Post-Release-Checklist: Difference between revisions

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(removed details about hgcentral, otherOrgs.ra and uniProt (they're in the QAing and Staging pages now), and added announcement section)
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This page capture the things to remember after the release of UCSC Genes for the new assembly.
This page capture the things to remember after the release of UCSC Genes for the new assembly.


== Update the metadata in hgcentral ==
= Announce the release =
* If this is a new gene set (not an update), set hgNearOk = 1 in the dbDb table to enable the Gene Sorter for this assembly.
* Make an announcement on the genome-announce mailing list
* add/update gdbPdb table to point the assembly to the protein database the gene set was built with.
* Add a news item to the Genome Browser front page
 
* Tweet the news (Ann usually does this)
== Check to see if otherOrgs.ra file is updated for this assembly ==
* this is in kent/src/hg/hgGene/hgGeneData/$org/$db/otherOrgs.ra
== Protein database README files and links==
* Include the new assembly in this README file: goldenPath/proteinDB/proteinsYYMMDD/database/README.txt (and edit it out of the previous file, if applicable).
* in the downloads.html file, update the "Protein database for <assembly>" link.


= Contact various collaborators =
= Contact various collaborators =

Revision as of 00:11, 24 February 2012

This page capture the things to remember after the release of UCSC Genes for the new assembly.

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.

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