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: wheat, rice, maize, Tree species (cacao), Musa, barley, sorghum, potato, sweet potato, yam
  • Feedback on the TD template

• Notes:
  • Wheat TD version #5 was uploaded just prior to the PhenoHarmonis meeting (to where?)
  • Rosemary shared the validated mappings duringt he workshop, so MAL will be able to upload onto the Planteome Github
  • Rice almost done
  • Reinhard is almost done with the TDs for the potato, sweet potato

Leo is leaving the project as of May 30th- lack of funds and moving on to other things

• Leo working on the guide lines for the TDs
• Who will Continue work on TD, or is it dying?- Julian taking a few crops over,
• EA, and MAL will be working on the remainder in their free time.
• EA wants to hire someone new, but no funds, is applying for several grants. Agroportal has no funding .
• H2020 program not too secure funding
• Genticin (??) Platform more reliable
• PJ offered to talk to Leo about options if he is interested

• Weds afternoon- Visit to https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform
  • High throughput phenotyping platform, rotate through different crop experiments
  • Pascal's database,
  • should try to access the list of evaluation data and the traits
  • Analyzed final data, to test on
  • how to address HTP phenotyping experiments?
  • Follow-up with Astrid Junker, list of traits? :
  • Francois Tardieu - leader at PhenoArch- LC will contact

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

Discussion from meeting:

• Data sets with multiple reps of measurements- How do we capture this?
• single germplasm annotation with stable phenotypes
• multiple reps and/or multiple experiments
• GO - gaf2 has no way of capturing that
• TASSEL scheme or database schema would handle this??
• limit on our side
• Do we need a new evidence code to associate genotype and phenotype??
  • experiment average of reps, average of locations
• column 16 - new relationship - tells users that the score was averaged somehow
• Variables from CO should indicate if it is an average or a single datapoint
• MAL sent a rice data set from Cecile Grenier (CIRAD/CIAT Colombia) which contains replicated data measurements

2. Planning for ICBO/BioCreative Conference

• Link to program: ICBO + BioCreative

• BS will arrive the day before, and leave early on Friday
• Currently have 67 submissions, but only 12 people have registered
• PJ will send a reminder to the authors of the submitted papers:
  • 1. In order to have your accepted submission included in the proceedings ​of the meeting, ​at least one author from each paper must register for ​the meeting​.​
  • 2. Where authors are involved in more than one submission, a distinct author must register for each accepted paper.
• good to have a number of people to support the workshops

• Plant Biodiversity Workshop
  • Title: Tools and Applications for Data Standards and Knowledge Sharing in Plant Biodiversity
  • Workshop type: Project Workshop (Project specific talks + Discussions)
  • Organizer: Laurel Cooper, Oregon State University
  • Co-organizer(s): Dennis Wm. Stevenson, Chelsea Specht, Marie-Angelique LaPorte

• Will set up a meeting with the co-organizers later this week.
• Link to Google Doc: https://docs.google.com/document/d/1GK51a9J5v91nP7OiIB9XuEbDZyo3FmhlJ4N4_MqvvW0/edit?usp=sharing

3. Planning for Post-ICBO Curator Workshop

• The idea is this would be similar to the one held at OSU in November 2015
• Venue: Alumni Center, just need a single room

• Proposed Dates: Three days: Monday Aug 8th to Weds Aug 10th, (or possibly right before the ICBO mtg?), or maybe Friday May 5th to Sunday May 7th??
  • Lol out Sunday Aug 7th for family responsibilities
• If people come for the week of ICBO, are they able to stay for an additional 5 days to a week? BS: no, MAL: ?

• People can come for the ICBO meeting and then stay for the plant-specific, more hand's on session
  • People have to stay through the weekend- we can pay for the stay in the dorms
  • If they come to this meeting, we can pay for their ICBO registration.

• Who is interested in attending?- Ideally 5-6 people
  • Indian researcher has contacted - working to get TO terms added, rice gene annotations, PJ will send his info to LC

• Target wheat and maize researchers, primarily from CIMMYT ?, also rice
  • CIMMYT/CGIAR Characterization of Maize Page
• EA: Are you interested in genebank data or evaluation data? It is managed differently- starting with genebank data and can also work with evaluation data- different people- should discuss with Kate, CIMMYT will refer to the data managers, Kate could suggest a person from scientific team.

• Focus on the people who are developing the TDs, annotations to germplasm, gene bank repositories, traits
• Good to set the standards,
  • Julian Pietragalla- IBP, Mexico
  • Kate - maize data manager, entry point to
  • Rosemary Shrestha - wheat data manager
  • Need an additional wheat/Maize breeder- ask Julian??

• Could also go through the Wheat IS to find people with data sets...

4.Planteome Ontology Updates

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

Upcoming Meetings and Workshops

9th International Conference on Formal Ontology in Information Systems (FOIS 2016), Annecy, France on July 6th-9th, 2016

• http://www.iaoa.org/fois2016/

• BS is attending
• most technically sophisticated ontology meeting, non computational
• what relations should we use, how are ontologies taught?, what an object is?
• High level ontology design and engineering
• Planteome could present results in 2018, when we have some results - held every two years

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