11594d79515c4bcdec42959a0881d840a26ab908 jnavarr5 Thu Oct 23 14:08:20 2025 -0700 Need 'useast' in the URL, no Redmine diff --git src/hg/utils/otto/orphanet/parseOrphadata.py src/hg/utils/otto/orphanet/parseOrphadata.py index f9d616a7d75..107ccd0cc66 100755 --- src/hg/utils/otto/orphanet/parseOrphadata.py +++ src/hg/utils/otto/orphanet/parseOrphadata.py @@ -209,31 +209,31 @@ # References - Ensembl, OMIM, HGNC refList = gene.find('ExternalReferenceList') geneDict['externalRefList'] = [] for ref in refList.iter("ExternalReference"): # iterate through reference list refName = ref.find("Source").text refID = ref.find("Reference").text # Find Ensembl reference if ref.find("Source").text.lower() == "ensembl": ensemblId = ref.find("Reference").text geneDict['ensembl'] = str(ensemblId) # Grab the Ensembl reference link geneDict[ - 'ensemblLink'] = 'https://ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=' + ensemblId + 'ensemblLink'] = 'https://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=' + ensemblId # Capture ensembl info if ensemblId in ensemblDict.keys(): geneDict['chr'] = ensemblDict[ensemblId].chr geneDict['start'] = ensemblDict[ensemblId].start geneDict['end'] = ensemblDict[ensemblId].end geneDict['strand'] = ensemblDict[ensemblId].strand # Find OMIM reference if refName.lower() == 'omim': geneDict['OMIM'] = str(refID) # Find HGNC reference if refName.lower() == 'hgnc': geneDict['HGNC'] = str(refID)