Merge pull request #39 from Knowledge-Graph-Hub/35-change-folder-name…

…-from-kgmetadata Change main resource dir name from `kgmetadata` to `resource`
Knowledge-Graph-Hub · Jan 28, 2025 · 8549cf9 · 8549cf9
2 parents 7a9742c + a2ff493
commit 8549cf9
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Showing 53 changed files with 378 additions and 402 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -3,12 +3,12 @@ on:
   # Allows for on-demand build
   workflow_dispatch:
   # Automatically rebuilds when somebody edits a markdown file in
-  # the kgmetadata/ directory
+  # the resource/ directory
   push:
     branches:
       - main
     paths:
-      - 'kgmetadata/*.md'
+      - 'resource/*.md'
 
 jobs:
   build:

diff --git a/Makefile b/Makefile
@@ -29,7 +29,7 @@
 ### Configuration
 
 # All KG .md files
-KGS := $(wildcard kgmetadata/*.md)
+KGS := $(wildcard resource/*.md)
 
 # All principles .md files
 PRINCIPLES := $(wildcard principles/*.md)

diff --git a/_config.yml b/_config.yml
@@ -264,8 +264,8 @@ ontologies:
   preferredPrefix: http
   products:
   - description: OWL release of Biolink-Model
-    id: biolink_model.owl.ttl
-    ontology_purl: http://purl.obolibrary.org/obo/biolink_model.owl.ttl
+    id: biolink-model.owl.ttl
+    ontology_purl: http://purl.obolibrary.org/obo/biolink-model.owl.ttl
     title: Biolink-Model OWL release
   repository: https://github.com/biolink/biolink-model/
   restype: data model
@@ -644,6 +644,30 @@ ontologies:
   title: mixs
   tracker: https://w3id.org/mixs
   uri_prefix: https://w3id.org/
+- activity_status: active
+  contact:
+    label: Sandrine Muller
+    orcid: 0000-0001-5998-3003
+  description: A Translator Knowledge Provider for molecular data.
+  domain: health
+  homepage: ''
+  id: molecular-data-kp
+  layout: ontology_detail
+  ontology_purl: http://purl.obolibrary.org/obo/molecular-data-kp.owl
+  preferredPrefix: http
+  products:
+  - description: KGX nodes for Molecular Data KP
+    format: kgx
+    id: nodes.tsv
+    ontology_purl: https://molepro.s3.amazonaws.com/nodes.tsv
+  - description: KGX edges for Molecular Data KP
+    format: kgx
+    id: edges.tsv
+    ontology_purl: https://molepro.s3.amazonaws.com/edges.tsv
+  repository: ''
+  restype: knowledge graph
+  title: Molecular Data KP
+  tracker: ''
 - activity_status: active
   contact:
     label: Gustavo Glusman, Guangrong Qin
@@ -990,6 +1014,25 @@ ontologies:
   title: swisslipid
   tracker: https://github.com/biopragmatics/pyobo/issues
   uri_prefix: http://purl.obolibrary.org/obo/
+- activity_status: active
+  contact:
+    label: Edgar Gatica
+  description: A Translator Knowledge Provider applying text-mined assertions.
+  domain: information
+  homepage: ''
+  id: text-mining-kp
+  layout: ontology_detail
+  ontology_purl: http://purl.obolibrary.org/obo/text-mining-kp.owl
+  preferredPrefix: http
+  products:
+  - description: Text Mining KP KGX distribution
+    format: kgx
+    id: targeted_assertions.tar.gz
+    ontology_purl: https://storage.googleapis.com/translator-text-workflow-dev-public/kgx/UniProt/targeted_assertions.tar.gz
+  repository: ''
+  restype: knowledge graph
+  title: Text Mining KP
+  tracker: ''
 - activity_status: active
   contact:
     email: [email protected]
@@ -1024,54 +1067,6 @@ ontologies:
   title: uniprot
   tracker: https://github.com/biopragmatics/pyobo/issues
   uri_prefix: http://purl.obolibrary.org/obo/
-- activity_status: active
-  contact:
-    email: ''
-    github: ''
-    label: Sandrine Muller
-    orcid: 0000-0001-5998-3003
-  description: A Translator Knowledge Provider for molecular data.
-  domain: health
-  homepage: ''
-  id: molecular-data-kp
-  layout: ontology_detail
-  ontology_purl: http://purl.obolibrary.org/obo/molecular-data-kp.owl
-  preferredPrefix: http
-  products:
-  - description: KGX nodes for Molecular Data KP
-    format: kgx
-    id: nodes.tsv
-    ontology_purl: https://molepro.s3.amazonaws.com/nodes.tsv
-  - description: KGX edges for Molecular Data KP
-    format: kgx
-    id: edges.tsv
-    ontology_purl: https://molepro.s3.amazonaws.com/edges.tsv
-  repository: ''
-  restype: knowledge graph
-  title: Molecular Data KP
-  tracker: ''
-- activity_status: active
-  contact:
-    email: ''
-    github: ''
-    label: Edgar Gatica
-    orcid: ''
-  description: A Translator Knowledge Provider applying text-mined assertions.
-  domain: information
-  homepage: ''
-  id: text-mining-kp
-  layout: ontology_detail
-  ontology_purl: http://purl.obolibrary.org/obo/text-mining-kp.owl
-  preferredPrefix: http
-  products:
-  - description: Text Mining KP KGX distribution
-    format: kgx
-    id: targeted_assertions.tar.gz
-    ontology_purl: https://storage.googleapis.com/translator-text-workflow-dev-public/kgx/UniProt/targeted_assertions.tar.gz
-  repository: ''
-  restype: knowledge graph
-  title: Text Mining KP
-  tracker: ''
 principles:
 - id: fp-000-summary
   layout: principle

diff --git a/_includes/ontology_table.html b/_includes/ontology_table.html
@@ -21,7 +21,7 @@
     <tr class="obsolete">
       {% endif %}
       <td>
-        <a href="kgmetadata/{{ ont.id }}.html">
+        <a href="resource/{{ ont.id }}.html">
           {% if ont.is_obsolete %}
           <s> {{ ont.id }} </s>
           {% else %} {{ ont.id }} {% endif %}
@@ -48,12 +48,12 @@
         <mark>inactive</mark>
         {% else %} {{ ont.description | truncate: 140 }} {% endif %}
         <small>
-          <a href="kgmetadata/{{ ont.id }}.html"> Detail </a>
+          <a href="resource/{{ ont.id }}.html"> Detail </a>
         </small>
       </td>
       <td>
         <a
-          href="kgmetadata/{{ont.id}}.html"
+          href="resource/{{ont.id}}.html"
           class="btn btn-outline-primary"
           aria-label="More details for {{ ont.title }}"
           title="More details"

diff --git a/assets/js/custom.js b/assets/js/custom.js
@@ -309,7 +309,7 @@ jQuery(document).ready(function() {
                     let template = `
                         <tr class="${tr_class}">
                             <th scope="row">
-                                <a href="kgmetadata/${id}.html">
+                                <a href="resource/${id}.html">
                                     ${id}
                                 </a>
                             </td>

diff --git a/kg.Makefile b/kg.Makefile
@@ -2,7 +2,7 @@ DB = ../../semantic-sql/db
 
 DYNAMIC = neo reacto sgd swisslipid uniprot hgnc drugbank ecosim drugcentral
 
-all: $(patsubst %,kgmetadata/%.md,$(DYNAMIC))
+all: $(patsubst %,resource/%.md,$(DYNAMIC))
 
 ontology/%.md:
 	runoak -i $(DB)/$*.db ontology-metadata --all -O md > $@.tmp && mv $@.tmp $@
diff --git a/registry/kgs.jsonld b/registry/kgs.jsonld
@@ -340,8 +340,8 @@
             "products": [
                 {
                     "description": "OWL release of Biolink-Model",
-                    "id": "biolink_model.owl.ttl",
-                    "ontology_purl": "http://purl.obolibrary.org/obo/biolink_model.owl.ttl",
+                    "id": "biolink-model.owl.ttl",
+                    "ontology_purl": "http://purl.obolibrary.org/obo/biolink-model.owl.ttl",
                     "title": "Biolink-Model OWL release"
                 }
             ],
@@ -816,6 +816,38 @@
             "tracker": "https://w3id.org/mixs",
             "uri_prefix": "https://w3id.org/"
         },
+        {
+            "activity_status": "active",
+            "contact": {
+                "label": "Sandrine Muller",
+                "orcid": "0000-0001-5998-3003"
+            },
+            "description": "A Translator Knowledge Provider for molecular data.",
+            "domain": "health",
+            "homepage": "",
+            "id": "molecular-data-kp",
+            "layout": "ontology_detail",
+            "ontology_purl": "http://purl.obolibrary.org/obo/molecular-data-kp.owl",
+            "preferredPrefix": "http",
+            "products": [
+                {
+                    "description": "KGX nodes for Molecular Data KP",
+                    "format": "kgx",
+                    "id": "nodes.tsv",
+                    "ontology_purl": "https://molepro.s3.amazonaws.com/nodes.tsv"
+                },
+                {
+                    "description": "KGX edges for Molecular Data KP",
+                    "format": "kgx",
+                    "id": "edges.tsv",
+                    "ontology_purl": "https://molepro.s3.amazonaws.com/edges.tsv"
+                }
+            ],
+            "repository": "",
+            "restype": "knowledge graph",
+            "title": "Molecular Data KP",
+            "tracker": ""
+        },
         {
             "activity_status": "active",
             "contact": {
@@ -1247,6 +1279,31 @@
             "tracker": "https://github.com/biopragmatics/pyobo/issues",
             "uri_prefix": "http://purl.obolibrary.org/obo/"
         },
+        {
+            "activity_status": "active",
+            "contact": {
+                "label": "Edgar Gatica"
+            },
+            "description": "A Translator Knowledge Provider applying text-mined assertions.",
+            "domain": "information",
+            "homepage": "",
+            "id": "text-mining-kp",
+            "layout": "ontology_detail",
+            "ontology_purl": "http://purl.obolibrary.org/obo/text-mining-kp.owl",
+            "preferredPrefix": "http",
+            "products": [
+                {
+                    "description": "Text Mining KP KGX distribution",
+                    "format": "kgx",
+                    "id": "targeted_assertions.tar.gz",
+                    "ontology_purl": "https://storage.googleapis.com/translator-text-workflow-dev-public/kgx/UniProt/targeted_assertions.tar.gz"
+                }
+            ],
+            "repository": "",
+            "restype": "knowledge graph",
+            "title": "Text Mining KP",
+            "tracker": ""
+        },
         {
             "activity_status": "active",
             "contact": {
@@ -1290,68 +1347,6 @@
             "title": "uniprot",
             "tracker": "https://github.com/biopragmatics/pyobo/issues",
             "uri_prefix": "http://purl.obolibrary.org/obo/"
-        },
-        {
-            "activity_status": "active",
-            "contact": {
-                "email": "",
-                "github": "",
-                "label": "Sandrine Muller",
-                "orcid": "0000-0001-5998-3003"
-            },
-            "description": "A Translator Knowledge Provider for molecular data.",
-            "domain": "health",
-            "homepage": "",
-            "id": "molecular-data-kp",
-            "layout": "ontology_detail",
-            "ontology_purl": "http://purl.obolibrary.org/obo/molecular-data-kp.owl",
-            "preferredPrefix": "http",
-            "products": [
-                {
-                    "description": "KGX nodes for Molecular Data KP",
-                    "format": "kgx",
-                    "id": "nodes.tsv",
-                    "ontology_purl": "https://molepro.s3.amazonaws.com/nodes.tsv"
-                },
-                {
-                    "description": "KGX edges for Molecular Data KP",
-                    "format": "kgx",
-                    "id": "edges.tsv",
-                    "ontology_purl": "https://molepro.s3.amazonaws.com/edges.tsv"
-                }
-            ],
-            "repository": "",
-            "restype": "knowledge graph",
-            "title": "Molecular Data KP",
-            "tracker": ""
-        },
-        {
-            "activity_status": "active",
-            "contact": {
-                "email": "",
-                "github": "",
-                "label": "Edgar Gatica",
-                "orcid": ""
-            },
-            "description": "A Translator Knowledge Provider applying text-mined assertions.",
-            "domain": "information",
-            "homepage": "",
-            "id": "text-mining-kp",
-            "layout": "ontology_detail",
-            "ontology_purl": "http://purl.obolibrary.org/obo/text-mining-kp.owl",
-            "preferredPrefix": "http",
-            "products": [
-                {
-                    "description": "Text Mining KP KGX distribution",
-                    "format": "kgx",
-                    "id": "targeted_assertions.tar.gz",
-                    "ontology_purl": "https://storage.googleapis.com/translator-text-workflow-dev-public/kgx/UniProt/targeted_assertions.tar.gz"
-                }
-            ],
-            "repository": "",
-            "restype": "knowledge graph",
-            "title": "Text Mining KP",
-            "tracker": ""
         }
     ]
 }