WormBase-Caltech Weekly Calls

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September 3, 2015

Development instances at Caltech

  • Caltech wants to provide a Beta testing environment for curators/users. we'll have to rely on juancarlos.wormbase.org as cost/benefit analysis is unfavourable to consider other options.

GObA (Graph of Ontology-based Annotations)

Anatomy enrichment tool

  • Enter list of genes, get a list of anatomy terms
  • Developed originally by David Angeles
  • Being incorporated and worked on by Raymond

Community allele-phenotype annotations

  • Outreach: sending out e-mails to relevant people
    • Not done yet
  • May be good to travel out to labs to give instructions, outreach
  • We'll gather a list of labs that publish phenotypes and contact them
  • We can also push the micropublication process

Logical Extensions of Gene Ontology (LEGO)

  • Further developments being made on Noctua and other LEGO software
  • Lots of discussion on LEGO modeling, how to best do it
  • Testing is scheduled
  • Protein complexes in cellular component ontology?
    • GO will collaborate with Protein Ontology group to work out how to capture that info
  • Molecular function ontology annotation approach is being refactored
  • Noctua being used for phenotype annotations, would be good to see how

Phentoype-association file: Attributing phenotypes to genes via genetic interaction

  • Can we (and how do we) capture genes as involved in a process, for example, SynMuv genes in vulva development
  • The phenotype association file currently only on direct phenotype annotations, not interaction-based phenotypes
  • Gene Ontology captures these events (associations to a process, for example) with the evidence code, Inferred from Genetic Interaction