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
Planning and formulating a vision for the workplan- Planteome Ontologies
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