From 54e1321e9ea4e58d57e11557c7d7833ac3ac68ee Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Wed, 29 Jul 2020 16:02:31 -0700
Subject: [PATCH 1/2] WIP/EXPERIMENTAL: blml specification of GPI

---
 specs/gpi.yaml | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 specs/gpi.yaml

diff --git a/specs/gpi.yaml b/specs/gpi.yaml
new file mode 100644
index 0000000..d23e13c
--- /dev/null
+++ b/specs/gpi.yaml
@@ -0,0 +1,56 @@
+## IN PROGRESS
+
+prefixes:
+  biolink: 'https://w3id.org/biolink/vocab/'
+  biolinkml: 'https://w3id.org/biolink/biolinkml/'
+  gff3: todo
+
+classes:
+  gene product:
+    slots:
+      - id
+      - symbol
+      - name
+      - synonyms
+      - type
+      - taxon
+      - parent
+      - xrefs
+      - properties
+
+slots:
+  id:
+    identifier: true
+    
+  symbol:
+    type: symbol type
+    multivalued: false
+          
+  name:
+    type: string
+    multivalued: false
+    mappings:
+      - biolink:name
+      - gff3p:name
+
+  synonyms:
+    type: string
+    multivalued: true
+    mappings:
+      - biolink:synonym
+
+  type:
+    type: category type
+    multivalued: false
+      
+types:
+  symbol type:
+    pattern: "^\S+$"
+    base: str
+    uri: xsd:string
+
+  category type:
+    typeof: uriorcurie
+    description: >-
+      A primitive type in which the value denotes a class within the biolink model.
+    

From f29a6f93b4a94b96e69b72e48f73db0c9b91cc5a Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Wed, 29 Jul 2020 20:13:17 -0700
Subject: [PATCH 2/2] adding missing fields

---
 specs/gpi.yaml | 66 ++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 58 insertions(+), 8 deletions(-)

diff --git a/specs/gpi.yaml b/specs/gpi.yaml
index d23e13c..4085bbf 100644
--- a/specs/gpi.yaml
+++ b/specs/gpi.yaml
@@ -3,7 +3,7 @@
 prefixes:
   biolink: 'https://w3id.org/biolink/vocab/'
   biolinkml: 'https://w3id.org/biolink/biolinkml/'
-  gff3: todo
+  gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md'
 
 classes:
   gene product:
@@ -18,30 +18,74 @@ classes:
       - xrefs
       - properties
 
+  gene product properties:
+    slots:
+      - todo
+
 slots:
   id:
     identifier: true
+    required: true
+    mappings:
+      - biolink:id
+      - alliancegenome:primaryId
+      - gff3:ID
     
   symbol:
-    type: symbol type
+    range: symbol type
     multivalued: false
+    required: true
+    mappings:
+      - alliancegenome:symbol
+      - rdfs:label
           
   name:
-    type: string
+    range: string
     multivalued: false
+    required: true
     mappings:
       - biolink:name
-      - gff3p:name
+      - gff3:Name
 
   synonyms:
-    type: string
+    range: string
     multivalued: true
     mappings:
       - biolink:synonym
-
+      - alliancegenome:synonyms
+      - gff3:Alias
+      - skos:altLabel
+      
   type:
-    type: category type
+    range: category type
     multivalued: false
+    required: true
+    mappings:
+      - biolink:type
+      - alliancegenome:soTermId
+      - gff3:type
+      - rdfs:type
+
+  taxon:
+    range: taxon type
+    multivalued: false
+    required: true
+    mappings:
+      - alliancegenome:taxonId
+      - RO:0002162
+      
+  parent:
+    range: gene product
+    multivalued: false  ##?
+    mappings:
+      - gff3:Parent
+
+  xrefs:
+    range: string
+    multivalued: true
+    mappings:
+      - alliancegenome:crossReferences  # inlined
+      - gff3:Dbxref
       
 types:
   symbol type:
@@ -53,4 +97,10 @@ types:
     typeof: uriorcurie
     description: >-
       A primitive type in which the value denotes a class within the biolink model.
-    
+
+  taxon type:
+    typeof: uriorcurie
+    pattern: "^NCBITaxon:\d+$"
+    description: >-
+      A primitive type in which the value denotes a class within the biolink model.
+