Merge pull request biolink#257 from biolink/datadesc

Representing dataset metadata in BioLink Model. I'll back the __init__.py changes out in the next pull request.
cbizon · Aug 20, 2019 · a23f344 · a23f344
2 parents 9d08f79 + aaa6618
commit a23f344
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Showing 6 changed files with 13,710 additions and 2 deletions.
diff --git a/biolink-model.yaml b/biolink-model.yaml
@@ -1137,6 +1137,54 @@ slots:
       A grouping for any property that holds between a node and a value
     domain: named thing
 
+  title:
+    is_a: node property
+    domain: data set version
+    slot_uri: dct:title
+
+  source data file:
+    is_a: node property
+    domain: data set version
+    range: data file
+    slot_uri: dcterms:source
+
+  source web page:
+    is_a: node property
+    domain: data set summary
+    slot_uri: dcterms:source
+
+  retrievedOn:
+    is_a: node property
+    domain: source file
+    range: date
+    slot_uri: pav:retrievedOn
+
+  versionOf:
+    is_a: node property
+    domain: data set version
+    range: data set
+    slot_uri: dct:isVersionOf
+
+  source version:
+    is_a: node property
+    domain: source file
+    slot_uri: pav:version
+
+  downloadURL:
+    is_a: node property
+    domain: distribution level
+    slot_uri: dct:downloadURL
+
+  distribution:
+    is_a: node property
+    domain: data set version
+    range: distribution level
+    slot_uri: void:Dataset
+
+  type:
+    is_a: node property
+    slot_uri: rdf:type
+
   id:
     is_a: node property
     identifier: true
@@ -1632,6 +1680,46 @@ classes:
       - UMLSSC:T168
       - UMLSST:food
 
+  data file:
+    is_a: named thing
+    class_uri: EFO:0004095
+
+  source file:
+    is_a: data file
+    slots:
+      - source version
+      - retrievedOn
+
+#  data set descriptor:
+#    abstract: true
+#    mixin: true
+
+  data set:
+    is_a: named thing
+    class_uri: IAO:0000100
+
+  data set version:
+    is_a: data set
+    slots:
+      - title
+#      - description
+      - source data file
+      - versionOf
+      - type
+      - distribution
+
+  distribution level:
+    is_a: data set version
+    mixin: true
+    slots:
+      - downloadURL
+
+  data set summary:
+    is_a: data set version
+    mixin: true
+    slots:
+      - source web page
+
   biological entity:
     is_a: named thing
     abstract: true

diff --git a/biolink/__init__.py b/biolink/__init__.py
@@ -1,8 +1,9 @@
 # Biolink model file locations
 import os
+from typing import Union
 
 basedir = os.path.abspath(os.path.join(__file__, '..', '..'))
-BIOLINK_MODEL_YAML = os.path.join(basedir, 'biolink-model.yaml')
+BIOLINK_MODEL_YAML = os.path.join(basedir, 'biolink-model.yaml')  # type: Union[bytes, str]
 BIOLINK_MODEL_JSONLD = os.path.join(basedir, 'context.jsonld')
 BIOLINK_MODEL_SHEX = os.path.join(basedir, 'shex', 'biolink-model.shex')
 BIOLINK_MODEL_RDF = os.path.join(basedir, 'rdf', 'biolink-model.ttl')