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?

This may not be too much of an issue as it looks like they already have a common #.

Example: Wheat Trait Ontology: CO_321: http://www.cropontology.org/ontology/CO_321/Wheat

Wheat Plant Anatomy and Development Ontology: http://www.cropontology.org/ontology/CO_121/Wheat%20Plant%20Anatomy%20and%20Development%20Ontology

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?

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

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

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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