Post-Release-Checklist

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

Update the metadata in hgcentral

• 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.
• add/update gdbPdb table to point the assembly to the protein database the gene set was built with.

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

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 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.