WormBase-Caltech Weekly Calls

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2017 Meetings





May 4, 2017

Strategies for GO-CAM (Noctua) curation

  • GO-CAM (Gene Ontology - Causal Activity Model(ing))
  • Proposal for curation report page (Kimberly)
  • Paper-by-paper approach vs. big-picture approach
  • Kimberly presented proposal for curation tool:
    • Given a list of genes and keywords, tool could pull up all relevant annotations to help start with GO CAM model building
    • Tool could return GO annotations, expression patterns, phenotypes, interaction-based phenotypes, etc.
  • Could have a table to fill out that could then be imported into Noctua
  • Can we use SObA to visualize relevant annotations for a set of genes? Help visualize common vs. distinct annotations?
  • Process could highlight the need for micropublications


  • Raymond & Juancarlos have been working on autocomplete tool for search bar; not trivial

May 11, 2017

Phenotype Strain curation (ky)

  • Changing Strain tag in the Phenotype class, which is used as a primary object for annotating a phenotype to, to clarify its purpose.
  • A Strain tag also exists in phenotype assay, which is meant to capture the parent strain in which a mutant or other primary object (transgene or rearrangement) is part of.
  • These two tags have been causing confusion for curators and it causes errors upon the dump, in addition strains entered into the Control_strain field of the phenotype form are throwing errors during the dump as they are being recognized as "Strains".
  • The dumper does not allow more than one primary phenotype affected object, it can be Variation OR Strain.
  • Control_strain data from the phenotype form are being dumped as "Strain", not Control_strain. Chris will work with Juancarlos to fix

Metabolic curation (ky)

  • Michael Witting has hired a student to curate elegans metabolic data.
  • I will be talking to him to see what we can provide to help them share these curated data with WB. This might be as minimal as an spreadsheet although if they are submitting their own data, I will aim for a micropublication template. If there is another curator that wants to sit in on a call with Michael and me, that would be appreciated.
  • Mary Ann will join the call

CGC login

  • CGC site now has a login. While we will be able to access all the info without logging in (the log in is required for placing an order or viewing an order history), do we need want a login?
  • Aric talked with people at wormbase a while ago about the changes, was there any decision about if there will be a wormbase group login. I asked if they will be using logins to track activity on the site, he said no.
  • We do not need to do anything, we have the access we need.

Methods in Molecular Biology

  • Received comments back from editor, Chris going through them now
  • Chris is working through the comments; will send around to staff

SObA Gene Ontology interface

  • Raymond and Juancarlos have resolved most suggestions
  • Have settled on a search scheme
  • Haven't yet implemented highlighting GO Slim nodes; will work on
    • Maybe allow user to request "highlighting" of GO Slim nodes
    • Button "Show GO Slim terms"? Default highlighting of GO Slim nodes?
  • URL should still be active

Progress report

  • There is a WormBase progress report and an AGR progress report
  • Send WB reports to Paul

Phenotype display

  • Putting phenotype remarks in their own column; in-line evidence
  • Adam & Sibyl are working on phenotype display from Datomic
  • We can wait until they ask us to review to make comments about phenotype display
  • What about changes to phenotype model? Will make changes to phenotype model soon, but display shouldn't wait

Database migration

  • 3 year vision request; where do we want to be in 3 years?
  • ACEDB to Datomic? AGR dependent activities? May need to consider both

May 11, 2017

GO SObA update

May 18, 2017

Texas Women University visit report

  • Tissue enrichment tool
  • Cytoscape
  • WormMine and Simplemine
  • User's traffic
  • Micropubs