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| 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.
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| == Data Involved ==
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| * Databases
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| ** Assembly Database (e.g. hg18) -- usually about 60 tables (more details on this [[#Tables_in_the_Assembly_Database | below]])
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| ** UniProt Database (e.g. sp080707)
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| ** Proteome Database (e.g. proteins080707)
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| * Files
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| ** Index files to speed searching (e.g. /gbdb/hg18/knownGene.ix and /gbdb/hg18/knownGene.ixx)
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| ** Known Gene list for Google to index (e.g. /usr/local/apache/htdocs/knownGeneList/hg18/*)
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| ** hgdownload files (e.g. /goldenPath/proteinDB/proteins080707/database/README.txt)
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| == Tables in the Assembly Database ==
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| 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.
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| == Details About UniProt and Proteome Databases ==
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| == Staging on hgwbeta ==
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| As usual, the new databases and tables will be built on hgwdev. After QAing on hgwdev, the whole set should be staged on hgwbeta.
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| [[Category:Browser_QA]]
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Latest revision as of 19:26, 10 March 2011
This page is no longer maintained.