WormBase-Caltech Weekly Calls

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

January

February

March

April

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 (I initially said 4000) 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