WormBase-Caltech Weekly Calls July 2019

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July 11th, 2019

Alliance all hands meeting

  • Raymond: would be interested in discussing ontologies and their usage in the Alliance
    • Phenotype, anatomy ontologies, GO, etc.
    • Ontology browsers, SObA

IWM workshop

  • Videos ready for upload
  • Wen and Raymond now have access to outreach@wormbase.org account; will upload videos

Protocol videos

  • Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase?
  • Can make each video a Video Weblog so people can make comments, etc.

July 25, 2019

Anatomy ontology

  • Raymond added back some deprecated cell group terms as obsolete terms

Life stage ontology

  • Who will take charge of it? Raymond or Chris?
  • OBO-to-ACE script is working
  • OBO is working (?) in SObA and WOBr
  • Chris will take over life stage ontology; Daniela & Raymond will send Chris location of OBO-to-ACE script
  • Chris will send release OBO to Raymond to test WOBr and SObA

Anatomy term acronyms

  • Some anatomy terms: can the name be changed?
    • e.g. "DTC" is main label for "distal tip cell"
    • e.g. "HMC" is main label for "head mesodermal cell"
    • e.g. "gon herm dtca" is main label for "anterior distal tip cell"
  • Karen: would be good to still point out a "public name" or "common name"
    • Chris: we may need to select a specific OWL annotation property to dump into OBO so our scripts can recognize them and populate ACEDB/Datomic; will look into; may require model change

Author first pass

  • Paul: spent about 30-40 minutes doing author first pass for a micropublication
  • Entities need to be listed 10+ times (fixed threshold) to be recognized, but micropubs won't usually have this many occurrences of terms
  • Need a better way to report allele details; curation of alleles can happen at Caltech or Hinxton; need to discuss
  • Google summer of code: add to schedule so we can post requests/openings
  • Karen: Could implement something like Apollo? Talk to Nathan?
  • How can we optimize micropub author first pass?
  • Need to minimize/eliminate redundant curation effort
  • Curation forms could hide fields that have already been curated; OR, show existing curated data to form users
  • Paul: Can we have submission form build a report to send to user, but possibly not store locally?
    • Karen: May be counter to the intent of micropublication where we want authors to submit data in parallel to submission/publication process
  • Eventually there shouldn't be any author first pass for micropublications
  • For now we will exclude micropublications from AFP
  • Can NIH funded groups be pressured to submit data? We need the pipeline to operate smoothly (and properly) before making a requirement