Post-Release-Checklist: Difference between revisions
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=== Alert Ensembl === | === 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. | 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. Note they also do want to be notified for rn4 even though it is not Known Genes, and they may want to be notified for assemblies with Known-Gene-like gene tracks. | ||
[[Category:Browser_QA]] | [[Category:Browser_QA]] | ||
[[Category:Browser QA UCSC Genes]] | [[Category:Browser QA UCSC Genes]] | ||
Revision as of 18:08, 24 February 2012
This page capture the things to remember after the release of UCSC Genes for the new assembly.
wiki pages about known genes
QAing UCSC Genes
UCSC Genes tables
UCSC Genes Staging Process
Post-Release-Checklist
Announce the release
- Make an announcement on the genome-announce mailing list
- Add a news item to the Genome Browser front page
- Tweet the news (Ann usually does this)
Contact various collaborators
Exon Primer Links
For human and mouse, 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
For human, contact HGNC: hgnc at genenames dot org to let them know about the update. They will need to rebuild their ucsc2hgnc mappings table.
Galaxy
Galaxy may want to update and/or pre-load these data. Contact Anton at Galaxy (anton at bx.psu.edu) 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.
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. Note they also do want to be notified for rn4 even though it is not Known Genes, and they may want to be notified for assemblies with Known-Gene-like gene tracks.
