WormBase-Caltech Weekly Calls January 2014

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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
  • Models deadline
  • Curating pseudogenes
  • Part-time help

lin-15 - Creating a page for it

*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 people do not.
*There are many lin-15AB alleles, e.g., n765. Where in WB can we see that one 
allele affects more than one gene, is this something a lin-15 operon page can 

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. 
Tim Schedl:
I think there should be a lin-15 page that explains the original allele/ 
why it was called lin-15 and then refers the user to the lin-15A and lin-15B 
pages.  The lin-15 page need not have any/much other information, although 
a description of the define allele would be useful.  
Just killing the lin-15 page might lead to confusion for someone who 
does not know the history (which is the majority of current worm researchers).
  • Mary Ann would like to attribute as many strains as possible to lin-15A or lin-15B
  • lin-15 is the only gene/locus with ONLY a "Public_name"
  • Can lin-15 be the CGC name? What about synonyms/"Other_names"
  • Should the operon of lin-15 be called "lin-15"? Can we apply descriptions to operons?
  • Proposal: create a "Name" tag for operons?
  • Important: We need a page for the "lin-15" entity, for historical reasons at least, either as a gene or an operon (something else?)
  • Allele attribution, e.g. n765? others?

Models deadline

  • Models deadline first conference call of the (upload) month?
  • Proposal to EBI
    • First conference call of the "Upload" month (3rd conference call of the cycle, usually), finalize models
    • Paul Davis has 1 week to finish the models.wrm file and tag it for the official release
    • Once tagged, the "final" models.wrm file can be tested by curators for ~1 week before data upload for citace build by Wen
    • So, for example, on the current calendar we are on, we would have the following dates:
      • WS243 model submission deadline : March 6th, 2014
      • Paul finishes tagging WS243 models.wrm: March 13th, 2014
      • Curators can test official WS243 models.wrm file: March 14th, 2014 - March 24th, 2014
      • CITace data upload for WS243: March 28th (Friday), 2014 (Caltech curators submit ace files to Wen before Tues. March 25)
      • WS244 model submission deadline: May 1st, 2014
      • Paul finishes tagging WS244 models.wrm: May 8th, 2014
      • Curators can test official WS244 models.wrm file: May 9th, 2014 - May 26th, 2014
      • CITace data upload for WS244: May 30th (Friday), 2014 (Caltech curators submit ace files to Wen before Tues. May 27)

Curating Pseudogenes (Kimberly)

  • Two cases have come up recently wrt functional annotation of pseudogenes.
  • drh-2 - a Dicer-related helicase for which there is apparently protein evidence and some functional studies (although it is part of an operon)
      • klp-10 - a kinesin-related protein that lacks a critical motif was recently converted to a pseudogene
  • Pseudogene status is listed discreetly under Type in the summary box display, but I wonder if we need to communicate this information more prominently and/or explain the classification in the concise description (CD).
  • Typically, we haven't written CDs for genes WB classifies as pseudogenes, but in the case of drh-2, there are papers that suggest it is functional.
  • How best to reconcile all this data? Should we contact authors of the papers? What should we do with experimental data attached to pseudogenes?
  • Consensus: users should have access to all relevant information, including any conflicting evidence (in a concise description) and why a gene should or shouldn't be considered a pseudogene

Part-time help

  • Part-time help (undergrads, etc.); Paul was wondering if we thought we could use any
  • Mary Ann: allele curation, check through papers for true positives (appropriate for undergrads)
    • Could undergrads at Caltech use the Hinxton curation tools? Would they need a "sponsored" account or something?
    • Or, more simply, papers could be scanned for data and results sent to Mary Ann
  • Karen: downloading papers and supplemental information (high school students could do this)