Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Literature acquisition: still needs work | * Literature acquisition: still needs work | ||
** Using SVM vs. Textpresso search to find relevant papers | ** Using SVM vs. Textpresso search to find relevant papers | ||
+ | ** Species based SVM? Currently use string matching to derive different corpora | ||
+ | ** Finding genes and determining which species those genes belong to? |
Revision as of 18:16, 11 June 2020
Contents
Previous Years
2020 Meetings
June 4, 2020
Citace (tentative) upload
- CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
- Citace upload to Hinxton on Friday, July 10th
Caltech reopening
- Paul looking to get plan approved
- People that want to come to campus need to watch training video
- Masks available in Paul's lab
- Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
- Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
- Need to coordinate, maybe make a Google calendar to do so (also Slack)
- Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
- Also, need to submit who you were in contact with for contact tracing
- Form is used all week, and hold on to it until asked to be submitted
- If someone goes in to the office, they could print several forms for people to pick up in WB offices
Nameserver
- Nameserver was down
- CIT curators would still like to have a single form to interact with
- Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
- Still putting genotype and all info for a strain in the reason/why field in the nameserver
- We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
- Hinxton is pulling in CGC strains, how often?
- Caltech could possibly get a block of IDs
Alliance SimpleMine
- Any updates? 3.1 feature freeze is tomorrow
- Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
June 11, 2020
Name Service
- Testing site now up; linked to Mangolassi
- CGI from Juancarlos not accepting all characters, including double quotes like "
- Example submission that fails via CGI
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | α β Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “ ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
- Juancarlos will look into and try to fix
Alliance Literature group
- Textpresso vs. OntoMate vs. PubMed
- Still some confusion about what the different tasks can be performed in each tool
- Working on collecting different use cases
- Sentence-based search is big strength of Textpresso
- At latest meeting performed some large searches for OntoMate and Textpresso
- Literature acquisition: still needs work
- Using SVM vs. Textpresso search to find relevant papers
- Species based SVM? Currently use string matching to derive different corpora
- Finding genes and determining which species those genes belong to?