May 24th, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday May. 24th, 2016
• Time: 8:15am PDT (GMT-7)

• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/400883197

• Attendees: LC, AM, MAL, BS, EA, PJ

• Regrets: CM

• File:Ontology Zoom Meeting 5-24-16 audio only.m4a
• File:Ontology Zoom Meeting 5-24-16 video.mp4

Agenda

1. Update from PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France

• Planteome members attending: LC, MAL, AM, EA, GG, JD

• Reports from the meeting:
• Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home or http://tinyurl.com/hzsho6v

• About 70+ Participants attended: PhenoHarmonIS_List-of-participants

• Link to the agenda: PhenoHarmonIS Agenda

Planteome Presentations:

• Monday afternoon: oral presentation (10 mins) LC: "The Planteome Project"

• Monday late afternoon: Poster presentation- LC, AM, MAL: Planteome Poster

• Tuesday morning: oral presentation (10 min)- AM: "Annotating germplasm using the Plant Trait Ontology in Planteome"

• Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"

• Tuesday afternoon: Hands-on Session (2.5 hours)- LV:
  • Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam
  • Feedback on the TD template

• Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop
  • 9 participants, 7 crop species:
    • Nordine El- Hassouni - CIRAD - rice
    • Trushar Shah- IITA, Kenya - cassava, cowpea, and banana
    • Jeffery Detras - IRRI - rice
    • Reinhard Simon - Centro Internacional de la Papa (CIP), Peru - potato/sweet potato
    • Manuel Riuz - CIRAD, France / CIAT, Colombia - rice
    • Cecile Grenier - CIRAD/CIAT Colombia - rice
    • Ashley DuVal - Mars, Inc USA - cacao
    • Anthony Bolger - RWTH Aachen University - Institute for Biology 1, Germany
    • Astrid Junker - IPK Gatersleben, Germany - HTP phenotyping
  • Outcomes:
    • No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.
      • the work is never truly "automated" -
      • everything requires a human checkpoint.
    • reference ontology space makes it very difficult to standardize workflow
      • no one is an expert on all things we attempt to capture
      • collaborating with other application ontologies or working groups is necessary
    • High throughput phenotyping requires an entirely new standard vocabulary
      • perhaps could be captured with a new set of "methods"?
      • Only a few measurements are taken
      • most of the "traits" are calculations and inferences

2. Planning for ICBO/BioCreative Conference

• Link to program: ICBO + BioCreative Program

3. Planning for Post-ICBO Curator Workshop

• The idea is this would be similar to the one held at OSU in November 2015

• Dates??
• Who is interested in attending ?
• Should we send out a survey?

• If people come for the week of ICBO, are they able to stay for an additional 5 days to a week?

• Other options: Perhaps do in September before OSU starts?

4.Planteome Ontology Updates

• "Soft Release" of Plant Ontology, still working out a few issues for the Plant Trait Ontology

Upcoming Meetings and Workshops

BioOntologies SIG of the Intelligent Systems for Molecular Biology (ISMB); July 8-12, 2016, Orlando, Florida

• Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
  • Short papers, up to 4 pages (will be published in JBMS)
  • Poster abstracts, up to 1 page
  • Flash updates, up to 1 page

7th International Conference on Biological Ontology and BioCreative 2016 Aug 1st to 4th, Corvallis, OR

• Link to program: ICBO + BioCreative Program
• Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589