May 24th, 2016 Ontology Working Group Meeting

From Planteome.org
Jump to navigation Jump to search

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday May. 24th, 2016
  • Time: 8:15am PDT (GMT-7)
  • Attendees: LC, AM, MAL, BS, EA, PJ
  • Regrets: CM

Agenda

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

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

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

  • 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

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
  • 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

  • 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

Retrieved from "https://wiki.planteome.org/index.php?title=May_24th,_2016_Ontology_Working_Group_Meeting&oldid=3241"