WormBase-Caltech Weekly Calls

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Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

January 9, 2014


  • Apologies from Mary Ann - in Strasboug. Might try and Skype in. - Mary Ann joined in at the end of the call.
  • Curation of protein complexes - will wait until Chris can join in.
  • Set up a time next week to go over what more needs to be done for the construct/variation/transgene class - Main people being Mary Ann, Daniela, Chris, and Karen, others are welcome. Visit the construct model requests here
  • Raymond gave an update on WObr. Juancarlos has learned enough Catalyst to create a workable ontology browser on the caltech wormbase sandbox.
    • The browser can accommodate all ontologies used by Caltech curators (all GO, Phenotype, Anatomy, Life Stage, Disease)
    • A browser will be on each respective ontology page;
      • direct and indirect gene connections will be displayed in a list format
      • there was a request that the gene connections to ontology terms display the indirect annotations with direct annotations in parenths
    • various ontology browsers can be in their own widgets where desired.
    • still need to set up the search function from the main wb search
  • Caltech Models due Thursday 16 January 2014
  • Caltech WS242 data due into Citace by Tuesday Jan 28.
  • Biocuration 2014

January 16, 2014


  • WOBr discussion
  • Author-person issues
  • Timeline for construct model
  • Topic Curation

Author/Person issues

  • User was looking for papers for a specific person
  • Person was an author, but did not have a WBPerson object
  • Cecilia will contact user
  • Make author names searchable? ~32,000 authors without a person object
  • How many authors (without a WBPerson) have multiple (5+?) papers?
  • Proposal 1: make WBPersons for authors with 5 or more articles, and/or sort results of a search by number of publications
  • Proposal 2: Search for WBPerson (no autocomplete function); if no WBPerson, look up authors (prioritized search)

Timeline for ?Construct model

  • For WS243?
  • Mapping primers used for expression constructs or reporters
  • Integration of sequence features
  • Examples of the new Crispr/CAS (genome editing) alleles (curated with flanking sequences)
  • AddGene plasmids etc.
  • Karen will move ahead with the ?Construct model just for the context of genome-editing alleles
  • Other contexts can be added later

Topic Curation

  • Is there a way to update curators if a new paper is added to the current focus topic?
  • No, but curators can just send around an e-mail and/or query through the topic OA and curation status form

WormBase Ontology Browser (WOBr)

  • Juancarlos can now modify WormBase widgets, but would need to learn how ACEDB is handled, if required
  • We want to workout a pipeline for widget/website modifications, proposals etc.
  • WOBr is not working off of ACEDB
  • Note: WOBr is going to be a widget on the Ontology Term page (all other ACEDB-based info will be present on page)
  • General structure:
  • Association files needed: Disease, Life stage
  • Curators are now testing and commenting on WOBr
  • Difficult to implement: display of evidence codes, sorting by species
    • Will consider for second generation WOBr
  • Do we want species-specific WOBr? C. elegans WOBr? Yes, probably; not clear how to implement
    • WormBase ontologies are currently species-agnostic
    • Maybe we should have species-specific ontology terms/pages
  • When displaying the number of associated gene products, we could/should? distinguish the number of gene products from C. elegans versus other species (or ALL species)
  • Direct vs. indirect/inferred annotations, how to display at different points? Ignore numbers for ancestor terms? Speed is an issue
  • The new Solr update may allow for precalculated/precached number calculations, which should improve speed

January 23, 2014


  • Biocuration 2014
    • Mary Ann's flights are booked.
    • Shall we ask for a WormBase booth/helpdesk table?

Biocuration Meeting April 2014, OICR, Toronto, CA

  • http://biocuration2014.events.oicr.on.ca/biocuration
  • Mary Ann going
  • Xiaodong may go, present info presented at IWM
  • Wen considering, may want to see what's up for RNAseq etc.
  • February 10, 2014 is abstract deadline, March registration deadline
  • More WormBase curators?
  • Registration discount for "International Society for Biocuration" members

Topic Curation

  • Considerations for WS243
  • Innate immunity, response to pathogens?
  • Good to work on something for which a WormBook chapter exists
  • Jonathan Ewbank, "Signaling in the immune response" 2006 WormBook chapter
  • Creg Darby, "Interactions with microbial pathogens" 2005 WormBook chapter
  • Action items: Look over two WormBook chapters, collect relevant genes and send to EBI/Hinxton, collect relevant papers
  • What are the distinct challenges for EBI/Hinxton? Is it the number of genes? Number of protein coding genes? Are we sticking to "Core" species only? Which ones?


  • Tuesday morning 10am, 1-28-2014 deadline
  • Models available tomorrow (Friday 1-24-2014)

January 30, 2014


  • lin-15 - can we keep a page alive for this? Should it be considered a gene or can we fix up it up better as an operon? It has been assigned to operon CEOPX140, but searching for lin-15 in the operon class does not work, is there an other_name tag in the operon class to store 'lin-15'. 'lin-15' is frequently published object. Although many people in the field know that it is a complex locus comprised of two separate genes, lin-15A and lin-15B, many other people do not.
    • Mary Ann:
    • There are no plans to kill the lin-15 gene object at this time.
    • I agree that the operon object is rather vague. That it is the lin-15 operon could currently only be curated in the Description tag, which is not ideal. Should we propose a Name (or similar) tag for the ?Operon model?
    • The operon object is linked from lin-15A and lin-15B and is visible in the Overview on their respective Gene Summary pages.
  • Models deadline first conference call of the (upload) month?