WormBase-Caltech Weekly Calls

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May 2015

May 7, 2015

Disease variants

  • Ranjana, Karen, and Chris will work out a pipeline to link elegans gene variations and phenotypes to homologous human disease gene variations. This is separate from any automated pipeline that can be set up by Hinxton.
  • Tim Schedl brought up: would be good to connect conserved/syntenic mutations
  • Human disease mutations should be mapped to C. elegans/nematode variants
  • Is there an ortholog? Is the mutation location conserved? Is there a mutation at the site in both orthologs?
  • Authors refer to C. elegans mutations as a model; may or may not be strictly conserved
  • Need to consider what can be done automatically, and what needs to be curated manually
  • We could consider curating connections between mutations and protein domains, and predict affects on function
  • Query use case: what mutations exist in SH3 domains?
  • We could perform two-way mappings: human disease variants to worms/elegans AND elegans/worm mutations to human protein sequence
  • First need to identify all protein sequences of "sufficient" identity/orthology between human and elegans proteins
  • Discuss with Michael Paulini et al


Grant Progress Report

  • Statistics for WS248
  • Want to report progress to data display on web
  • Xiaodong will write section on binding sites, gold-standard regulatory regions, sequence features updates
  • Daniela can write short bit on sequence feature OA


Pathway curation: metabolites

  • Karen talking with Michael Witting
  • Sent Karen list of >2700 metabolites and is curating those verified to be elegans metabolites from publications; wants incorporated into WB with IUPAC names etc.
  • Michael working mostly off of KEGG pathways; metabolites have KEGG IDs
  • Not necessarily an applicable ontology of metabolites, as far as we know
  • Worm-specific vs. general biological metabolites
  • Would be good to connect enzyme commission (EC) numbers to metabolites
  • We can add tag to ?Molecule data model to capture endogenous molecules/metabolites

Community Annotation

  • Biggest backlog: allele-phenotype
  • We want simplest, minimal form necessary
  • We need (minimally): who is curating, allele, phenotype, and reference
  • Need good look-ups for phenotypes, references
  • We can (later) increase the detail
  • Allele names can be entered (ideally) in one field that handles both registered terms, and new terms (with warning)
    • Allele designations must be registered
  • Confirmation screen
  • We want a prominent "Submit Data" button and/or tab (Allele-Phenotype could be a drop down option at top)
    • Users click on this and (at least for now) are redirected to the Allele-Phenotype form (only)
    • Option to submit other data
  • We will accept PubMed IDs for papers (only)
  • We will keep allele data (allele nature, temperature sensitivity, etc. as optional entries)


May 14, 2015

WormBase/ParaSite shopping bag souvenirs for 2015 IWM

  • Daniel looked into costs and styles
  • We can choose from a number of material colors as well as print colors
  • Having two distinct logos will cost more
  • There is a reinforced option that is about 14 cents more per bag
  • We can order locally (saves on shipping costs)
  • Cost break down estimates: base $1.06 per bag, +$0.35 per bag for extra logo, +$0.14 per bag for reinforced