a26e6bfa1bc310a809138e7c39bdcf5ea29a79ef lrnassar Tue Jul 16 17:13:07 2024 -0700 Nesting OMIM into a single superTrack, refs #25682 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 825f835..3f15a07 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -3695,66 +3695,30 @@ shortLabel Stan Jurkat NRSF/REST/Upstate longLabel Stanford ChIP-chip (Jurkat cells, NRSF/REST/Upstate ChIP) priority 12 track rgdQtl override shortLabel RGD Human QTL track nibbImageProbes override group expression track allenBrainAli override group expression track eponine override -track omimLocation -shortLabel OMIM Cyto Loci -longLabel OMIM Cytogenetic Loci Phenotypes - Gene Unknown -group phenDis -visibility hide -color 0, 80, 0 -type bed 4 -hgsid on -url http://www.omim.org/entry/ -tableBrowser noGenome -noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org - -track omimGene2 -shortLabel OMIM Genes -longLabel OMIM Gene Phenotypes - Dark Green Can Be Disease-causing -group phenDis -visibility dense -color 0, 80, 0 -type bed 4 -hgsid on -url http://www.omim.org/entry/ -tableBrowser noGenome omimGeneMap omimGeneMap2 omimPhenotype omimGeneSymbol omim2gene -noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org - -track omimAvSnp -shortLabel OMIM Alleles -longLabel OMIM Allelic Variant Phenotypes -group phenDis -visibility hide -color 0, 80, 0 -type bed 4 -hgsid on -url http://www.omim.org/entry/ -tableBrowser noGenome omimAv omimAvRepl -noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org - track cosmic shortLabel COSMIC longLabel COSMIC: Catalogue Of Somatic Mutations In Cancer group phenDis visibility hide color 200, 0, 0 type bed 4 hgsid on url http://cancer.sanger.ac.uk/cosmic/mutation/overview?id= release alpha track cosmicNew shortLabel COSMIC longLabel COSMIC: Catalogue Of Somatic Mutations In Cancer group phenDis @@ -4358,68 +4322,30 @@ searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 searchTable kiddEichlerDiscG248 searchMethod exact query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%" xrefTable kiddEichlerToNcbi xrefQuery select name, cloneAcc from %s where cloneAcc = '%s' termRegex AC[0-9]{6} searchPriority 52 -searchName omimAvSnpAcc -searchTable omimAvSnp -searchMethod exact -searchType bed -shortCircuit 1 -semiShortCircuit 1 -termRegex ([0-9]{6})\.([0-9]{4}) -searchPriority 10 -padding 50 - -searchName omimGene2Acc -searchTable omimGene2 -searchMethod exact -searchType bed -shortCircuit 1 -semiShortCircuit 1 -termRegex ([0-9]{6}) -searchPriority 10 -#release beta,public - -#searchName omimGene2AccBb -#searchTable omimGene2bb -#searchMethod exact -#searchType bigBed -#shortCircuit 1 -#semiShortCircuit 1 -#termRegex ([0-9]{6}) -#searchPriority 10 -#release alpha - -searchName omimGeneLocAcc -searchTable omimLocation -searchMethod exact -searchType bed -semiShortCircuit 1 -termRegex ([0-9]{6}) -searchPriority 10 - track fox2ClipSeqComp compositeTrack on shortLabel FOX2 CLIP-seq longLabel FOX2 Adaptor-trimmed CLIP-seq reads subGroup1 view Tracks reads=Reads density=Density clusters=Clusters group regulation visibility hide type bed 3 . dataVersion January 2009 track fox2ClipSeqCompViewreads shortLabel Reads view reads visibility pack parent fox2ClipSeqComp @@ -4935,30 +4861,33 @@ subGroups view=dose class=path level=cur track clinGenTriploSensitivity parent doseSensitivity shortLabel Triplo Sensitivity longLabel ClinGen Triplo Sensitivity visibility dense priority 2 type bigBed 9 + bigDataUrl /gbdb/$D/doseSensitivity/clinGenTriploSensitivity.bb mouseOverField mouseOver subGroups view=dose class=path level=cur include phastBias.ra +include omim.ra beta,public +include omim.alpha.ra alpha + searchName decipherId searchTable decipher termRegex [0-9]+ searchType bed searchPriority 50 release public searchName decipherSnvsId searchTable decipherSnvs termRegex [0-9]+ searchType bed searchPriority 50 searchTable ensGene searchType genePred