|
|
Line 37: |
Line 37: |
| [[WormBase-Caltech_Weekly_Calls_June_2019|June]] | | [[WormBase-Caltech_Weekly_Calls_June_2019|June]] |
| | | |
− | | + | [[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
| |