Difference between revisions of "WormBase-Caltech Weekly Calls"
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− | + | ||
= 2020 Meetings = | = 2020 Meetings = | ||
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=== Caltech reopening === | === Caltech reopening === | ||
* Paul looking to get plan approved | * Paul looking to get plan approved | ||
− | * People that want to come to campus | + | * People that want to come to campus need to watch training video |
* Masks available in Paul's lab | * 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 | * Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room | ||
Line 56: | Line 56: | ||
=== Nameserver === | === Nameserver === | ||
− | * Nameserver down | + | * Nameserver was down |
* CIT curators would still like to have a single form to interact with | * 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 | * 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 | * 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 | * We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out | ||
− | * Hinxton is pulling in CGC strains | + | * 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 |
Revision as of 18:57, 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 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