089c09e98db52e92da694ab1a0c8891c1a7fd3e8 gperez2 Thu Apr 2 15:50:07 2026 -0700 Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM. diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra index 2b7e4d211f3..935d648a5a4 100644 --- src/hg/makeDb/trackDb/refSeqComposite.ra +++ src/hg/makeDb/trackDb/refSeqComposite.ra @@ -1,214 +1,214 @@ track refSeqComposite compositeTrack on shortLabel NCBI RefSeq longLabel RefSeq genes from NCBI group genes visibility dense type genePred dragAndDrop subTracks noInherit on #subGroup1 view Views aNcbiRefSeq=NCBI_RefSeq zUcscRefSeq=UCSC_RefSeq allButtonPair on dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqVersion.txt priority 2 -dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="http://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="https://www.informatics.jax.org//marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$" +dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="https://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="https://www.informatics.jax.org//marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$" dbPrefixLabels hg="HGNC" dm="FlyBase" ce="WormBase" rn="RGD" sacCer="SGD" danRer="ZFIN" mm="MGI" xenTro="XenBase" track ncbiRefSeq parent refSeqComposite on color 12,12,120 shortLabel RefSeq All longLabel NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 1 track ncbiRefSeqCurated color 12,12,120 parent refSeqComposite on shortLabel RefSeq Curated longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 2 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite off shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 3 track ncbiRefSeqOther color 32,32,32 parent refSeqComposite off shortLabel RefSeq Other longLabel NCBI RefSeq Other Annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) priority 4 searchIndex name searchTrix /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.ix bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.bb type bigBed 12 + labelFields gene skipEmptyFields on - urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="https://www.informatics.jax.org//marker/$$" + urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$" FlyBase="https://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="https://www.informatics.jax.org//marker/$$" track ncbiRefSeqPsl priority 5 parent refSeqComposite off shortLabel RefSeq Alignments longLabel RefSeq Alignments of RNAs type psl indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsMaxZoom 10000.0 showCdsAllScales . baseColorDefault diffCodons pslSequence no baseColorUseSequence extFile seqNcbiRefSeq extNcbiRefSeq baseColorUseCds table ncbiRefSeqCds idXref ncbiRefSeqLink mrnaAcc name color 0,0,0 pepTable ncbiRefSeqPepTable track ncbiRefSeqGenomicDiff parent refSeqComposite off priority 6 type bigBed 9 + skipEmptyFields on shortLabel RefSeq Diffs longLabel Differences between NCBI RefSeq Transcripts and the Reference Genome bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb itemRgb on track refGene override parent refSeqComposite off shortLabel UCSC RefSeq longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*) color 12,12,120 type genePred refPep refMrna idXref hgFixed.refLink mrnaAcc name priority 7 baseColorUseCds given baseColorDefault genomicCodons track ncbiRefSeqHgmd parent refSeqComposite off priority 9 type genePred shortLabel RefSeq HGMD longLabel NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons track ncbiOrtho parent refSeqComposite off shortLabel NCBI Orthologs longLabel NCBI Gene Orthologs type bigBed 9 + bigDataUrl /gbdb/$D/ncbiOrtho/ncbiOrtho.bb visibility hide labelFields hugo,name searchIndex hugo,name searchTrix /gbdb/$D/ncbiOrtho/ncbiOrtho.ix defaultLabelFields hugo color 136,0,204 priority 10 mouseOver $url searchName ncbiRefSeqCuratedName2 searchTable ncbiRefSeqCurated searchMethod prefix query select chrom, txStart,txEnd, name from %s where name2 like '%s%%' searchPriority 1.07200 searchName ncbiRefSeqPredictedName2 searchTable ncbiRefSeqPredicted searchMethod prefix query select chrom, txStart,txEnd, name from %s where name2 like '%s%%' searchPriority 1.07201 searchName ncbiRefSeqCuratedProtAcc searchTable ncbiRefSeqCurated searchType genePred searchMethod prefix xrefTable ncbiRefSeqLink xrefQuery select id,protAcc from %s where protAcc like '%s%%' termRegex [NY]P_[0-9]+(\.[0-9]+)? dontCheck XP_[0-9]+(\.[0-9]+)? searchPriority 2.07201 searchName ncbiRefSeqPredictedProtAcc searchTable ncbiRefSeqPredicted searchType genePred searchMethod prefix xrefTable ncbiRefSeqLink xrefQuery select id,protAcc from %s where protAcc like '%s%%' termRegex XP_[0-9]+(\.[0-9]+)? dontCheck [NY]P_[0-9]+(\.[0-9]+)? searchPriority 2.07203 searchName ncbiRefSeqCuratedProduct searchTable ncbiRefSeqCurated searchType genePred searchMethod fuzzy xrefTable ncbiRefSeqLink xrefQuery select id,product from %s where product like '%%%s%%' searchPriority 2.07201 searchName ncbiRefSeqPredictedProduct searchTable ncbiRefSeqPredicted searchType genePred searchMethod fuzzy xrefTable ncbiRefSeqLink xrefQuery select id,product from %s where product like '%%%s%%' searchPriority 2.07203 searchTable ncbiRefSeqCurated searchMethod exact searchType genePred semiShortCircuit 1 termRegex [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07202 searchName ncbiRefSeqCuratedNoVersion searchTable ncbiRefSeqCurated query select chrom,txStart,txEnd,name from %s where name like '%s.%%' semiShortCircuit 1 termRegex [NY][MRP]_[0-9]{6}[0-9]* dontCheck [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07202 searchTable ncbiRefSeqPredicted searchMethod exact searchType genePred semiShortCircuit 1 termRegex X[MR]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07204 searchName ncbiRefSeqPredictedNoVersion searchTable ncbiRefSeqPredicted query select chrom,txStart,txEnd,name from %s where name like '%s.%%' semiShortCircuit 1 termRegex X[MR]_[0-9]{6}[0-9]* dontCheck X[MR]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07204 searchTable ncbiRefSeqOther searchPriority 2.07207 searchType bigBed searchName ncbiOrtho searchTable ncbiOrtho searchType bigBed searchPriority 21