Difference between revisions of "WormBase-Caltech Weekly Calls"

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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

Revision as of 15:32, 1 August 2019