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September 6, 2012

Canopus

• Will become a server (heavy outside access)
• Raymond will take precautions to restore properly; should take a week or less
• Used for:
  • Picture curation
  • Virtual worm web page & FTP

Grant Writing

• Approach & future plans - do we need to discuss and add more to proposal?
• Virtual worm access to data
• Browsing data
  • Browse genes/proteins by class/GO annotation
• Intermine queries
  • Queries can be saved and used again later (available to other users)
  • Results can be stored and displayed on web pages
• Displaying large scale expression (microarray) data (from SPELL)
  • SPELL data currently stored in relational (MySQL?) form
  • We could extend the WormBase web app to interact with SPELL data
  • RESTful-compliant data serving would be best

Migration away from ACEDB?

• Scalability - ACEDB does not scale to genome-scale studies
• We (EBI & OICR) spend a lot of time building ACEDB database
• ACEDB not actually used so much
• Makes more sense to adopt a more central database
• Migration would take place over entire grant cycle
• We should continue extending models as we see fit, in the meantime

Massmails

• Discuss again with Paul about Worm Breeder's Gazette and WormBook.

September 13, 2012

Grant

• Two things to work on:
  • 1) Metrics and quality control
    • Metrics: Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments/papers and we have ~62% coverage")
      • SVM form (in development) vs Curation Status form (needs work/update); can generate numbers for coverage to display on the web?
      • What is the vision of a new Curation Status form? (Daniela will write something)
      • Stats with new SVM results on pre-2000 papers: state them in grant as pre-2000 corpus
    • Quality Control: How do we demonstrate that our curation is correct/accurate?
      • Sampling First-pass curation (false negative estimates)
      • WormBase person would check on case-by-case basis the accuracy of data (e.g. expression pattern, RNAi experiment, etc.); what percent do you need to check to ensure good quality control? Blind/independent re-curation? Collection of facts to use for metrics
      • Contact senior author on a paper to check the quality of data from a paper; experts for a process; prioritize based on who responds to author-first-pass
      • Data-type specific issues
      • Internal consistency checks
      • Ontology based curation checks (granularity; branch-consistency)
  • 2) Training and user interaction
    • Screencasts and FAQs list (Chris will write some sentences)
    • User guide status? Currently needs major revamp and new information (old Wiki User Guide is now obsolete)
    • Online chat: has been broken for months; should it only be allowed for logged-in users?
• Daily updates with low-connectivity data (not relying on sequence mapping) from PostgreSQL database?
  • Have different CGI forms to populate the data on the website?
• Are we committed to migrating away from ACEDB? Who then is responsible for managing data models?
  • Migrate to Chado? Do we need detailed plan for this?
  • FlyBase has migrated; they like Chado, but the migration was painful

Worm Breeder's Gazette & WormBook outreach

• Mass mailings should be an Opt-in system, as opposed to blanket mass mailings
• One mass mail for each to ask about Opting-in to e-mail alerts?
• Regional & International worm meetings; don't hand all e-mails over to meeting organizers.

Itai Yanai expression datasets

• Including images from microarray expression data directly from paper for now
• Plan is to generate time-course expression data 'on-the-fly' later on so that other data sources can be compared and included in the same graph, given that they are the same type of data
• Eventually, the paper images will be superceded by the new, calculated 'on-the-fly' images

Phenotype Images?