Ontology Working Group Meeting, Tuesday May 26th, 2015

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Agenda

Who: LC, MAL, CM, PJ, BS

Absent: EA, JE etc

  • Connection details:

Topic: Planteome Ontology WG Meeting

Update from Barry on the UN Initiative:

  • UN is adopting ontologies to describe indicators for sustainable development
  • Barry is workimg with Ramona and Pier B
  • Goals have been published
  • Wide ranging set of goals to encompass agriculture, health, environment
  • 'Plant Stress Ontology' is of interest
  • Plant Experimental Conditions Ontology (PECO/EO)-Plant Stress Ontology- aspects of overlap

Report from Bioversity team

Marie Angelique:

  • Leo is working on adding columns in the trait template for entity and attribute- will be useful for linking to the reference ontologies
  • One trait dictionary per crop, Excel format, defined columns, uploaded in CO system and then exported as OBO and SKOS
  • Not sure how to deal with disease resistance - what are the entity and attribute ? Link to PDO terms for the disease name
  • Question of sharing the trait dictionary file- should be stored on GitHub, at least for the four focus crops: cassava, wheat, maize, rice
  • Currently the trait dictionaries are stored in Dropbox, waiting for curator validation and approval
  • Ideally, the working versions could be stored on GitHub

Discussion of the id space for Crop Ontologies:

  • Having 20-30 separate id spaces (or namespaces) can be done, but is not too convenient, they would have to each be registered in the OBO library
  • A single common prefix would be preferable, can be something like CO_IBP:XXXXXXX
  • The numbering scheme could have a leading number with the taxon id (from NCBI??), or use the existing numbering scheme (e.g. cassava CO_334:xxxxxxx)
    • How would we deal with the crop ontologies that have more than one for an individual species? Only wheat and banana
  • All the codes are listed on the GCP Pantheon Page: [1]- "This is out of date, as the GCP project has ended
  • Wheat are both the same: CO-321, but the banana ones are different

Example:

Report from OSU

  • Laurel, Justin E and Pankaj
  • Progress on AmiGO2 browser development: http://dev.planteome.org/amigo
    • Report from All Hands meeting: Working on creating an planteome importer owl file to simplify the loading of the ontologies via the golr Makefile. Working on a catalog xml file to redirect URI in the importer OWL. (JE)
    • The issue with loading both the Plant Environment (EO) and Plant TO where loading both causes the EO to disappear from AmiGO- this appears to be fixed
  • From Justin Elser: Let me know if any other ontologies are missing. I am going to start working on how to get a smaller slice of the ncbi one loaded up.
    • Is including the NCBI a priority? How is the slice being created? Looks like only 68 terms so far
  • Missing from current version:
    • GO-BP, MF and CC???
    • ChEBI
    • Need to remove Uberon
    • Can we just have a slice of the Cell Ontology?

Updates on the transition to Github: https://github.com/Planteome

  • Model is a separate repository for each ontology under the organization of the Planteome

Plant Trait Ontology

  • Plant Trait Ontology repo has been created, along with the SVN history - testing is underway
  • File was renamed "plant-trait-ontology.obo"
  • TO development browser (http://palea.cgrb.oregonstate.edu/amigo/TO_dev) is now set up to read from the OBO file on the GitHub, rather than the one on the SVN
    • This updates nightly and is a useful tool for the curators
    • Now also includes the PDO
  • To-Do:
  • Need to move the other associated other files from the SVN: cross product files, trait lists, owl file etc
  • Will need to change where collaborating sites are pulling the TO from: Bioportal, EBI OLS, OBO Foundry, Gramene (?), others?

Action Items:

  • Move the rest of the ontology files from the SVN folder (JE): which ones are the priority?
  • Remove the other test repo "planteome-ref-ontologies" (JE). LC transferred the only comment (from CM) to the plant-trait-ontology repo.

Other Repositories on GitHub:

  • Need to rename the CGIAR/IBP prefix for their files. EA will clarify with her colleague at the IBP. - Any news? None yet

From the last meeting:

  • Discussion of including the trait dictionaries in the GitHub repos:
  • Managing the files as excel files with the users, and this can be converted to a simple OBO file using MAL's script (for loading on the CO site)
  • Could be uploaded as the OBO or a TSV file- closer to the source and works well with Github
  • Could load the OBO, TSV and SKOS files together in the repo and use the wiki and issue trackers

Updates on new hires

  • Post-doc position at OSU- Six candidates were interviewed and an offer has been made, new person should join in late June or early July.
  • Post-doc position at Aberystwyth University, UK- GG is advertising, closing date is mid-June
  • Post-doc position at NYBG- No news on this yet

Updates on work on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)

Tabled for next meeting

Discussion of format for meetings

- Rotate hosting and presenting

Schedule for future meetings:

  • Next Ontology meetings- Every other Tuesday 8:15 AM (GMT-7:00) Pacific Time
    • June 9th, 2015
    • June 23rd, 2015
    • July 7th- Laurel is on vacation, but someone else can host?
    • July 21st
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