WormBase-Caltech Weekly Calls September 2017

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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


  • 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

September 28, 2017

Updating the Phenotype Form

  • http://www.wormbase.org/submissions/phenotype.cgi
  • Current form allows users to submit multiple genetic perturbations simultaneously
  • This was originally intended to make it easier for users to submit multiple experimental results
  • Now we are finding that users want to submit double mutant phenotypes, but we need a way to distinguish multiple alleles in a complex genotype (single experiment) from multiple alleles, each observed individually for phenotypes (multiple experiments)
  • Some are confusing the "Allele" field for the genetic background of an RNAi experiment
  • Also, optional details like inheritance pattern, mutation effect, and temperature sensitivity cannot be unambiguously assigned to one allele if multiple are submitted
  • Some solutions:
    • Make it clear that each submission represents a single experiment; then, multiple perturbations would represent complex genotypes
    • If we make it single experiment at a time, we could offer a way to keep the same fields populated for next submission (for easier editing/filling out)
    • Get rid of inheritance pattern, mutation effect, and temperature sensitivity fields
    • Allow multiple experiments to be submitted simultaneously, but create distinct submission blocks for each experiment
    • Add a checkbox that indicates multiple perturbations are all part of the same complex genotype
    • Have separate forms for single perturbation phenotypes and complex genotype phenotypes
    • Have a CANTO-style submission process with multiple steps with a decision tree

Mary Ann's transition

  • Paul, Mary Ann will talk to Tim about transition of responsibilities
  • Will consider who will take over different curation tasks
  • Congrats to Mary Ann and best of luck!!

NAR Paper

Jae's experience so far

  • Jae is trying out phenotype curation
  • Working with the OA and curation status form
  • Learning GO-CAM/Noctua with Kimberly
  • Million mutation project alleles not all necessarily in the OA
    • Will need to request alleles to be loaded into the OA, unless we load all of them, but will slow the OA
    • Could include only those mentioned in literature according to Textpresso
    • Variations now coming from Geneace; having already(?) filtered out most gk* alleles
  • Protein-protein, genetic interactions; will discuss with Chris & Kimberly