d3e77d28330c5c21d88a9deaef31d80dadd966ea
lrnassar
Mon Jan 5 11:09:33 2026 -0800
Squashing stale pennantIcons, no RM.
diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 8fa57a3a02d..5bb72086f6d 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -215,31 +215,30 @@
dataVersion /gbdb/$D/bbi/varChatVersion.txt
html varChat.html
track pubtator
shortLabel PubTator Variants
longLabel dbSNP variants and other genetic variants grounded to dbSNP by tmVar; collected by PubTator3
visibility dense
type bigBed 9 +
bigDataUrl /gbdb/$D/pubs2/pubtatorDbSnp.bb
noScoreFilter on
exonNumbers off
itemRgb on
parent varsInPubs pack
urls pubmedIds="https://www.ncbi.nlm.nih.gov/pubmed/$$"
mouseOver $name found in ${numPubmedIds} PubMed articles
- pennantIcon New red ../goldenPath/newsarch.html#080125 "Released Aug. 01, 2025"
html varsInPubs
track varaico
shortLabel Varaico Variants
longLabel Varaico Variants extracted from full text publications, titles, and abstracts
visibility dense
type bigBed 9 +
bigDataUrl /gbdb/$D/bbi/varaico.bb
noScoreFilter on
exonNumbers off
# itemRgb on
dataVersion release 2 (20251110)
parent varsInPubs pack
urls outlink="$$" selectedPmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" rgene="https://www.ncbi.nlm.nih.gov/nuccore/$$"
mouseOver $hgncSymbol $variantOrigStrs in: $author ($journal, $year) - $title
Number of publications: $articlesCount
Variant Effect: $variantEffect
@@ -5566,31 +5565,30 @@
longLabel HUGO Gene Nomenclature
bigDataUrl /gbdb/$D/hgnc/hgnc.bb
type bigBed 9 +
labelFields symbol, geneName, name, uniprot_ids, ensembl_gene_id, ucsc_id, refseq_accession
defaultLabelFields symbol
mouseOver Symbol: $symbol
ID: $name
Alias symbol: $alias_symbol
Previous symbols: $prev_symbol
filterValues.locus_type Y RNA,long non-coding RNA,micro RNA,misc RNA,ribosomal RNA,small nuclear RNA,small nucleolar RNA,transfer RNA,vault RNA,T cell receptor gene,T cell receptor pseudogene,complex locus constituent,endogenous retrovirus,gene with protein product,immunoglobulin gene,immunoglobulin pseudogene,pseudogene,readthrough,unknown
group genes
url https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$$
urlLabel HGNC Details:
searchIndex name
searchTrix /gbdb/$D/hgnc/search.ix
skipEmptyFields on
itemRgb on
noScoreFilter on
-pennantIcon Updated red ../goldenPath/newsarch.html "Updated July 31, 2025"
searchTable hgnc
searchMethod exact
searchType bigBed
searchPriority 1.02
shortCircuit 1
track ncbiRefSeqSelect
parent refSeqComposite off
priority 8
type genePred
shortLabel RefSeq Select and MANE
longLabel NCBI RefSeq Select and MANE subset: A single representative transcript
trackHandler ncbiRefSeq
idXref ncbiRefSeqLink mrnaAcc name