Contacting the Community
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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> Please help WormBase's effort to encourage community curation by writing or updating gene descriptions that appear in the 'Overview' widget on WormBase webpages. We have identified the following genes from publications, that have been linked to you or members of your lab: <gene list>. Proper attribution will be given to all submissions and displayed on the WormBase website. Please use the link below to access the gene description submission form, guidelines on how to use the form, and related information can be found in the form. http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/community_gene_description.cgi Thank-you and Regards WormBase Consortium
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