.md +++ b/docs/_posts/ahmedlone127/2023-06-13-ner_living_species_biobert_pipeline_en.md @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_living_species_biobert](htt ## Predicted Entities +`SPECIES`, `HUMAN` + {:.btn-box} diff --git a/docs/_posts/ahmedlone127/2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md b/docs/_posts/ahmedlone127/2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md index 13dc36ccc2..b2cbb6f358 100644 --- a/docs/_posts/ahmedlone127/2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md +++ b/docs/_posts/ahmedlone127/2023-06-16-jsl_rd_ner_wip_greedy_clinical_pipeline_en.md @@ -22,6 +22,9 @@ This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical] ## Predicted Entities +`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL` + + {:.btn-box} @@ -117,4 +120,4 @@ nlu.load("en.med_ner.jsl_rd_wip_greedy.pipeline").predict("""The patient is a 21 - TokenizerModel - WordEmbeddingsModel - MedicalNerModel -- NerConverterInternalModel \ No newline at end of file +- NerConverterInternalModel diff --git a/docs/_posts/ahmedlone127/2023-06-16-ner_cellular_biobert_pipeline_en.md b/docs/_posts/ahmedlone127/2023-06-16-ner_cellular_biobert_pipeline_en.md index 5bd345c8e9..b7df3a8257 100644 --- a/docs/_posts/ahmedlone127/2023-06-16-ner_cellular_biobert_pipeline_en.md +++ b/docs/_posts/ahmedlone127/2023-06-16-ner_cellular_biobert_pipeline_en.md @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_cellular_biobert](https://n ## Predicted Entities +`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`. + {:.btn-box} diff --git a/docs/_posts/ahmedlone127/2023-06-16-ner_human_phenotype_gene_biobert_pipeline_en.md b/docs/_posts/ahmedlone127/2023-06-16-ner_human_phenotype_gene_biobert_pipeline_en.md index 55a570b7b1..40c50eefd2 100644 --- a/docs/_posts/ahmedlone127/2023-06-16-ner_human_phenotype_gene_biobert_pipeline_en.md +++ b/docs/_posts/ahmedlone127/2023-06-16-ner_human_phenotype_gene_biobert_pipeline_en.md @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biober ## Predicted Entities +`GENE`, `HP`. + {:.btn-box} diff --git a/docs/_posts/ahmedlone127/2023-06-16-ner_living_species_biobert_pipeline_en.md b/docs/_posts/ahmedlone127/2023-06-16-ner_living_species_biobert_pipeline_en.md index face995d65..1a1f58b85c 100644 --- a/docs/_posts/ahmedlone127/2023-06-16-ner_living_species_biobert_pipeline_en.md +++ b/docs/_posts/ahmedlone127/2023-06-16-ner_living_species_biobert_pipeline_en.md @@ -22,6 +22,8 @@ This pretrained pipeline is built on the top of [ner_living_species_biobert](htt ## Predicted Entities +`SPECIES`, `HUMAN` + {:.btn-box} diff --git a/docs/_posts/ahmet-mesut/2024-01-18-hpo_resolver_pipeline_en.md b/docs/_posts/ahmet-mesut/2024-01-18-hpo_resolver_pipeline_en.md index 6d10db0446..f1c3a47bf3 100644 --- a/docs/_posts/ahmet-mesut/2024-01-18-hpo_resolver_pipeline_en.md +++ b/docs/_posts/ahmet-mesut/2024-01-18-hpo_resolver_pipeline_en.md @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java" This advanced pipeline extracts human phenotype entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Human Phenotype Ontology (HPO) codes. It also returns associated codes from the following vocabularies for each HPO code: - MeSH (Medical Subject Headings)- SNOMED- UMLS (Unified Medical Language System ) - ORPHA (international reference resource for information on rare diseases and orphan drugs) - OMIM (Online Mendelian Inheritance in Man). +## Predicted Entities + +`HP` + {:.btn-box} diff --git a/docs/_posts/ahmet-mesut/2024-01-25-mesh_resolver_pipeline_en.md b/docs/_posts/ahmet-mesut/2024-01-25-mesh_resolver_pipeline_en.md index cefa02e745..4e62f92b99 100644 --- a/docs/_posts/ahmet-mesut/2024-01-25-mesh_resolver_pipeline_en.md +++ b/docs/_posts/ahmet-mesut/2024-01-25-mesh_resolver_pipeline_en.md @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java" This advanced pipeline extracts clinical entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Medical Subject Heading (MeSH) codes. +## Predicted Entities + +`TREATMENT`, `PROBLEM`, `TEST` + {:.btn-box} diff --git a/docs/_posts/akrztrk/2024-01-18-hpo_resolver_pipeline_en.md b/docs/_posts/akrztrk/2024-01-18-hpo_resolver_pipeline_en.md index 7a8bd36966..fc6f9df973 100644 --- a/docs/_posts/akrztrk/2024-01-18-hpo_resolver_pipeline_en.md +++ b/docs/_posts/akrztrk/2024-01-18-hpo_resolver_pipeline_en.md @@ -26,6 +26,10 @@ deploy: This advanced pipeline extracts human phenotype entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Human Phenotype Ontology (HPO) codes. It also returns associated codes from the following vocabularies for each HPO code: - MeSH (Medical Subject Headings)- SNOMED- UMLS (Unified Medical Language System ) - ORPHA (international reference resource for information on rare diseases and orphan drugs) - OMIM (Online Mendelian Inheritance in Man). +## Predicted Entities + +`HP` + {:.btn-box} @@ -45,6 +49,7 @@ This advanced pipeline extracts human phenotype entities from clinical texts and
{% include programmingLanguageSelectScalaPythonNLU.html %} + ```python from sparknlp.pretrained import PretrainedPipeline diff --git a/docs/_posts/akrztrk/2024-01-25-mesh_resolver_pipeline_en.md b/docs/_posts/akrztrk/2024-01-25-mesh_resolver_pipeline_en.md index da4419ccb7..cc77b56825 100644 --- a/docs/_posts/akrztrk/2024-01-25-mesh_resolver_pipeline_en.md +++ b/docs/_posts/akrztrk/2024-01-25-mesh_resolver_pipeline_en.md @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java" This advanced pipeline extracts clinical entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Medical Subject Heading (MeSH) codes. +## Predicted Entities + +`TREATMENT`, `PROBLEM`, `TEST` + {:.btn-box} diff --git a/docs/_posts/bunyamin-polat/2024-01-17-hpo_resolver_pipeline_en.md b/docs/_posts/bunyamin-polat/2024-01-17-hpo_resolver_pipeline_en.md index a30cb77b30..aecccc5953 100644 --- a/docs/_posts/bunyamin-polat/2024-01-17-hpo_resolver_pipeline_en.md +++ b/docs/_posts/bunyamin-polat/2024-01-17-hpo_resolver_pipeline_en.md @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java" This advanced pipeline extracts human phenotype entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Human Phenotype Ontology (HPO) codes. It also returns associated codes from the following vocabularies for each HPO code: - MeSH (Medical Subject Headings)- SNOMED- UMLS (Unified Medical Language System ) - ORPHA (international reference resource for information on rare diseases and orphan drugs) - OMIM (Online Mendelian Inheritance in Man). +## Predicted Entities + +`HP` + {:.btn-box} diff --git a/docs/_posts/bunyamin-polat/2024-01-25-mesh_resolver_pipeline_en.md b/docs/_posts/bunyamin-polat/2024-01-25-mesh_resolver_pipeline_en.md index 58110e33d5..81e0363927 100644 --- a/docs/_posts/bunyamin-polat/2024-01-25-mesh_resolver_pipeline_en.md +++ b/docs/_posts/bunyamin-polat/2024-01-25-mesh_resolver_pipeline_en.md @@ -20,6 +20,10 @@ use_language_switcher: "Python-Scala-Java" This advanced pipeline extracts clinical entities from clinical texts and utilizes the `sbiobert_base_cased_mli` Sentence Bert Embeddings to map these entities to their corresponding Medical Subject Heading (MeSH) codes. +## Predicted Entities + +`TREATMENT`, `PROBLEM`, `TEST` + {:.btn-box} diff --git a/docs/_posts/murat-gunay/2022-03-21-jsl_rd_ner_wip_greedy_clinical_pipeline_en_3_0.md b/docs/_posts/murat-gunay/2022-03-21-jsl_rd_ner_wip_greedy_clinical_pipeline_en_3_0.md index 5ddbba13cf..52bb59a7d5 100644 --- a/docs/_posts/murat-gunay/2022-03-21-jsl_rd_ner_wip_greedy_clinical_pipeline_en_3_0.md +++ b/docs/_posts/murat-gunay/2022-03-21-jsl_rd_ner_wip_greedy_clinical_pipeline_en_3_0.md @@ -21,6 +21,11 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [jsl_rd_ner_wip_greedy_clinical](https://nlp.johnsnowlabs.com/2021/04/01/jsl_rd_ner_wip_greedy_clinical_en.html) model. +## Predicted Entities + +`Injury_or_Poisoning`, `Direction`, `Test`, `Route`, `Admission_Discharge`, `ImagingTest`, `Units`, `Death_Entity`, `Oxygen_Therapy`, `Relationship_Status`, `Triglycerides`, `Duration`, `Alcohol`, `Date`, `OtherFindings`, `BodyPart`, `Drug`, `Hyperlipidemia`, `Respiration`, `Birth_Entity`, `VS_Finding`, `Age`, `ManualFix`, `Social_History_Header`, `Family_History_Header`, `Medical_Device`, `Labour_Delivery`, `BMI`, `Fetus_NewBorn`, `Temperature`, `Section_Header`, `Communicable_Disease`, `ImagingFindings`, `Psychological_Condition`, `Obesity`, `Sexually_Active_or_Sexual_Orientation`, `Modifier`, `Vaccine`, `Symptom`, `Kidney_Disease`, `Pulse`, `Oncological`, `EKG_Findings`, `Medical_History_Header`, `Cerebrovascular_Disease`, `Blood_Pressure`, `Diabetes`, `O2_Saturation`, `Heart_Disease`, `Employment`, `Frequency`, `Disease_Syndrome_Disorder`, `Pregnancy`, `RelativeDate`, `Procedure`, `Overweight`, `Race_Ethnicity`, `Hypertension`, `Imaging_Technique`, `Test_Result`, `Treatment`, `Substance`, `Clinical_Dept`, `LDL`, `Measurements`, `Diet`, `Substance_Quantity`, `Allergen`, `Gender`, `RelativeTime`, `Score`, `Total_Cholesterol`, `Vital_Signs_Header`, `Height`, `Smoking`, `Form`, `Strength`, `Weight`, `Time`, `Dosage`, `HDL` + + {:.btn-box} diff --git a/docs/_posts/murat-gunay/2022-03-21-ner_cellular_biobert_pipeline_en_3_0.md b/docs/_posts/murat-gunay/2022-03-21-ner_cellular_biobert_pipeline_en_3_0.md index 2dbc3148ce..3dbaaa2613 100644 --- a/docs/_posts/murat-gunay/2022-03-21-ner_cellular_biobert_pipeline_en_3_0.md +++ b/docs/_posts/murat-gunay/2022-03-21-ner_cellular_biobert_pipeline_en_3_0.md @@ -21,6 +21,10 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [ner_cellular_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_cellular_biobert_en.html) model. +## Predicted Entities + +`DNA`, `protein`, `cell_type`, `cell_line`, `RNA`. + {:.btn-box} diff --git a/docs/_posts/murat-gunay/2022-03-21-ner_deid_subentity_augmented_i2b2_pipeline_en_3_0.md b/docs/_posts/murat-gunay/2022-03-21-ner_deid_subentity_augmented_i2b2_pipeline_en_3_0.md index 1eed1622a1..c2b0be2cd0 100644 --- a/docs/_posts/murat-gunay/2022-03-21-ner_deid_subentity_augmented_i2b2_pipeline_en_3_0.md +++ b/docs/_posts/murat-gunay/2022-03-21-ner_deid_subentity_augmented_i2b2_pipeline_en_3_0.md @@ -21,6 +21,10 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [ner_deid_subentity_augmented_i2b2](https://nlp.johnsnowlabs.com/2021/11/29/ner_deid_subentity_augmented_i2b2_en.html) model. +## Predicted Entities + +`MEDICALRECORD`, `ORGANIZATION`, `PROFESSION`, `HEALTHPLAN`, `DOCTOR`, `USERNAME`, `URL`, `LOCATION-OTHER`, `DEVICE`, `CITY`, `DATE`, `ZIP`, `STATE`, `PATIENT`, `COUNTRY`, `STREET`, `PHONE`, `HOSPITAL`, `EMAIL`, `IDNUM`, `BIOID`, `FAX`, `AGE` + {:.btn-box} [Live Demo](https://demo.johnsnowlabs.com/healthcare/NER_DEMOGRAPHICS/){:.button.button-orange} [Open in Colab](https://colab.research.google.com/github/JohnSnowLabs/spark-nlp-workshop/blob/master/tutorials/streamlit_notebooks/healthcare/NER_DEMOGRAPHICS.ipynb){:.button.button-orange.button-orange-trans.co.button-icon} diff --git a/docs/_posts/murat-gunay/2022-03-21-ner_human_phenotype_gene_biobert_pipeline_en_3_0.md b/docs/_posts/murat-gunay/2022-03-21-ner_human_phenotype_gene_biobert_pipeline_en_3_0.md index edf12b4f2b..3fc92a6c65 100644 --- a/docs/_posts/murat-gunay/2022-03-21-ner_human_phenotype_gene_biobert_pipeline_en_3_0.md +++ b/docs/_posts/murat-gunay/2022-03-21-ner_human_phenotype_gene_biobert_pipeline_en_3_0.md @@ -21,6 +21,10 @@ use_language_switcher: "Python-Scala-Java" This pretrained pipeline is built on the top of [ner_human_phenotype_gene_biobert](https://nlp.johnsnowlabs.com/2021/04/01/ner_human_phenotype_gene_biobert_en.html) model. +## Predicted Entities + +`GENE`, `HP`. + {:.btn-box}