WormBase-Caltech Weekly Calls August 2016

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August 4, 2016

Parasite Paper Pipeline and Curation Status Tracking

  • ~4% of Journal articles (roughly, but not precisely, translates to curatable papers) mention both Caenorhabditis species and parasite species
  • We discussed last week the options for accurately tracking data type flagging and curation status for these papers
  • SVM does not flag data at the species level, but we need a way to distinguish curation status based on species or it will be difficult to get accurate numbers for Caltech and Hinxton
  • One option would be to have separate status tables
    • Lump Caltech and Hinxton species together or distinguish each species separately?
  • Other options?

Intellectual lineage graph

  • Raymond - are we ready to implement as a widget on person page?
  • Can toggle to show only direct relationships
  • Will eventually be able to toggle by relationship type
  • These will simplify complex graphs


  • Yuling is tying up loose ends for MGI SVM before he leaves

AGR Timeline meeting

  • Timeline still pretty high-level but making progress

Complex genotype to phenotype annotation

  • Chris - still planning to work out details over models mailing list
  • We can go ahead with the creation of phenotype report objects to encapsulate complex genotypes
  • Another approach to consider is whether or not to create "set" objects that contain sets of, for example, alleles, genes, etc.
  • We could potentially reuse sets as they come up again in different contexts, or in replicate experiments

Teleconference line

  • New AT&T conference call is OK, not great
  • BlueJeans is too expensive for our purposes

August 11, 2016


  • Would like to make more prominent on homepage
  • Expanding micropublications to phenotype
    • Would we require images, photographs of mutant worms
    • Can clone phenotype form, but remove requirement for publication; also add funding sources
    • Would negative data require controls?

August 18, 2016

Citace local upload August 30


  • Raymond installing new network card
  • Recent network crashes, unclear why
  • Raymond sent a help desk ticket to IMSS; no response so far
  • Michael and Ranjana have gotten network errors as well (when trying to deal with automated descriptions)

Models updating

  • Wen has GitHub page bookmarked to retrieve latest models.wrm file
  • Older CVS system had used explicit release ID in name of file; not same now with GitHub
  • With GitHub, it could be easy to script retrieval of latest models.wrm file

Anatomy ontology, from OBO to OWL

  • Major reason to do it: make direct connections to terms in other ontologies
  • Can take advantage of other anatomy ontologies
  • Should the WBbt "cell" be synonymous with generic "cell" or be referred to as "C. elegans cell"?
  • Import versus cross-reference approach to linking ontologies

Noctua, LEGO curation

  • Weekly meetings, Monday mornings
  • Nearly ready to release Noctua for use
  • Ongoing discussion about use of relations from the relations ontology; maybe need some new terms
  • Idea is to make Noctua the main GO annotation tool, for simple or complex annotations
  • People still using legacy GAF file, need to transition to OWL format
  • Training session at end of month (next week)
  • GO meeting at USC in November; will dedicate the following week to Noctua/LEGO training workshop (Monday Nov 7th?)
  • While curating need to consider whether a molecular function regulates a process or is part of a process; requires explicit positioning
  • Need to deal with annotations to a generic gene product versus a specific gene product (one or all isoforms, for example)
  • Would want a "enabled by product of" relation for genes
  • Chris M concerned with having too many relations for curators to know/keep track of
  • Training material should be available from the Noctua homepage

Community Phenotype annotation

  • Still sending out emails, reached stopping point, for now (emailed most authors within last month)
  • Still getting consistent responses from authors
  • Working on homepage widget to display top contributors


  • Daniela had sent out solicitations for expression data; some people expressed interest, but haven't heard back
  • We could take the phenotype form and modify for micropublication