Contacting the Community

List of papers in WormBase

• This is the lsit of papers that come into WormBase, in real time, latest are at the bottom:

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=WpaXref

Criteria for choosing papers for community gene descriptions

• 1. Should have paper editor tag-- pubmed_final final
• 2. Should have paper editor tag--Status valid
• 3. Should have paper editor tag--Type Journal_article
• 4. Should not have paper editor tag--Curation flags E-mailed_community_gene_descrip
• 5. Should not have been e-mailed for author first pass, in the last 3 months
• 6. Should have a PDF in WormBase
• 7. Should have: First author has a WBPerson with an e-mail address
• 8. Should not have an entry in the 'Reference' field of the OA, postgres table, con_paper (meaning it should not have been used in a concise description

E-mailing the community

From Juancarlos: On tazendra, in this directory : /home/postgres/work/pgpopulation/concise_description/20150702_papgenes_after_lastupdate

• gene_to_published_after - has a set of WBGenes + locus + count of papers + list of papers with a gene connection after the gene's date last updated (unsorted, but if you copy the file to your machine and put it in excel or something like that, you can sort it)

• pis_to_papers_with_genes_published_after - has PIs sorted in descending order by count of papers that mention a gene that has a gene connection after the gene's date last updated. So, possibly some papers have multiple genes, but are counted just once.

• This script takes some 40 minutes to run, because we're taking the date last updated, then for each of the 138056 doing a separate query to get paper-gene connections with a timestamp after that. So if we keep working on this script, it'd be kind-of-good to work out what we want since it takes so (relatively) long to run.

• Chris has a similar list for newmutant-flagged papers that still need curation, so you can both talk about what you want to do next.

Letter for e-mail for Community Annotation

 
Dear Dr. <name>
In an effort to keep the gene descriptions in WormBase updated, we are requesting your assistance to either update an existing gene description or write a new description when none exists, based on your publication:

Leight ER, Murphy JT, Fantz DA, Pepin D, Schneider DL, Ratliff TM, Mohammad
DH, Herman MA, Kornfeld K. Conversion of the LIN-1 ETS protein of
Caenorhabditis elegans from a SUMOylated transcriptional repressor to a
phosphorylated transcriptional activator. Genetics. 2015
Mar;199(3):761-75. doi: 10.1534/genetics.114.172668. Epub 2015 Jan 7.
PubMed PMID: 25567989


Gene descriptions appear in the 'Overview' widget on WormBase gene pages. We would greatly appreciate if you, or any of the other authors, could take a moment to update the gene description for <gene> using our simple web-based tool:

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/community_gene_description.cgi

If you have any questions, comments or concerns, please let us know.

Thank you so much!

Best Regards,
The WormBase Gene Description Team

Letter for allele-phenotype requests

Subject: Contribute phenotype data to WormBase: Leight et al (2015) Genetics
From:    "Christian A Grove" <cgrove@caltech.edu>
Date:    Mon, October 5, 2015 1:19 pm
To:      kornfeld@wustl.edu
--------------------------------------------------------------------------


Dear Kerry Kornfeld,

In an effort to improve WormBase's coverage of allele-based phenotypes,
WormBase is requesting your assistance to annotate mutant allele
phenotypes from your paper:


Leight ER, Murphy JT, Fantz DA, Pepin D, Schneider DL, Ratliff TM, Mohammad
DH, Herman MA, Kornfeld K. Conversion of the LIN-1 ETS protein of
Caenorhabditis elegans from a SUMOylated transcriptional repressor to a
phosphorylated transcriptional activator. Genetics. 2015
Mar;199(3):761-75. doi: 10.1534/genetics.114.172668. Epub 2015 Jan 7.
PubMed PMID: 25567989


We would greatly appreciate if you, or any of the other authors, could
take a moment to contribute allele-phenotype connections using our simple
web-based tool:


http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/allele_phenotype.cgi


If you have any questions, comments or concerns, please let us know.

Thank you so much!

Best regards,

The WormBase Phenotype Team