WBConfCall 2018.03.01-Agenda and Minutes

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WormBase SAB Meeting Date

  • Decide on date for SAB meeting



  • Anything we need to know?

Open Tickets


WormBase SAB Meeting Date

  • Best dates for the meeting are July 12th-13th 2018 in Toronto. (There is a Caenorhabditis evolution meeting at Hinxton this year, 5-7 July ).
  • SAB advisors will be contacted to check their availability


Quick update

  • Paul K

said Advisory board wanted us to explain AGR management structure and overall objectives better.

  • Paul S

Will send the AGR SAB Staff Report to the group

In April NIH panel will decide what will happen after our 1.5 years of funding...... therefore we need a detailed implementation plan.

With respect to the April meeting implementation plan (1.5 years):. This should include not only what can we get done in the next 1.5 years (detailed), but include some info of longer term plans and challenges we think we will face. This sketch needs vision of the 5 year plan showing the cohesion of the AGR group members (common infrastructure and common curation efforts).

Working Group Updates for 1.5 year plan:

The following gave perspectives/plans for the working groups on which they sit.

Chris G: Interactions:

  • Currently, the interactions working group is focusing physical interactions, including protein-protein, protein-DNA, protein-RNA, RNA-RNA types
  • Once we have sorted out physical interactions, we will move on to genetic interactions, followed by regulatory interactions
  • Each interaction type will likely take ~6 months, so at the end of 1.5 years we should have this data available on the Alliance website
  • Will also work out network visualization tools, like Cytoscape

Daniela R: Gene Expression

  • Links to MOD gene expression pages

Ranjana K: Gene descriptions

  • Goal: produce a short text description for every gene in AGR where biological data is available.
  • 1.5 year plan:
    • produce a gene description describing gene molecular function, biological processes involved in, and cellular localization based on Gene Ontology (GO data)
    • reports detailing amount of GO data for MOD genes
    • learn to trim terms by traversing ontology tree and/or slim terms to increase readability
    • include disease data based on disease annotation that uses DO terms, following the same strategies used for GO

Chris G: Disease and Phenotype

  • Currently the disease group has been focused on integrating alleles into the Alliance and disease display; more genetic entities, like strains, genotypes, fish, etc. to follow
  • Group is getting close to finalizing a disease term slim to use for disease ribbons on gene report pages
  • We are transitioning now into phenotype data; still need to generate a common data model for phenotypes
  • We are reviewing the ontologies and controlled vocabularies that each MOD is currently using for phenotype curation
  • We hope to have decided on appropriate ontologies and slim terms for a phenotype ribbon type of data display
  • At the end of 1.5 years, we will have all relevant genetic entities on Alliance website with disease and phenotype data display for each

Kevin H: Orthology:

  • This group has achieved the goals in its original mandate. Will wind down and perhaps a group can move on to pralogs

Adam W: Said to let the architecture working group know if your working group needs assistance with infrastructure plans.

Paul S: Outside the working groups – think more about community Curation. Lynn Crosby from FlyBase has interest in heading up a working group dealing with community curation.