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== Post Release Checklist for UCSC Genes ==
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]]<br>
[[UCSC Genes tables]]<br>
[[UCSC Genes Staging Process]]<br>
[[Post-Release-Checklist]]
 
== Announce the release ==
* Make an announcement on the genome-announce mailing list
**It's a longer format like [https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce this].
* Add a news item to the Genome Browser front page
* Tweet the news (Anyone in QA can do this see [http://genomewiki.ucsc.edu/genecats/index.php/Facebook_update Facebook/Twitter Update ] page).


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


* Update the metadata in hgcentral:
=== Exon Primer Links ===
::set hgNearOk and hgPbOk = 1 in the dbDb table.
For human and mouse, send an email to Tim Strom (TimStrom@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. *Note: without an existing dbSNP track, Tim will not be able to install the ExonPrimer feature.
:: 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 in:
::kent/src/hg/hgGene/hgGeneData/$org/$db/otherOrgs.ra
* Add the link to the protein database /goldenPath/proteinDB/proteinsYYMMDD/database/ in:
:: 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).


* Exon Primer Links
=== HGNC Links to us===
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.
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.


* HGNC Links to us
=== UniProtKB ===
Contact Michael Lush: hgnc at genenames dot org to let him know about the update.  He will need to rebuild his ucsc2hgnc mappings table.
For all but sacCer and danRer, create a special file for the folks at UniProt to create their cross-references to us. Run makeUniProtFile.csh on hgwdev.  This will create a file an the appropriate downloads directory, e.g.:
hgwdev:/usr/local/apache/htdocs-hgdownload/goldenPath/hg19/UCSCGenes/
and then ask for a push of the file to hgdownload.


* Galaxy (may want to update and/or pre-load these data)
Contact Anton at Galaxy to let him know about the update.


* UniProtKB
Send an email to UniProt (uniprot-prod@ebi.ac.uk), notifying them of the new UCSC Genes release.
Create a speical file for the folks at UniProt. See this file for a sample of what they are looking for: hgwdev:/usr/local/apache/htdocs/goldenPath/hg18/UCSCGenes/uniProtToUcscGenes.txt


You can use this script to create the file: makeUniProtFile.csh


After creating this file, push it to the hgdownload machine.  Then 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.
The current download URLs are:


* Exoniphy
ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/UCSCGenes/uniProtToUcscGenes.txt
Exoniphy is a companion track (in the Genes group). It is created by Adam Seipel's group at Cornell. Contact Adam to ask him to create this track for this UCSC Genes release.
ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/UCSCGenes/uniProtToUcscGenes.txt
ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10/UCSCGenes/uniProtToUcscGenes.txt
ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/UCSCGenes/uniProtToUcscGenes.txt
ftp://hgdownload.soe.ucsc.edu/goldenPath/rn4/UCSCGenes/uniProtToUcscGenes.txt
ftp://hgdownload.soe.ucsc.edu/goldenPath/ce6/UCSCGenes/uniProtToUcscGenes.txt
ftp://hgdownload.soe.ucsc.edu/goldenPath/dm3/UCSCGenes/uniProtToUcscGenes.txt


* Alert Ensembl:
=== Alert Ensembl ===
Please e-mail this information to Glenn Proctor <glenn@ebi.ac.uk> and cc Ewan Birney <birney@ebi.ac.uk>. They would like UCSC Gene IDs, and coordinates and/or sequences. One problem is
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>, and Fiona Cunningham <fiona@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.
that they handle randoms differently to us and display individual scaffolds instead of an artificially created random chromosome like we do.  We might also send them the knownToEnsembl table, too.




[[Category:Browser_QA]]
[[Category:Browser_QA]]
[[Category:Browser QA UCSC Genes]]
[[Category:Browser QA UCSC Genes]]

Latest revision as of 19:44, 28 January 2019

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
    • It's a longer format like this.
  • Add a news item to the Genome Browser front page
  • Tweet the news (Anyone in QA can do this see Facebook/Twitter Update page).

Contact various collaborators

Exon Primer Links

For human and mouse, send an email to Tim Strom (TimStrom@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. *Note: without an existing dbSNP track, Tim will not be able to install the ExonPrimer feature.

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.

UniProtKB

For all but sacCer and danRer, create a special file for the folks at UniProt to create their cross-references to us. Run makeUniProtFile.csh on hgwdev. This will create a file an the appropriate downloads directory, 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 UniProt (uniprot-prod@ebi.ac.uk), notifying them of the new UCSC Genes release.


The current download URLs are:

ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.soe.ucsc.edu/goldenPath/rn4/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.soe.ucsc.edu/goldenPath/ce6/UCSCGenes/uniProtToUcscGenes.txt ftp://hgdownload.soe.ucsc.edu/goldenPath/dm3/UCSCGenes/uniProtToUcscGenes.txt

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>, and Fiona Cunningham <fiona@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.

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