WormBase-Caltech Weekly Calls
From WormBaseWiki
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 on spreadsheet
- 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?
Alliance priorities?
- Transcription regulatory networks
- Interactions can focus on network viewer eventually
- May want different versions/flavors of interaction viewers
- May also want to work closely with GO and GO-CAMs
- Gene descriptions can focus on information poor genes, protein domains, etc.
Sandbox visual cues
- Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
- AFP and Micropub dev sites have indicators
- Could play with changing the background color? Maybe too hard to look at?
- Change the color of the title of the form, e.g. the OA?
- Will add red text "Development Site" at top of the OA form
Evidence Code Ontology
- Kimberly and Juancarlos have worked on a parser
- Will load into ACEDB soon
June 18, 2020
Undergrad phenotype submissions
- Chris gave presentation to Lina Dahlberg's class about community phenotype curation
- Class took survey about experience with presentation and experience trying to curate worm phenotypes
- Survey results: https://www.dropbox.com/s/00cit5aitv8yu27/Dahlberg_class_survey_results.xlsx?dl=0
- Some students didn't benefit, but most did; nice feedback!
- Lina intends to publish/micropublish the survey results so please don't share
Special characters in OA/Postgres
- There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
- In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
- It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters