WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2018 Meetings
- 2.1 July 5, 2018
- 2.2 July 19, 2018
- 2.3 July 26th, 2018
GoToMeeting link: https://www.gotomeet.me/wormbase1
July 5, 2018
Community Curation Mass Email update
- Emails (1 per paper) sent (most batches 75 at a time): 3,227 total
- June 11: 5
- June 20: 15
- June 21: 82
- June 22: 6
- June 25: 75
- June 26: 80
- June 28: 363
- June 29: 600
- June 30: 300
- July 1: 450
- July 2: 1,251
- Email success rate:
- 482 emails bounced (15%)
- 74 bounced emails had a backup email (2%)
- 292 bounced emails had no backup (12%)
- 88% of emails were successfully sent
- 52 out of office replies (2%)
- 482 emails bounced (15%)
- Total community annotations received since June 11: 718 (115 papers)
- June 13: 24 (3 papers)
- June 14: 8 (3 papers)
- June 17: 1 (1 paper)
- June 20: 13 (3 papers)
- June 21: 13 (4 papers)
- June 25: 13 (4 papers)
- June 26: 20 (7 papers)
- June 28: 17 (8 papers)
- June 29: 131 (8 papers)
- June 30: 4 (2 papers)
- July 1: 24 (5 papers)
- July 2: 184 (36 papers)
- July 3: 179 (20 papers)
- July 4: 27 (9 papers)
- July 5: 62 (pre-meeting) (4 papers)
- We may want to give people the option to "opt-out" either for a paper or for all emails or both
- May be good to ask SAB and users at meetings how they feel about these email requests
- Is it worthwhile to send requests about same paper to same people after a wait period?
SAB Literature Curation overview
- Outline: https://docs.google.com/document/d/1OUHoFYC3deEmZvgzmOtmxpt5iBrVio9sAZG66kRHwsE/edit?usp=sharing
- Want to ask about:
- Data type history, current types, priorities going forward?
- Community curation? Pilot results, should we expand?
- Data type vs. topic-based curation?
- Val Wood and PomBase have found topic-based curation to be more efficient
- Alliance working groups:
- data type focused
- Has affected our curation approach
WS267 Citace upload
- July 20th, upload to Hinxton
- July 17th, local CIT upload
- Some minor tag name changes
- Changes to GO_annotation to accommodate RO terms
Curation Status Form: flagged vs. validated papers
- Papers validated by curators are not necessarily considered flagged
- Author first pass forms: prepopulated with SVM, string-matches
- Curation First Pass: are forms still used?
- TFP (Textpresso first pass) not currently used?
July 19, 2018
- Val Wood would be interested in using SObA for PomBase
- Some immediate action items to deal with for expanding SObA to other ontologies and databases
- Maybe highlight leaf nodes with more granular information? Already available in unweighted view
- SAB suggested continuing site visits for WormBase tutorials
- SAB suggested host institution provide funds; we can at least ask
July 26th, 2018
Temporarily Withdrawn Paper (WBPaper00054672)
- A recently epublished Genetics paper (2018 Jun 26) "...has been temporarily removed at the authors' request, to allow review of a companion article. The article 301078 will appear in a future issue of GENETICS."
- We already have the PDF in postgres, but I don't see the paper in TPC yet.
- Is there anything we should do here? Temporarily remove the PDF from postgres?
Expression display on the anatomy page
- Suggested last week to have a way to display genes and associated evidences on the anatomy page. Rank order by number of evidences.
- Mock here: https://docs.google.com/presentation/d/1HE_QhJrs5oScmORdiAAdTxfavAnF6NUQhtJGWvcC7EQ/edit#slide=id.p2