WormBase-Caltech Weekly Calls
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Contents
Previous Years
2015 Meetings
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