WormBase-Caltech Weekly Calls

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October 1, 2015


  • General discussion on DOI handling for micropublications and using the ?Paper model
  • Project started with expression pattern submissions
  • Micropublications were displayed on ?Expr_pattern pages on WormBase/WormBook
  • We do currently assign a DOI to these URLs/pages
  • If we put the micro publications in Wormbook shall we request a different DOI? May be enough to request a DOI for WormBook, with just a link to the respective WormBase page
  • Daniela has requested changes to ?Expr_pattern model to accommodate micropublication
    • So many of the tags were shared (or could be shared) with the ?Paper class
  • If micropublications will be indexed by MEDLINE, we could use our standard paper pipeline to capture paper data
    • Any lag in indexing is likely negligible (~1 day)
  • Daniela & Paul asked NLM to change the title of WormBook from "WormBook: An online review of C. elegans biology" to just "WormBook" to accommodate a broader scope; haven't heard back yet

Community Curation paper

  • Due at end of October
  • Daniela communicating with Mary Ann; should micropublications be mentioned?
  • Database issue that is published concurrently with the BioCurator meeting
  • Hopefully we have some feedback by the time we need to make revisions (end of January)
  • E-mails to authors for concise description and allele-phenotype will go out today/soon

WS251 citace upload tomorrow

Community editing of concise descriptions

  • Would like community to edit manually-written and automated gene descriptions
  • Would be nice to have a link to the concise description form from gene overview/existing description
  • Same for allele-phenotype form

Traveling to labs

  • Soliciting community contributions AND providing user help/guidance
  • Need to emphasize the importance of MODs and why they need support
  • We should cater our discussions to what the labs specifically work on
  • Could start with 2-4 days of trial; half-day at campuses
  • Needs to be short talk/seminar (not an hour, much shorter)
  • Should we go to local/area meetings
  • Will likely be effective to have one-on-one discussions with PIs, lab members

October 8, 2015

Soliciting community curation

  • Juancarlos, Ranjana and Chris working on a pipeline to e-mail authors
  • Will try to automate as much as possible
  • Will avoid e-mailing authors that have already been AFP e-mailed in the last 3 months
  • Juancarlos writing scripts to generate list of valid papers with relevant e-mail information
  • Would be good to parse corresponding author and first author from paper XMLs, but publishers are not uniform in their format

SObA in Cytoscape

  • Juancarlos working on adapting SObA to Cytoscape
  • Would allow zooming in for details, zooming out to hide details

Help Desk query

  • Looking for all mutations in a Million Mutation strain
  • Currently, large queries on website point users to FTP site, but without direction
  • Would be good to provide more clear directions to users (point to specific file)
  • We used to have a mechanism for users to download a flat file for large datasets, but missing now

Community Curation paper

  • Will wait for the right time to write, after feedback, etc.
  • Biocurator meeting is in April, by which time we will hopefully have good results to present (talk/poster/workshop).

Cell Ontology project

  • Didn't get funding on first round application
  • However, may get funded through GO
  • Species agnostic, but tries to draw connections between human and C. elegans cell types
  • Example, human epithelial cells using FGF/Wnt etc. connected to C. elegans epithelial cells using FGF/Wnt etc.


  • WormBook gets indexed by NCBI/PubMed
  • We want micropublications to be indexed
  • Marie-Anne Felix asked about species descriptions
  • We have a micropublication form for expression data; can we build for other data types?
  • Data in form does not, currently, read into Postgres
  • Would be good to automatically generate a PDF