Post-Release-Checklist: Difference between revisions
m (→Update the metadata in hgcentral: clarified what hgNearOk does) |
(→Add the link to the protein database /goldenPath/proteinDB/proteinsYYMMDD/database/: clarified downloads.html link, changed title of section) |
||
| Line 7: | Line 7: | ||
== Check to see if otherOrgs.ra file is updated for this assembly == | == Check to see if otherOrgs.ra file is updated for this assembly == | ||
* this is in kent/src/hg/hgGene/hgGeneData/$org/$db/otherOrgs.ra | * 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 06:00, 23 February 2012
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
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.
Exoniphy
Exoniphy is a companion track (in the Genes group). It is created by Adam Siepel'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.
