0967c36677fccbce9d80eb6e2aa21eed04759ebe
gperez2
  Fri Dec 20 17:42:53 2024 -0800
Announcing the release of the NCBI Gene Orthologs track, refs #30262

diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra
index 2b7e4d2..876a338 100644
--- src/hg/makeDb/trackDb/refSeqComposite.ra
+++ src/hg/makeDb/trackDb/refSeqComposite.ra
@@ -1,214 +1,215 @@
 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/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$"
 dbPrefixLabels hg="HGNC" dm="FlyBase" ce="WormBase" rn="RGD" sacCer="SGD" danRer="ZFIN" mm="MGI" xenTro="XenBase"
+pennantIcon Updated red ../goldenPath/newsarch.html#122024 "December 20, 2024"
 
         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/$$"
 
         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