Merge pull request #983 from biolink/982

adding target for fixes #982

.github/workflows/verify_pull_request.yml

@@ -0,0 +1,33 @@
+name: Verify Pull Request
+
+on:
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build-pipenv:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install pipenv
+      uses: dschep/install-pipenv-action@v1
+
+    - name: Install dependencies
+      run: |
+       pipenv install --dev
+
+    - name: Test with unittest
+      run: |
+        pipenv run python -m unittest discover -p 'test_*.py'

biolink-model.yaml

@@ -233,6 +233,30 @@ enums:
       "supported by real-world evidence":
       "supported by clinical evidence":
 
+  druggable_gene_category_enum:
+    permissible_values:
+      "Tclin":
+        description: >-
+          These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.
+      "Tbio":
+        description: >-
+          These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy
+          the activity thresholds detailed below.
+      "Tchem":
+        description: >-
+          These targets do not have known drug or small molecule activities that satisfy the activity
+          thresholds detailed below AND satisfy one or more of the following criteria:
+          target is above the cutoff criteria for Tdark
+          target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s)
+          with an Experimental Evidence code
+      "Tdark":
+        description: >-
+          These are targets about which virtually nothing is known. They do not have known drug or small
+          molecule activities that satisfy the activity thresholds detailed below AND satisfy two or
+          more of the following criteria:
+          A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or
+          less than or equal to 50 Antibodies available according to http://antibodypedia.com.
+
   drug_availability_enum:
     description: >-
     permissible_values:
@@ -1676,6 +1700,24 @@ slots:
       tag: biolink:canonical_predicate
       value: true
 
+  target for:
+    is_a: related to at instance level
+    description: >-
+      A gene is a target of a disease when its products are druggable and when a drug interaction with the gene
+      product could have a therapeutic effect
+    annotations:
+      biolink:canonical_predicate:
+        tag: biolink:canonical_predicate
+        value: true
+    domain: gene
+    range: disease
+
+  has target:
+    is_a: related to at instance level
+    inverse: target for
+    domain: disease
+    range: gene
+
   active in:
     is_a: related to at instance level
     domain: gene or gene product
@@ -10323,6 +10365,27 @@ classes:
           gene in which variation is correlated with the disease,
           may be protective or causative or associative, or as a model
 
+  druggable gene to disease association:
+    is_a: gene to disease association
+    slot_usage:
+      subject:
+        range: gene or gene product
+        description: >-
+          gene in which variation is correlated with the disease
+          in a protective manner, or if the product produced by the gene can be targeted by a small molecule and
+          this leads to a protective or improving disease state.
+      predicate:
+        subproperty_of: target for
+      has evidence:
+        range: druggable_gene_category_enum
+    defining_slots:
+      - subject
+      - object
+      - predicate
+    mixins:
+      - entity to disease association mixin
+      - gene to entity association mixin
+
   variant to gene association:
     description: >-
       An association between a variant and a gene, where the variant has