115c6d24a46472bd44400f1fe9b38541364138ad
lrnassar
  Fri Sep 4 17:53:17 2026 -0700
Add a search rule so a deprecated versioned NP_ accession resolves to RefSeq Historical.

A superseded protein accession was answered by hgFixed.refLink, which stores
accessions without versions, so NP_000005.2 and NP_000005.3 returned the same
gene. The new rule looks the accession up in ncbiRefSeqLinkHistorical and jumps
to the deprecated transcript instead. It excludes accessions that are still
current so their searches are untouched, and is semiShortCircuit so it replaces
the version-blind answer rather than adding a second result. refs #38248

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 9e09bdcc5fe..5a885f6b7ff 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -5610,30 +5610,40 @@
 dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqHistoricalVersion.txt
 shortLabel RefSeq Historical
 longLabel NCBI RefSeq Historical Transcript Versions
 color 12,12,120
 idXref ncbiRefSeqLinkHistorical mrnaAcc name
 baseColorUseCds given
 baseColorDefault genomicCodons
 
 searchTable ncbiRefSeqHistorical
 searchMethod exact
 searchType genePred
 semiShortCircuit 1
 termRegex [N][MR]_[0-9]{6}[0-9]*\.[0-9]+
 searchPriority 20
 
+searchName ncbiRefSeqHistoricalProtAcc
+searchTable ncbiRefSeqHistorical
+searchType genePred
+searchMethod exact
+semiShortCircuit 1
+xrefTable ncbiRefSeqLinkHistorical
+xrefQuery select id,protAcc from %s where protAcc = '%s' and protAcc not in (select protAcc from ncbiRefSeqLink)
+termRegex [NY]P_[0-9]{6}[0-9]*\.[0-9]+
+searchPriority 20.1
+
 
 include alphaMissense.ra
 
 include mitoMap.ra
 
 include exonprimers.ra alpha
 include colorsDbLegacy.ra alpha
 
 include g2p.ra
 include varFreqs.ra
 include phasedVars.ra
 
 track dnaMethylation
 superTrack on
 shortLabel DNA Methylation