fix: use create-pull-request action for JSON-LD updates in non-PR context

.github/workflows/ci-lint-validate-convert.yml

@@ -3,7 +3,9 @@ name: Make JSON-LD and Build Dependencies Table
 on:
   pull_request:
     branches: 'main'
-    paths: 'HTAN.model.csv'
+    paths: 
+      - 'HTAN.model.csv'
+      - '.github/workflows/ci-lint-validate-convert.yml'
   release:
     types: [published]
   workflow_dispatch:
@@ -117,10 +119,20 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Push changes in non-PR context
+      - name: Create PR for JSON-LD updates
         if: steps.check_pr.outputs.is_pr == 'false'
-        run: |
-          git push origin HEAD:${{ github.ref_name }}
+        uses: peter-evans/create-pull-request@v5
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Update HTAN.model.jsonld"
+          branch: update-jsonld
+          title: "Update HTAN.model.jsonld"
+          body: "This PR updates HTAN.model.jsonld with the latest changes."
+          base: main
+          committer: GitHub <noreply@github.com>
+          author: aditigopalan <aditigopalan@users.noreply.github.com>
+          signoff: false
+          delete-branch: true
 
   build-dependencies:
     name: Build Dependencies Table

HTAN.model.jsonld

@@ -4910,9 +4910,6 @@
                 {
                     "@id": "bts:OvarianCancerSurgicalOutcome"
                 },
-                {
-                    "@id": "bts:ReadIndicator"
-                },
                 {
                     "@id": "bts:ExpressionUnits"
                 },
@@ -4940,6 +4937,9 @@
                 {
                     "@id": "bts:Race"
                 },
+                {
+                    "@id": "bts:ReadIndicator"
+                },
                 {
                     "@id": "bts:SlicingMethod"
                 },
@@ -33919,7 +33919,7 @@
         {
             "@id": "bts:ReadIndicator",
             "@type": "rdfs:Class",
-            "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",
+            "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads 1 (I1), Index Reads 2 (I2),  or Other",
             "rdfs:label": "ReadIndicator",
             "rdfs:subClassOf": [
                 {
@@ -33942,6 +33942,9 @@
                 {
                     "@id": "bts:I1"
                 },
+                {
+                    "@id": "bts:I2"
+                },
                 {
                     "@id": "bts:Other"
                 }
@@ -53883,6 +53886,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:I2",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "I2",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:ReadIndicator"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "I2",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:CDNAOffset",
             "@type": "rdfs:Class",