make hgnc: seconday identifier and see if omim still works

yeastgenome · Sep 22, 2021 · a03a39c · a03a39c
1 parent de62042
commit a03a39c
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Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/diopt-orthologs/src/main/java/org/intermine/bio/dataconversion/DioptOrthologsConverter.java b/diopt-orthologs/src/main/java/org/intermine/bio/dataconversion/DioptOrthologsConverter.java
@@ -148,7 +148,11 @@ private String getGene(String g, String org) throws ObjectStoreException {
         if(gene == null) {
             System.out.println("creating new gene..." + g);
             gene = createItem("Gene");
-            gene.setAttribute("primaryIdentifier", g);
+            if(g.startsWith("HGNC:")){
+                gene.setAttribute("secondaryIdentifier", g);
+            }else {
+                gene.setAttribute("primaryIdentifier", g);
+            }
             gene.setReference("organism", org);
             genes.put(g, gene);
         }

diff --git a/ncbi-gene/src/main/java/org/intermine/bio/dataconversion/NcbiGeneConverter.java b/ncbi-gene/src/main/java/org/intermine/bio/dataconversion/NcbiGeneConverter.java
@@ -157,12 +157,16 @@ private void createGeneByTaxonId(String taxonId, GeneInfoRecord record,
         // xref
         for (String key : record.xrefs.keySet()) {
             for (String id : record.xrefs.get(key)) {
-                createCrossReference(gene.getIdentifier(), id, key, true);
+                if(key.startsWith("HGNC")){
+                    gene.setAttribute("secondaryIdentifier", id);
+                }else {
+                    createCrossReference(gene.getIdentifier(), id, key, true);
+                }
             }
         }
 
         for (String ensemblId : record.ensemblIds) {
-            gene.setAttribute("secondaryIdentifier", ensemblId);
+            //gene.setAttribute("secondaryIdentifier", ensemblId);
             createCrossReference(gene.getIdentifier(), ensemblId, "Ensembl", true);
         }