Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
== 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