Difference between revisions of "WormBase-Caltech Weekly Calls"
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[[WormBase-Caltech_Weekly_Calls_May_2019|May]] | [[WormBase-Caltech_Weekly_Calls_May_2019|May]] | ||
+ | [[WormBase-Caltech_Weekly_Calls_June_2019|June]] | ||
− | + | [[WormBase-Caltech_Weekly_Calls_July_2019|July]] | |
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− | === | + | == August 1, 2019 == |
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− | === | + | === Life stage public names missing in WS271 === |
− | * | + | * Did we ever get a patch in for this? |
− | * | + | * WormMine only has WBls IDs (no public name) for almost all life stages |
− | * | + | * Wen will resend the patch file |
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+ | === 2020 WB NAR paper === | ||
+ | * Who's contributing? | ||
+ | ** Raymond, Chris, Ranjana, Valerio, Daniela, Kimberly | ||
+ | * Topics | ||
+ | ** Automated descriptions | ||
+ | ** Ontology tools (SObA) | ||
+ | ** Community curation | ||
+ | ** Author first pass | ||
− | == | + | === 2019 IWM Workshop videos === |
+ | * On YouTube, but not public yet | ||
+ | * Chris will make them public and send links to Ranjana for the blog post | ||
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− | == | + | == August 15, 2019 == |
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− | === | + | === GO Alliance slim terms === |
− | * | + | * We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance |
− | * | + | * May need to watch out for terms that don't apply to worms |
+ | * Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?) | ||
− | === | + | === Phenotype ontology patternization === |
− | * | + | * Now have 676 terms patternized (27% of 2,506 terms total) |
− | * | + | * Have reviewed the class hierarchy, collecting list of unexpected class subsumptions |
− | + | * Issues to address collected here: https://docs.google.com/document/d/1IWtQbEQ-elM-U5SQyU4VfIH3vdJp6taVMGViIjGyVks/edit?usp=sharing | |
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− | == | + | == August 22, 2019 == |
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− | === | + | === Obsolete ontology terms in Postgres === |
− | * | + | * There are currently 172 GO annotations in the GO OA referring to obsolete GO terms |
− | + | ** https://docs.google.com/spreadsheets/d/14iG3-s0GrZ3_W87iOjD6tZiQiUJklRRjgs6ARFWi9E4/edit?usp=sharing | |
− | + | * We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres | |
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Revision as of 19:27, 16 August 2019
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2019 Meetings
August 1, 2019
Life stage public names missing in WS271
- Did we ever get a patch in for this?
- WormMine only has WBls IDs (no public name) for almost all life stages
- Wen will resend the patch file
2020 WB NAR paper
- Who's contributing?
- Raymond, Chris, Ranjana, Valerio, Daniela, Kimberly
- Topics
- Automated descriptions
- Ontology tools (SObA)
- Community curation
- Author first pass
2019 IWM Workshop videos
- On YouTube, but not public yet
- Chris will make them public and send links to Ranjana for the blog post
August 15, 2019
GO Alliance slim terms
- We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance
- May need to watch out for terms that don't apply to worms
- Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?)
Phenotype ontology patternization
- Now have 676 terms patternized (27% of 2,506 terms total)
- Have reviewed the class hierarchy, collecting list of unexpected class subsumptions
- Issues to address collected here: https://docs.google.com/document/d/1IWtQbEQ-elM-U5SQyU4VfIH3vdJp6taVMGViIjGyVks/edit?usp=sharing
August 22, 2019
Obsolete ontology terms in Postgres
- There are currently 172 GO annotations in the GO OA referring to obsolete GO terms
- We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres