WormBase-Caltech Weekly Calls

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2016 Meetings

January 7, 2016

SAB 2016

• Schedule for Caltech talks:
  • SAB wiki: http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks
  • Mary Ann, Chris, and Ranjana will discuss how to condense and streamline a presentation on community curation
  • We should have a talk about LEGO curation and pathways; Kimberly happy to present
    • LEGO adoption can be made cross-MOD and encourage collaboration
  • Maybe move micropublication talk to the end of the day; it will generate a lot of discussion; will try earlier in the day, 5 min talk, 5 min discussion before longer discussion
  • Maybe include discussion of expression summary description in Gary Williams talk about large scale expression data and visualization

Expression summaries

• We want to consolidate large-scale expression data into a human-readable summary
• Would be good to consolidate large-scale and small-scale expression data
• We will adapt anatomical expression data for the SObA graph in future

Phenotype form

• Now on sandbox, allows for RNAi transgene data
• Will finish up, write documentation and make live
• Will continue to send out e-mail requests

E-Merge Tech outsourcing

• Company called Chris asking if we would want them to curate for us
• Website: http://www.e-mergeglobal.com/
• Will send them some phenotype curation for some papers and ask them to curate new papers, as a pilot
• They will give us a cost estimate after a free pilot
• Will see if it is cost-effective; good to know what they charge

January 14, 2016

LEGO

• Sent out slides for an overview talk of LEGO and the Noctua curation tool. (Kimberly)

Collecting info for SAB

• Chris would like to collect summaries of curation progress over last year in a Google Doc
• Google doc: https://docs.google.com/document/d/1S8EjL20owW07RH9kIi8HbnTAtP5JierliBuyOo2oDVc/edit
• Would be good to include progress on various projects or curation efforts (or curation changes)
• Next week at group meeting we can review and decide what should be presented as the overview for curation to the SAB

January 21, 2016

SAB

• Agenda items for literature curation overview
• Todd will discuss outreach; Chris will talk to Todd about Caltech plans for outreach
• Cataloging web usage on WB site, SPELL, etc.
• We can discuss hosting all WB services and tools under the same web domain

Phenotype form

• New phenotype form is live: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/allele_phenotype.cgi
• We should point out response rate and paper coverage for community curation
• How long can we expect to complete curation for phenotype with current pipelines
• Can request PIs to check coverage of their allele phenotypes
• We want this to lead to development of pathways

The Allied Genetics Conference, Orlando, July 2016

• WB needs to decide who will go
• Intermine project will have their own room
• MODs will present together

January 28, 2016

SAB talks

• Literature curation overview
  • General publication trends for C. elegans and data types
  • Our coverage, backlogs, outreach and curation efforts
• Automated paper flagging and data identification (Karen)
  • SVM pipeline, keyword/string matching, data extraction
• Automated gene descriptions (Ranjana)
  • Manual writing doesn't scale (currently ~5000 descriptions)
  • Amenable to automation (pulling together primary data for descriptions)
  • Mention gene description form
• Community annnotation numbers (Mary Ann & Chris)
  • Other MODs efforts
  • WB submission forms and pilot response rates
• Micropublications
  • Incentivizing community contributions
  • Micropublication form
  • How data is displayed on WormBase
• LEGO
  • What it is, how it's different, why it's important
  • Priorities for LEGO models: signaling pathways, development, human disease biology (signal transduction, cilia pathology, etc.)
• SObA
  • WB uses ontologies extensively, many annotations
  • Need an easy-to-consume data display
  • Have WOBr
  • Convention is to provide list format of data display, e.g. mouse expression summary
  • SObA: intuitive summary view of ontology annotations from gene perspective
  • Ontology trimmed to display only relevant ontology terms
• What do we not have a talk about:
  • Human disease curation
  • SPELL/modSeek
  • Metabolite curation
• Google Doc: https://docs.google.com/document/d/1uvSIIecWTmVjhUPA8f4FHIECSTJhloy8Z2ocujx96Uw/edit