Ontology Working Group Meeting, Tuesday July 21st, 2015

Time: 8am PDT (GMT-7:00) Pacific Time (US and Canada)

• In attendance: LC, MAL, AM, EA

File:Ontology WG July 21st audio only.m4a

- Participants: Maria-Angelique, Elizabeth Arnaud, Lol, Austin

Priority 1

• Improving the IBP/CO trait dictionaries with trait names and methods and scales from the curators
• Will eventually make sure the trait is mapped to the ontologies
• lentil, pigeonpea, cowpea, 3 dictionaries need to upload
• OBO files generated computationally are intersection of trait and scale
• By the end of July: all trait dictionaries revised and sent to BIPP (no idea on this acronym)

   "Running a little behind schedule, but should have 10 done by end of Aug."

• For rest, waiting on validation of variables, and structure by the curators

   "variables = how the trait is measured."

• MAL- working on the file and OBO structure

   "still wanting to work on the mapping"
   - Mapping will not be a separate file, it will be imbedded
   - Needs to be validated first (the trait dictionary).
   - some already on Github
 - trait name, variable name, scale

- Priority 2:

 "PDO"
 - Disease ontology needs reviewed.
 - plan for overall structure needs made (next week)
 - Share google spreadsheet with us from the CO, done by french group
 - need to unify a plan from the 3 ontologies
 - Early August deadline

- OSU's targets

 - look at stress traits in TO
   - TO has been switched to Github
     "no longer updating the SVN"
   - Need to migrate the trackers
   - 
 - migrate PO and EO
 - identify overall plan for PDO pathogens
   - unclear as what should be a synonym 
 - Migrate PDO

• JE- working with seth and chris to fix AmiGO2

 - OWL conversion from OBO in process

• Upper level conversation

   - what dictionaries become ontologies?

Workshop planning

 - PJ and EA need to figure out who is getting trained on OWL
 - sessions for mapping?  Or just ontology demo
 - AM + MAL 
 - train for OWL
   - Need to know when
   - Austin
   - Afola Agbona ("Afolabi, Agbona (IITA)" <A.Afolabi@cgiar.org>)
     "cassava guy"
     - only one still using OBO
   - PAG meeting another option for OWL training
     "not ideal"
   - Teach someone OWL in 3 days?  This is tough for people with little exposure
   - need goals
     - Clear goals will be key 
       - nama working with afula, and soon to CIP
       - should ask her how far everyone she works with needs training in.
       - Maybe just CIP and banana people need the training
       - possible that no one needs to be upgraded
     - Better to try and teach OWL, or just stick to teaching OBO
     - if they are going to work in Planteome, OWL would be nice
     - the endgame of each person should determine what should be taught (OBO or OWL)
     - Background can decide what each person needs
       - bioinformaticist- easy to learn programs, tougher to learn biology
   - format
     - trait dictionary
     - excel
     - ontology format?
       - enriched relationships

Schedule:

- rice/wheat - still getting worked on

 "end of July is the goal"
 - rosemary and kate in charge of this
 - Kate- working on the dictionary and data management
 - rosemary is in charge of it

• Get George to join an ontology meeting

 "also his postdoc"
 - just get him in one of these meetings, and ask him about what he's doing, and find out if he can help us.
 - been difficult because of everyone's schedule.
 - Lets get a meeting going at PAG