Difference between revisions of "Contacting the Community"

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Thank you so much!
 
Thank you so much!
  
Best Regards,
+
Best Regards,<br/>
 
The WormBase Gene Description Team
 
The WormBase Gene Description Team
  

Revision as of 16:46, 22 October 2015

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 description requests

  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

List of papers generated using the above criteria: http://tazendra.caltech.edu/~acedb/ranjana/concise_list_to_email.html

Criteria for choosing papers for allele-phenotype requests

  1. Should be flagged for "newmutant"
  2. Should NOT be curated in Phenotype OA
  3. Should have paper editor tag-- pubmed_final final
  4. Should have paper editor tag--Status valid
  5. Should have paper editor tag--Type Journal_article
  6. Corresponding author should not have been e-mailed for author first pass, in the last 3 months
  7. Should have at least one gene connected via 'Inferred_automatically' script that connects genes from abstracts to papers or from manual first pass curation
  8. Should have flag "Primary_data' Primary flag.

Script location: Generate with script on tazendra at :

/home/acedb/ranjana/concise_emailing/generate_list_papers_concise_email.pl

See output at :

http://tazendra.caltech.edu/~acedb/ranjana/concise_list_to_email.html

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-mailing the community for gene descriptions

Subject: WormBase request for community curation of gene descriptions

Dear Authors,

In an effort to keep the gene descriptions in WormBase updated, we are requesting your assistance either to update an existing gene description or write a new gene description if none exists, for any genes studied in your publication:

PeerJ. 2015 Sep 1;3:e1213. doi: 10.7717/peerj.1213. eCollection 2015. Perilipin-related protein regulates lipid metabolism in C. elegans.


Gene descriptions appear in the 'Overview' widget on WormBase gene pages. We would greatly appreciate if you, or any of the other authors, could use our simple web-based tool, to either write or update gene descriptions:

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

Dear _____,

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:


<citation>


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


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