WormBase-Caltech Weekly Calls
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GoToMeeting link: https://www.gotomeet.me/wormbase1
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
- Videos ready for upload
- Wen and Raymond now have access to email@example.com account; will upload 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
- 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