Difference between revisions of "WormBase-Caltech Weekly Calls"
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=== Obsolete ontology terms in Postgres === | === Obsolete ontology terms in Postgres === | ||
| − | * There are currently 172 GO annotations in the GO OA referring to obsolete GO terms | + | * There are currently 172 GO annotations in the GO OA, 94 in Expr OA, and 54 in Pic OA referring to obsolete GO terms |
** https://docs.google.com/spreadsheets/d/14iG3-s0GrZ3_W87iOjD6tZiQiUJklRRjgs6ARFWi9E4/edit?usp=sharing | ** 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 | * We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres | ||
| + | |||
| + | === Community phenotype requests === | ||
| + | * Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019 | ||
| + | * 2,627 emails/papers requested | ||
| + | * 112 emails bounced; 4 resent to new addresses | ||
| + | * 205 Phenotype OA community annotations; 55 RNAi OA annotations, from 47 papers, by 42 distinct community curators (so far) | ||
| + | * Also, 3 worksheets submitted, for 4 papers | ||
| + | * 35 papers flagged as not having phenotypes | ||
| + | * 86 papers with responses (3% response; still early) | ||
| + | * Need to coordinate with the AFP request pipeline | ||
| + | |||
| + | === GO slim terms === | ||
| + | * SObA highlights Alliance slim terms, but doesn't correspond to ribbon | ||
| + | * Want to use same slim terms used for ribbons | ||
| + | * Add slim terms into ACEDB? One option | ||
| + | * Ribbon order of slim terms is an issue | ||
| + | * Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code | ||
| + | * Will have to manually synchronize with Alliance if Alliance changes its ribbon | ||
Revision as of 18:30, 22 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, 94 in Expr OA, and 54 in Pic OA referring to obsolete GO terms
- We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres
Community phenotype requests
- Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019
- 2,627 emails/papers requested
- 112 emails bounced; 4 resent to new addresses
- 205 Phenotype OA community annotations; 55 RNAi OA annotations, from 47 papers, by 42 distinct community curators (so far)
- Also, 3 worksheets submitted, for 4 papers
- 35 papers flagged as not having phenotypes
- 86 papers with responses (3% response; still early)
- Need to coordinate with the AFP request pipeline
GO slim terms
- SObA highlights Alliance slim terms, but doesn't correspond to ribbon
- Want to use same slim terms used for ribbons
- Add slim terms into ACEDB? One option
- Ribbon order of slim terms is an issue
- Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
- Will have to manually synchronize with Alliance if Alliance changes its ribbon
