WormBase-Caltech Weekly Calls
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Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2020 Meetings
January 9, 2020
Phenotype Curation Requests
- 1,229 emails sent Dec 3-6, 2019
- Received 194 annotations from 40 papers and from 37 distinct community curators
- 37 papers requested, 3 additional papers annotated
- 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
- 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
- 43 bounced emails
- 2 resent to new addresses
- 5 have backup email addresses (also sent)
Worm Area Meetings
- Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
- Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)
Reference widget Textpresso linkouts
- Now live on WormBase, WS274
- GitHub ticket
- Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes
- Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10
- Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10
- Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10
- Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10
- Known issue: searching on synonyms in addition to public name; Sibyl will fix
- Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10
- Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix
- Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10
- Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell
- Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10
- Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10
- Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym
- Rearrangement example: https://wormbase.org/species/all/rearrangement/sDp3#03--10
- Molecule example: https://wormbase.org/resources/molecule/WBMol:00003650#03--10
- Process examples:
- Michael has improved phrase search and combined supplemental documents with main paper documents; should roll out soon
WS276 Citace upload
- Hinxton upload Jan 31, 2020
- Citace upload on Tuesday, Jan 28, 2020
Author First Pass paper
- AFP resent to Database
- Automated descriptions about to be sent
- SObA, write for micropub? One micropub on SObA and another on comparative SObA
Noctua/GO-CAM
- New version of the Noctua form released next week
- Imports from WormBase?
- Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
- Need to work on annotation history on back end
- May have face-to-face meeting in Pasadena
Variation curation
- Have a backlog; Paul D is assigned but has been overwhelmed
- Have asserted this as a priority
- We have the allele-sequence form; where does it go? Hinxton
- Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
- Need to integrate curation with the Variant Effect Predictor (VEP) pipeline