Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
== June 4, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
=== Citace (tentative) upload ===
 
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 
* Citace upload to Hinxton on Friday, July 10th
 
  
=== Caltech reopening ===
+
==August 6th, 2020==
* Paul looking to get plan approved
+
===Experimental conditions data flow into Alliance===
* People that want to come to campus need to watch training video
+
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
* Masks available in Paul's lab
+
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
+
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
+
*So for data flow into Alliance:
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
+
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
+
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
* Also, need to submit who you were in contact with for contact tracing
+
* How do we handle genetic sex? Part of condition?
* Form is used all week, and hold on to it until asked to be submitted
+
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
+
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
 
 
=== 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::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; 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.
 

Revision as of 16:36, 6 August 2020

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August 6th, 2020

Experimental conditions data flow into Alliance

  • Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
  • We use the WB Molecule CV for Inducers and Modifiers in disease annotation
  • Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
  • So for data flow into Alliance:
    • In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
    • Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
  • How do we handle genetic sex? Part of condition?
    • Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
    • Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex