WormBase-Caltech Weekly Calls

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June 5, 2014

Agenda

• GAF vs GPAD/GPI file formats
  • GO still uses both, but is moving towards using GPAD/GPI as their preferred format.
  • We will always need GAF for WOBr?
• LEGO Curation/Noctua Development
  • Tool is still under significant development at Berkeley.
  • What are our plans/goals at Caltech? How best to align this with Berkeley development?

WormBase Ontology Browser (WOBr) for WS244 release

• User interface: would be good if curators could have a look and review again
• Latest GAFs added were for Life Stage and Disease
• GitHub WOBr tracker: https://github.com/azurebrd/wobr

GAF vs GPAD/GPI file formats

• GO traditionally uses GAF format
• May be migrating to GPAD/GPI [Gene Product Annotation Data / Gene Product Information] format in future
• Backend of Amigo2/WOBr uses owltools
• Kimberly discussing with GO team
• We already have scripts to convert GPAD to ACE format

LEGO curation / Noctua Development

• (Too?) much flexibility in what can be curated into Noctua
• Final data model may still need refinement?
• Need to wait for final word on data model before finalizing curation pipeline
• We may be able to develop curation tools ahead of final LEGO data model
• Would be good to have discussions about complex biological scenarios and how to best capture

Construct OA

• Karen and Juancarlos working on ?Construct OA
• Other OA's may need to be updated accordingly
• Wen will set up a local database with the proposed ?Construct model

Reactome tutorial

• 10am PDT tomorrow (Friday)
• WebEx conference
• Initial talk of curating chromosome segregation, may be too complex
• Paper sent around to summarize Reactome model and curation pipeline

New Topic for WS245

• Many possible topics; would be good to choose a topic that has some new papers and would be amenable to drawing a pathway
• We discussed: aging, apoptosis, defecation, feeding, ascarosides...
• We will try apoptosis
• Chris will look into and send around findings

Mapping of promoters

• We have annotated many promoters for expression patterns, for example, but have not been mapped to genome
• Ultimately want to map constructs (or components of constructs) to the genome
• Construct components should be converted to sequence feature objects (?Feature)

June 12, 2014

Agenda

• Topic 1
• Topic 2