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September 14, 2017

WB Grant

• Want to focus on community outreach
  • site visits, training, etc.
• Need to work on pathway models & diagrams
• Transcriptional regulatory network models need work
• Will look at regularly occurring quarterly milestones
  • Chris will look at curation goals, want ambitious but realistic
• Metabolomics? Maybe leave out since we need other funding to accomplish
• Would be good to generate lists of TF target genes and have available as a gene set/list for enrichment analyses and/or a WormMine list
• People can look over and make sure that we’re addressing important, exciting issues
• Put in blurb on “MicroReviews”
• Concise descriptions: people can contribute manually written descriptions, but would be best if people/labs took ownership for maintaining them
• How many papers did we get into the database in the past 5 years?

NAR Paper

• Punted until the end of the month
• Raymond fixing up to send around first draft

Author First Pass

• Proposing sending emails to authors AFTER SVM flagging, asking them to validate our automated flagging pipeline flags
• May want to incorporate other flagging methods like string matching
• We will want a mechanism such that each datatype flag requires action by the author, in order to get an official AFP flag, positive or negative, otherwise the paper does not get an AFP flag for that paper
• Maybe shouldn’t include data types in AFP form that are not actively being curated
• Want to strike a balance between too many and too few data types

Incentives for community curation

• Could consider not putting journal article (primary) papers on WB website until it has curation (by WB or community)
• We would like to collect a list of all regional worm meetings to reach out to
• How do we attribute annotations to community curators? Already a mechanism in place for concise descriptions and phenotype, but would need changes for other data types
• Have table of top community curators; will also work on having top contributors for past 2 or 3 months (Chris will discuss with Sibyl)

Leaving remark about corrections

• When authors make a typo about, e.g. a construct or transgene, can leave remark in the object in the OA

September 21, 2017

Grant

• Please review grant and send comments or revisions to Paul

Citace upload

• Check upload numbers from Wen; report any problems to her

Gene Ontology

• Number of complex terms being propagated to root terms
• There is a ticket to resolve this issue; Seth Carbon commented on it recently
• ~9000 terms ending up as direct descendants of root term "biological process"
• Same problem in AMIGO
• May be due to logical definitions

Reatcome/GO-CAM collaboration

• Kimberly will meet Monday with Reactome and GO-CAM folks to work together

Site visits

• We can start a Google spreadsheet of local meetings
• Curators can sign up for particular meetings
• We should gather the schedules and organize trips (chain of meetings to present)
• Each presentation could include all major topics of interest at WormBase (community curation, micropublications, Textpresso, etc.)
• Can include specific topics relevant to presenter, but should also be somewhat standardized
• Can include tutorials
• Also should include joining or presenting at individual lab meetings
• Daniela near some Texas meetings/labs
• Chris near Baltimore meeting and North Carolina triangle area meeting (Raleigh, Durham, Chapel Hill)
• Chris and Wen will present in Baltimore on March 16, 2018