90ab34106679395529b254e024c8b0f350547195
braney
  Wed Nov 27 16:54:26 2019 -0800
add myGene2 link from hgGene on hg38

diff --git src/hg/hgGene/hgGeneData/Human/links.ra src/hg/hgGene/hgGeneData/Human/links.ra
index 1907ef8..d342df8 100644
--- src/hg/hgGene/hgGeneData/Human/links.ra
+++ src/hg/hgGene/hgGeneData/Human/links.ra
@@ -1,141 +1,149 @@
 #Human-specific link info.
 
 #name gepis
 #shortLabel Gepis Tissue
 #tables kgXref
 #idSql select geneSymbol from kgXref x, knownGene k where kgID = '%s' and name= kgID and cdsStart <> cdsEnd
 #url http://research-public.gene.com/cgi-bin/genentech/genehub-gepis/web_search.pl?intype=1&xrefid=%s&species=human
 #priority 10
 
 name omim
 shortLabel OMIM
 tables hgFixed.refLink kgXref
 idSql select hgFixed.refLink.omimId from kgXref,hgFixed.refLink where kgID = '%s' and kgXref.refseq = hgFixed.refLink.mrnaAcc and hgFixed.refLink.omimId != 0
 url http://omim.org/%s
 priority 10
 
 name huge
 shortLabel HuGE
 tables huge
 idSql select huge.geneSymbol, l.value from kgXref, huge, knownToLocusLink l where kgID = '%s' and kgXref.geneSymbol = huge.geneSymbol and kgID=l.name
 url https://phgkb.cdc.gov/HuGENavigator/searchSummary.do?firstQuery=%s&action=search&Mysubmit=Search
 priority 10
 
 name geneTests
 shortLabel GeneTests
 tables geneTests kgXref
 idSql select geneTests.geneSymbol from kgXref, geneTests where kgID = '%s' and kgXref.geneSymbol = geneTests.geneSymbol
 url http://www.genetests.org/query?gene=%s
 priority 10
 
 name pga
 shortLabel SeattleSNPs PGA
 tables pga kgXref
 idSql select pga.geneSymbol from kgXref, pga where kgID = '%s' and kgXref.geneSymbol = pga.geneSymbol
 url http://gvs.gs.washington.edu/GVS/PopStatsServlet?searchBy=Gene+Hugo&target=%s
 priority 10
 
 name geneCards
 shortLabel GeneCards
 tables kgXref
 idSql select geneSymbol from kgXref x, knownGene k where kgID = '%s' and name= kgID and cdsStart <> cdsEnd
 url http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s
 priority 10
 
 name hugo
 shortLabel HGNC
 tables kgXref
 idSql select hgncId from kgXref,proteome.hgncXref where kgID = '%s' and geneSymbol=symbol
 url http://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/%s
 priority 10
 
 name cgap
 url http://cgap.nci.nih.gov/Genes/GeneInfo?ORG=Hs&CID=%s
 
 name hprd
 shortLabel HPRD
 tables knownToHprd 
 idSql select value from knownToHprd where name = '%s';
 url http://www.hprd.org/protein/%s 
 priority 10
 
 name reactome
 shortLabel Reactome
 tables proteome.spReactomeEvent kgXref
 idSql select spReactomeId.spID from proteome.spReactomeId,proteome.spVariant,kgXref where kgXref.kgID = '%s' and kgXref.spID=variant and spReactomeId.spID=parent;
 url http://www.reactome.org/content/query?q=%s
 priority 10
 
 name ensembl
 url http://www.ensembl.org/Homo_sapiens/geneview?transcript=%s
 
 name allenBrain
 shortLabel Human Cortex Gene Expression
 tables allenBrainGene
 idSql select a.geneSymbol from kgXref x, allenBrainGene a where x.geneSymbol=a.geneSymbol and kgId='%s'
 url http://human.brain-map.org/microarray/search/show?exact_match=false&search_term=%s&search_type=gene 
 priority 10
 
 name aceView
 shortLabel AceView
 tables jaxOrtholog
 idSql select geneSymbol from kgXref where kgID = '%s'
 priority 10
 url https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=%s
 
 name jaxOrtholog
 shortLabel MGI
 tables kgXref
 idSql select geneSymbol from kgXref x, knownGene k where kgID = '%s' and name= kgID and cdsStart <> cdsEnd
 url http://www.informatics.jax.org/searchtool/Search.do?query=%s
 priority 10
 
 name HInv
 shortLabel H-INV
 tables knownToHInv
 idSql select HInv.mrnaAcc from HInv, knownToHInv where knownToHInv.name = '%s' and HInv.geneId = knownToHInv.value
 url http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=%s
 priority 10
 
 name geneNetwork
 shortLabel GeneNetwork
 tables geneNetworkId
 idSql select Id from geneNetworkId, knownToRefSeq where Id = value and name='%s'
 url http://www.genenetwork.org/webqtl/WebQTL.py?cmd=sch&refseq=%s&species=human
 priority 10
 
 name stanfordSource
 shortLabel Stanford SOURCE
 tables kgXref
 idSql select mRNA from kgXref where kgID = '%s'
 url http://smd.stanford.edu/cgi-bin/source/sourceResult?organism=Hs&option=Number&criteria=%s&choice=Gene
 priority 10
 
 name nextProt
 shortLabel neXtProt
 tables knownToNextProt
 idSql select value from knownToNextProt where name = '%s';
 url http://www.nextprot.org/db/entry/%s
 priority 10
 
 name lynx
 shortLabel Lynx
 tables knownToLynx
 idSql select value from knownToLynx where name = '%s';
 url http://lynx.cri.uchicago.edu/gene/?geneid=%s
 priority 10
 
 name malacards
 shortLabel Malacards
 tables knownToMalacards
 idSql select knownToMalacards.value from kgXref, knownToMalacards where kgID = '%s' and kgXref.geneSymbol = knownToMalacards.value
 url http://malacards.org/search/results/%s
 priority 10
 
 name hgGeneGraph
 shortLabel Gene interactions
 tables hgFixed.ggSymbol kgXref
 idSql SELECT ggSymbol.geneSymbol FROM hgFixed.ggSymbol, kgXref where (kgXref.geneSymbol = ggSymbol.geneSymbol) and kgId='%s'
 url hgGeneGraph?gene=%s
 hgsid on
 priority 2
+
+name myGene2
+shortLabel myGene2
+tables knownToMyGene2
+idSql select value from knownToMyGene2 where name = '%s'
+url https://mygene2.org/MyGene2/variantsbygene?gene=%s
+priority 10
+