Post-Release-Checklist: Difference between revisions
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=== UniProtKB === | === UniProtKB === | ||
Create a speical file for the folks at UniProt. See this file for a sample of what they are looking for: | Create a speical file for the folks at UniProt. See this file for a sample of what they are looking for: | ||
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/UCSCGenes/uniProtToUcscGenes.txt | |||
Run makeUniProtFile.csh in the appropriate htdocs-hgdownload directory on hgwdev, e.g.: | |||
hgwdev:/usr/local/apache/htdocs-hgdownload/goldenPath/hg19/UCSCGenes/ | |||
and then ask for a push of the file to hgdownload. | |||
Send an email to Elisabeth Gasteiger (Elisabeth -dot- Gasteiger -at- isb -dash- sib -dot- ch) letting her know we are releasing a new UCSC Gene set. She will download the file and change their links to our web site. | |||
=== Exoniphy === | === Exoniphy === | ||
Revision as of 00:19, 9 February 2012
This page capture the things to remember after the release of UCSC Genes for the new assembly.
Update the metadata in hgcentral
- set hgNearOk and hgPbOk = 1 in the dbDb table.
- change defaultDb to the new assembly.
- add a record in the gdbPdb table that points the assembly to the recent protein database.
Check to see if otherOrgs.ra file is updated for this assembly
- this is in kent/src/hg/hgGene/hgGeneData/$org/$db/otherOrgs.ra
Add the link to the protein database /goldenPath/proteinDB/proteinsYYMMDD/database/
- in the downloads.html file
- Also, include the new assembly in this file: /goldenPath/proteinDB/proteinsYYMMDD/database/README.txt (and edit it out of the previous file).
Contact various collaborators
Exon Primer Links
Send an email to Tim Strom (http://ihg2.helmholtz-muenchen.de/) so that he knows we are releasing a new UCSC Gene set. He will need to prepare his website for the new UCSC IDs.
HGNC Links to us
Contact Michael Lush: hgnc at genenames dot org to let him know about the update. He will need to rebuild his ucsc2hgnc mappings table.
Galaxy
Galaxy may want to update and/or pre-load these data. Contact Anton at Galaxy to let him know about the update.
UniProtKB
Create a speical file for the folks at UniProt. See this file for a sample of what they are looking for: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/UCSCGenes/uniProtToUcscGenes.txt
Run makeUniProtFile.csh in the appropriate htdocs-hgdownload directory on hgwdev, e.g.: hgwdev:/usr/local/apache/htdocs-hgdownload/goldenPath/hg19/UCSCGenes/ and then ask for a push of the file to hgdownload.
Send an email to Elisabeth Gasteiger (Elisabeth -dot- Gasteiger -at- isb -dash- sib -dot- ch) letting her know we are releasing a new UCSC Gene set. She will download the file and change their links to our web site.
Exoniphy
Exoniphy is a companion track (in the Genes group). It is created by Adam Seipel's group at Cornell. Contact Adam (acs4 at cornell dot edu) to ask him to create this track for this UCSC Genes release.
Alert Ensembl
Notify Ensembl that there is a new UCSC Genes set: e-mail to Andy Yates <ayates@ebi.ac.uk> and cc Paul Flicek <flicek@ebi.ac.uk>, Fiona Cunningham <fiona@ebi.ac.uk>, and Javier Herrero <jherrero@ebi.ac.uk>. They use the UCSC Gene IDs in their external reference (xref) tables.
