WormBase-Caltech Weekly Calls

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2014 Meetings

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May 1, 2014

Progress report

• Curation status freezes have been collected (daily?)
• These can be used for report
• Review grant proposal: milestones, quarterly updates, etc.

LEGO - Paul Thomas' visit

• We want to work on/think about importing WB GO annotations into LEGO format
• Is .OWL format the final destination of LEGO data for us? Yes, probably
• Will we be able to automate the process and eventually port to WikiPathways or other pathway visualizer?
• Extended evidence codes? For capturing methods?
• We need some trial LEGO curation to start working out the process
• There is a communal desire to achieve a common format for pathways, whether it be SBML, SBGN, LEGO, etc. or some hybrid
• We would like to play around with how to import/interpret/export .OWL files for our data

Pathway curation

• Topic curation: a single (or pair of) curator(s) focusing on pulling together and drawing a pathway for a topic
• Labs adopting a pathway? Outreach, community annotation
• Reaching out to experts to confirm or proof read our pathways

WormBase Ontology Browser (WOBr)

• http://juancarlos.wormbase.org/tools/ontology_browser
• Getting closer to completion
• Working out how to handle different relationships, e.g. "part_of", "has_part"

May 8, 2014

Agenda

• Topic 1
• Topic 2