src/hg/hgGene/hgGeneData/links.ra 1.38

Index: src/hg/hgGene/hgGeneData/links.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgGene/hgGeneData/links.ra,v
retrieving revision 1.37
retrieving revision 1.38
diff -b -B -U 1000000 -r1.37 -r1.38
--- src/hg/hgGene/hgGeneData/links.ra	30 Jan 2009 23:32:28 -0000	1.37
+++ src/hg/hgGene/hgGeneData/links.ra	28 Apr 2009 16:29:12 -0000	1.38
@@ -1,156 +1,156 @@
 # This contains info to construct the quick links. 
 
 name genome
 shortLabel Genome Browser
 tables knownGene 
 idSql select chrom,txStart+1,txEnd from knownGene where name = '%s'
 url ../cgi-bin/hgTracks?position=%s:%s-%s
 nameFormat %s:%s-%s
 hgsid on
 dbInUrl on
 priority 1
 
 name family
 shortLabel Gene Sorter
 tables kgXref
 idSql select kgID from kgXref where kgID = '%s'
 url ../cgi-bin/hgNear?near_search=%s
 hgsid on
 dbInUrl on
 priority 1
 
 name visiGene
 shortLabel VisiGene
 tables knownToVisiGene
 idSql select value from knownToVisiGene where name = '%s'
 url ../cgi-bin/hgVisiGene?hgp_doId=%s
 hgsid on
 dbInUrl on
 priority 1
 
 name palTrack
 shortLabel Protein FASTA
 tables knownGene
 idSql select chrom,txStart+1,txEnd,name from knownGene where name = '%s'
 url ../cgi-bin/hgPal?g=knownGene&c=%s&l=%s&r=%s&i=%s
 hgsid on
 dbInUrl on
 priority 1
 
 name tbSchema
 shortLabel Table Schema
 tables knownGene
 idSql select 'this is a necessary placeholder %s'
 url ../cgi-bin/hgTables?hgta_group=%s&hgta_track=%s&hgta_table=%s&hgta_doSchema=describe+table+schema
 hgsid on
 dbInUrl on
 priority 5
 
 name uniProt
 shortLabel UniProtKB
 tables kgXref
 idSql select spId from kgXref where kgID = '%s'
 nameSql select spDisplayId from kgXref where kgID = '%s'
 url http://www.uniprot.org/uniprot/%s 
 priority 10
 
 #name refSeq
 #shortLabel RefSeq
 #tables kgXref
 #idSql select refseq from kgXref where kgID = '%s'
 #url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=%s&doptcmdl=GenBank&tool=genome.ucsc.edu
 #priority 10
 
 name entrezGene
 shortLabel Entrez Gene
 tables kgXref refLink
 idSql select refLink.locusLinkId from kgXref,refLink where kgID = '%s' and kgXref.refseq = refLink.mrnaAcc
 url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s
 priority 10
 
 #name genBank
 #shortLabel GenBank
 #tables kgXref
 #idSql select kgID from kgXref where kgID = '%s'
 #url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=%s&doptcmdl=GenBank&tool=genome.ucsc.edu
 #priority 10
 
 name pubMed
 shortLabel PubMed
 tables kgXref
 idSql select geneSymbol from kgXref where kgID = '%s'
 url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=PubMed&term=%s&doptcmdl=DocSum&tool=genome.ucsc.edu
 priority 10
 
 name gepis
 shortLabel Gepis Tissue
 tables kgXref
 idSql select geneSymbol from kgXref where kgID = '%s'
 url http://www.cgl.ucsf.edu/cgi-bin/genentech/genehub-gepis/web_search.pl?intype=1&xrefid=%s&species=human
 priority 10
 
 name treeFam
 shortLabel Treefam
 tables knownToTreefam
 idSql select value from knownToTreefam where name = '%s';
 url http://www.treefam.org/cgi-bin/TFinfo.pl?ac=%s
 priority 10
 
 name cgap
 shortLabel CGAP
 tables cgapAlias kgXref
 idSql select cgapID from cgapAlias,kgXref where kgID = '%s' and geneSymbol = alias;
 priority 10
 
 name stanfordSource
 shortLabel Stanford SOURCE
 tables kgXref
-idSql select mRNA from kgXref where kgID = '%s'
+idSql select geneSymbol from kgXref x, knownGene k where kgID = '%s' and name= kgID and cdsStart <> cdsEnd
 url http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceResult?option=Number&criteria=%s&choice=Gene
 priority 10
 
 name ensembl
 shortLabel Ensembl
 tables knownToEnsembl
 idSql select value from knownToEnsembl where name = '%s'
 priority 10
 
 #name modBase
 #shortLabel ModBase
 #tables hgFixed.modBaseLsSnp, kgXref
 #idSql select uniProtId from hgFixed.modBaseLsSnp where uniProtId = '%s'
 #nameSql select spDisplayId from kgXref where kgID = '%s'
 #url http://
 #priority 10
 
 #name lsSnpFunc
 #shortLabel LS-SNP Function
 #tables hgFixed.modBaseLsSnp, kgXref
 #idSql select uniProtId from hgFixed.modBaseLsSnp where uniProtId = '%s'
 #nameSql select spDisplayId from kgXref where kgID = '%s'
 #url http://alto.compbio.ucsf.edu/LS-SNP-cgi/SNP_query.pl?idvalue=%s&RequestType=QueryById&idtype=sprotID&PropertySelect=Functional
 #priority 10
 #
 #name lsSnpStruct
 #shortLabel LS-SNP Structure
 #tables hgFixed.modBaseLsSnp, kgXref
 #idSql select uniProtId from hgFixed.modBaseLsSnp where uniProtId = '%s'
 #nameSql select spDisplayId from kgXref where kgID = '%s'
 #url http://alto.compbio.ucsf.edu/LS-SNP-cgi/SNP_query.pl?idvalue=%s&RequestType=QueryById&idtype=sprotID&PropertySelect=Protein_structure
 #priority 10
 
 name allenBrain
 shortLabel Allen Brain Atlas
 tables knownToAllenBrain allenBrainUrl
 idSql select allenBrainUrl.url from knownToAllenBrain,allenBrainUrl where knownToAllenBrain.name = '%s' and knownToAllenBrain.value = allenBrainUrl.name
 url %s
 priority 10
 
 name wikiTrack
 shortLabel User annotations
 tables kgXref
 idSql select kgID from kgXref where kgID = '%s'
 url ../cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=none&hgg_do_wikiTrack=1
 dbInUrl on
 priority 10