UCSC Genes Staging Process

The UCSC Gene set is created at UCSC for three vertebrate organisms: human, mouse, and rat. It is built once during the initial release of a new assembly, then updated sporadically after that. The process for QAing, staging, and releasing an update to the UCSC Gene track is complicated enough that it deserves to be documented.

Data Involved

• Databases
  • Assembly Database (e.g. hg18) -- usually about 60 tables (more details on this below)
  • UniProt Database (e.g. sp080707)
  • Proteome Database (e.g. proteins080707)

• Files
  • Index files to speed searching (e.g. /gbdb/hg18/knownGene.ix and /gbdb/hg18/knownGene.ixx)
  • Known Gene list for Google to index (e.g. /usr/local/apache/htdocs/knownGeneList/hg18/*)
  • hgdownload files (e.g. /goldenPath/proteinDB/proteins080707/database/README.txt)

Tables in the Assembly Database

There are many tables involved in the UCSC Gene set. For a complete list of all possible tables ever used to support any UCSC Genes set in any of the three organisms, see: /cluster/bin/scripts/kgTables. If there are tables supporting the UCSC Gene set in the assembly you are working with that are not on this list, please add them to the list. You might also consider checking the list of tables in the pushQ entry against the list of tables for the previous UCSC Gene set (sometimes developers forget to build all of the necessary tables).

For the Summer 2008 update to the UCSC Gene set on hg18, the tables are:

affyHumanExonGs, affyHumanExonGsMedian, affyHumanExonGsRatio, affyHumanExonGsRatioMedian, bioCycMapDesc, bioCycPathway, ccdsKgMap, ceBlastTab, cgapAlias, cgapBiocDesc, cgapBiocPathway, chromInfo, dmBlastTab, drBlastTab, foldUtr3, foldUtr5, gnfAtlas2Distance, gnfU95Distance, humanHprdP2P, humanVidalP2P, humanWankerP2P, keggMapDesc, keggPathway, kg3ToKg4, kgAlias, kgColor, kgProtAlias, kgProtMap2, kgSpAlias, kgTxInfo, kgXref, knownAlt, knownBlastTab, knownCanonical, knownGene, knownGeneMrna, knownGenePep, knownIsoforms, knownToAllenBrain, knownToCdsSnp, knownToEnsembl, knownToGnf1h, knownToGnfAtlas2, knownToHInv, knownToHprd, knownToLocusLink, knownToPfam, knownToRefSeq, knownToSuper, knownToU133, knownToU133Plus2, knownToU95, knownToVisiGene, mmBlastTab, pbAnomLimit, pbResAvgStd, pbStamp, pepCCntDist, pepExonCntDist, pepHydroDist, pepIPCntDist, pepMolWtDist, pepMwAa, pepPi, pepPiDist, pepResDist, pfamDesc, rnBlastTab, scBlastTab, scopDesc, spMrna.

Staging on hgwbeta

As usual, the new databases and tables will be built on hgwdev. After QAing on hgwdev, the whole set should be staged on hgwbeta.

Post-Release

We typically like to announce the release of a new UCSC Gene set. Ask Donna to prepare an announcement for the website and genome-announce. Also see this page: Post-Release-Checklist.