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 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:

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 Author(s),

In an effort to improve WormBase's coverage of allele-based phenotypes, 
we are requesting your assistance to annotate mutant allele phenotypes 
from your papers. WormBase paper processing tools have predicted that 
the following paper contains allele-phenotype data for nematodes:

<citation>

If this paper does not reference nematode allele phenotypes, we apologize 
for taking your time and ask that you disregard this e-mail. Otherwise, 
WormBase 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

Community Contact & Curation Tracker CGI

Sandbox: http://mangolassi.caltech.edu/~postgres/cgi-bin/community_curation_tracker.cgi

Live: TBA

The Community Contact & Curation Tracker CGI allows curators (1) to get a filtered list of papers that fit the criteria for sending e-mail requests to authors, asking them to fill out the Concise Description Form or the Allele-Phenotype Form and (2) track the papers for which we've sent request e-mails. For each form (concise description & allele-phenotype), there is a "Ready" CGI to provide curators the filtered list of ready papers (#1 above) and a "Tracker" CGI to track progress of requests sent for each paper (#2 above).

New Mutant Ready CGI

For allele-phenotypes ("newmutant" data type), the "New Mutant Ready" CGI generates a filtered list of papers that:

1. have been predicted/indicated to have allele-phenotype data
2. have not been curated in the Phenotype OA (by WB curator or a community curator)
3. the corresponding author(s) has/have not been e-mailed for Author First Pass (AFP), concise descriptions, or allele-phenotypes in the last 3 months
4. the paper has not been e-mailed about for AFP, concise descriptions, or allele-phenotypes in the last 3 months

The CGI limits the number of papers displayed to 100.

The CGI has eleven (11) columns:

• generate
• WBPaper
• pmids
• first author initials
• first author's person name
• first author's person id
• first author's person emails
• corresponding author name
• corresponding person
• corresponding email
• pdfs

Column purposes:

• generate: this column only has a "generate email" button, which, when pressed, loads a new web page displaying an auto-generated e-mail to the corresponding and first authors with the form letter and PubMed citation in the body of the message. The contents of the target e-mail addresses, the subject line, and the body of the e-mail can all be edited at this stage. Once ready, the curator can click "send email" button to send off the e-mail. Recipients will receive the e-mail from outreach@wormbase.org. Any replies to that request e-mail will be automatically sent to the mailing list, curation@wormbase.org.

Back To Concise Descriptions