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July 11, 2013

Geneace daily dump

• EBI is moving nameserver location
• Getting real-time updates of gene list for genes in OA
• Michael Paulini set up nightly geneace dumps to FTP site
• We have gene file from nameserver: cgc name, public names, sequence name, live/dead status, gene IDs
• What data do we want additionally? Synonyms?

Spica has officially been moved to new machine

• Let Raymond know of any problems
• Would be good to track all accounts on Spica (and any other machine)
  • Can use log of all user logins

AMIGO 2 still moving forward

• AMIGO 2 might go live July 17th
• We should be able to start configuring for WormBase at that point

Process Pages/WikiPathways

• iFrame window doesn't work/load on Firefox; they are working on it
• iFrame window interactive display somewhat problematic
• Discussing Cytoscape as alternative?
• Using Cytoscape to display pathways would require significant development
• Some app available to load GPML from WikiPathways into Cytoscape, but JD couldn't get it working (yet)
• Having all process-related interactions in an Interactions widget on Process Pages
  • Users need a clearer legend explaining what the different edges mean
  • We need to modify some edges (e.g. flat ends do not mean repression; maybe they should)

Author First Pass Forms

• Currently we collect data from authors that we may not have intention of curating (at least right away)
• We can provide a disclaimer on the letter to authors explaining that some data may not be curated immediately
• All data is catalogued

Sequence Feature curation

• Xiaodong met with Gary Williams and Mary Ann Tuli at IWM
• Enhancer curation?
• Significant backlog on sequence feature curation
• Margie Ho asking about curated enhancers, regulatory regions
• Margie has 30 papers with highly annotated regulatory regions
• Gary W. is prioritizing curation of these now
• Gary will propose appropriate model changes (e.g. Add "silencer" and "enhancer" to method for GBrowse display)

User use case: All G-protein coupled receptors expressed in AWC neurons

• Quantitative expression data is not effectively linked to anatomy terms
• Wen will propose model fix to accommodate this association
• Genes expressed above some pre-defined threshold will be associated with a cell
• For example, Ping (in Paul's lab) will be performing AWC single cell profling
• AWA and BAG neurons has been profiled by tiling arrays
• Male linker cell by RNA-Seq (Erich and Mihoko)

Curation strategies

• Change our paper-by-paper curation
• We may be able to make use of a Textpresso categorization program to tag papers
• Caltech curators can then prioritize their curation based on a particular category or topic