WormBase-Caltech Weekly Calls March 2013

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March 7, 2013


  • Grant gets reviewed next week
  • Should hear results in ~two weeks

Gene Concise Description form

  • Ranjana, Kimberly working on form layout
  • Easy to use form, simple drop down menus to select, e.g., Species
  • Can users follow references for info?
  • Citing references in concise descriptions has, in the past, greatly increased workload/time to write
  • Prepopulated, precanned Textpresso info?
  • Send out to targeted members of the community, get feedback; Who should we ask for other species?
  • Curators could each try using form to make at least one concise descriptions, give feedback
  • Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..."
  • Can promote form at the International meeting

Galaxy Workshop

  • Screencast videos capturing use of Galaxy available
  • Chris will send around

Genetic Interaction Ontology

  • Perhaps add "what is expected" info during curation?
  • Good to have a comparison of curation with core set of common papers
    • Cross check for consistency of curation (at least terms should lay in same lineage, if not at same depth)

March 14, 2013

Cleaning up Citace Minus

  • Stemming from Paul Davis' GitHub ticket pointing out small-scale data problems
  • Bogus molecule objects (Chris will take care of)
  • Homol_data from RNAi (and the housing RNAi objects) can be removed
  • Ghost Expr_pattern objects, Wen taking care of (Xiaodong will remove from the Gene_regulation OA)
  • Will need to create a better (more robust) pipeline (with SOPs) for converting, for example, object names to WBID#'s
    • Once a conversion has been made, we need to check Postgres and Citace (& Citace Minus) for consistency
    • Need to minimize the burden on Wen to perform quality and consistency checks
    • Curators need to clean up/fix their data before a big change
    • Scenarios to foramlize:
      • Whole-class name changing
      • Model changes
  • Is there a list of classes (and objects?) that are held in Citace Minus?
    • Cross-references create complexity
  • We will suggest shifting the phase of the model proposal cycle: Propose to freeze all models one month before upload


  • AQL vs WQL vs AcePerl
  • We may consider working out more formal pipelines for submitting queries (maybe to Wen?)
  • AQL and WQL convenient but not necessarily efficient
  • AcePerl efficient, but has a learning curve
  • Todd highly recommends learning AcePerl as it has many advantages:
    • Learning AcePerl will provide skills to handle other generic queries
    • Whereas AQL and WQL will be obsolete when we leave ACeDB, AcePerl will still be useful (even if the details need updating)
    • Curators have GitHub access to all the AcePerl scripts, including those that generate FTP files

Under Testing

  • The "Under Testing" tag on GitHub issues is applied when something needs to be tested
  • Curators can filter for "Under Testing" issues and close them as they determine they are resolved

March 21, 2013

Protein browsing

  • KOGs vs eggNOG; eggNOG may be the most current
  • Would be nice to be able to (for each species or all species in WormBase) browse protein sets as orthologous groups by functional classification
  • Need to investigate

Microarray data

  • Data that were not provided (no changes observed in an experiment) leaves gaps in data
  • SPELL requires data for each experiment/probe (regardless of observation of change)
  • FTP site for downloads of data (independent from, but related to, SPELL); Wen needs regular access to
    • Can be hosted at Caltech FTP site (Todd can mirror over to main FTP site)
  • Add explanatory page to SPELL site

Dead genes

  • Historical_gene tag will be added to several class models: ?Interaction, ?Transgene, ?Antibody, etc.
  • How to handle GO annotations? GO will have mapping from proteins to GO terms, no need for new tag
  • Chris will send around model proposal to add the tag to relevant models
  • Curators will need to coordinate with Juancarlos how their respective OA dumpers should work

Beyond PDF conference

  • Karen attended
  • Peer-review process after open-access?
  • Provenance of data issues
  • ORCID collaboration
  • WormBase should coordinate WBPerson IDs with ORCID
  • Reproducibility of research: cataloging raw data and making it available
  • Authorea: data published as a GitHub repository
  • Discussions on contributing negative data
  • Rubriq: Peer review system

March 28, 2013

IWM Meeting

  • Workshops and talks topics
  • 2 Workshops (Kevin made Google Doc here (requires login):
  • Two workshop time slots: Thursday 1 hour (1:30 - 2:30pm), Saturday 1.5 hours (1:30 - 3pm)
    • Overview Workshop 1 (Thursday slot)
      • Sequence perspective (Hinxton/EBI member)
    • Data mining workshop (Thursday & Saturday slots)
      • Modmine with extra half-hour on Saturday
    • Overview Workshop 2 (Saturday slot)
      • Biology perspective (Caltech: Chris Grove)
        • Interactions, regulation
        • WikiPathways
        • Concise description forms
        • Expression Data in WormBase
  • Spreading the word:
    • Catch people during poster sessions (booth with ~4 posters)
      • Posters on: Wikipathways/Interactions, Species, Gene Expression & Regulation, Textpresso, Phenotypes & Diseases
      • Have projector displaying screen demos
      • We could create a template with a standard layout
      • Create posters with Illustrator or Scribus
    • WormBase events flyer to hand out or have placed in meeting program
  • WormBase give away ideas:
    • Mugs, aprons, gummy worms, LED light keychains, etc., etc.

Populating OA with variations for variation fields

  • Huge number of variations (>1,000,000!)
  • How to limit to relevant variations?
  • Can we split into "useful" vs. "generated" mutations/variations?
  • Splitting now on "Allele" tag
  • Add a new tag to the variation model?
  • Ask Hinxton to provide a file of all variations with a phenotype for FTP site
  • Also get full list of variations from Hinxton for our internal processing
  • Get abstracts (for posters, workshops, talks) ready by next conference call (next Thursday)

"Beyond the PDF" meeting

  • Who's driving the whole peer-review process?
  • Rebecca Lawrence Faculty of 1000 summary of Research Data Alliance (RDA) launch a world-wide open access data meeting - happening concurrently
  • Carol Tenopir - reading analysis
    • Successful researchers are very data-aware, read lots
  • Data format standards - defined by data repositories?
  • Action items: breakout groups (revolution group to completely reorganize data infrastructures)
  • Carole Goble: no need to "publish", just release data to public
  • Can follow up on action at http://www.force11.org/outcomes