WormBase-Caltech Weekly Calls

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November 1, 2012

SPELL data

• Including new RNA-seq datasets
• Comparing different RNA-seq datasets

Dedicated ~2 weeks for issues

• Dedicated time during release cycle to fix bugs and address GitHub issues

Intermine

• JD Wong started at WormBase this week; will focus on building WormBase instance of Intermine
• Developed FlyBase Intermine instance
• Once in place, we can build pre-canned queries that we can embed in WormBase pages (maybe in response to help desk inquiries)
  • E.g. Display meta information for a gene; "How many genes show this phenotype?"
• We have resources provisioned for building and hosting
• Low hanging fruit: access to ontologies, gene models, phenotypes, homology, orthology (things already made for Intermine)
• Focus first on central dogma stuff

SAB Meeting

• January 28th, 29th, 2013
• At Caltech

Concise description template

• Curator version versus a community (simpler) version
• 1) Transfer info from elegans to other species
• 2) Updates
• Easier to script when there is little information; harder when lots of info

Pathways

• Karen spoke to Alex Pico
• There could be tagged for "WormBase-approved" pathways
• Would be good to have worm community also contribute; "Community Pathways" widget
• Conflict resolution? There could be many contributions to the same pathway
• Is there a way to pull up conflicting versions of a pathway?
• Open system: any registered user can modify any pathway

Community Annotation

• Possibilities?
• Concise descriptions, pathways, what else?
• Expression patterns?
• Tables/templates of suggested data/types that authors could/should submit for a paper
• Annotation Apps? iPhone, Android, etc.
  • Controlled vocabulary, virtual worm, AMIGO ontology browser, etc.
• Annotation on tablets, other mobile devices? Read only?
• Web app versus native app
• Open Badges for micro-attribution, incentives
• ORCID for unique person IDs
• Possible Ontology Annotator version for community?
• Templates/forms would need to be very straight-forward and simple to use
• Maybe display a form alongside web display to inform users of how the two relate
• Training users: tutorials, workshops (2013 IWM?)
• Daily updates to website could be more satisfying for users