Ontology Working Group Meeting, Tuesday May 12th, 2015

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Agenda

Who: LC, JE, EA, MAL, CM Absent: PJ, BS, DWS etc

  • Connection details:
    • Topic: Planteome Ontology WG Meeting
    • Time: May 12, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada)
    • Join from PC, Mac, iOS or Android: https://zoom.us/j/774772939

Prelude: AmiGO2 browser work http://dev.planteome.org/amigo

1. Welcome to Marie Angelique Laporte- Bioversity

  • Marie Angelique has a background in Bioinformatics (MSc) and Ontology Engineering and Plant Functional Traits (PhD).

Previous experience includes:

  • Ontologies for automatically classifying remote sensing images
  • TRY database (https://www.try-db.org/TryWeb/Home.php), biggest database of plant traits, thesaurus in SKOS
  • FAO on the AgroVoc and GACS projects. GACS involves USDA, FAO and CABI (UK)
  • AgroVoc is a thesaurus of agriculture in the broad sense, 25 languages, but no traits, used to index documents in Agris, widely used by bibliographic databases
  • Worked previously with Elizabeth on the Crop Ontology project, working mostly in SKOS, modelling the ontologies in SKOS

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

  • Plant Trait Ontology repo has been created, along with the SVN history, - testing is underway

(Big Thanks to Justin E for his hard work and perseverance on this, with assistance from the Chris and Seth)

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

Repositories:

  • Need to rename the CGIAR/IBP prefix for their files. EA will clarify with her colleague at the IBP.
  • EA will send LC her Github id so we can add her to the organization
  • Currently, the the owl file is derived from the OBO file using OWL tools- OBO2OWL-
  • CM "Committing the derived files to the VCS, might not be the best strategy as we move forward.", eventually the ontology development will move to owl.

EA- 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
  • IBP team publishes the xls files on their site, need a single source for the latest trait dictionaries [1]
    • one page per crop, currently covers ten crops, e.g. cassava]
  • Could load the OBO, TSV and SKOS files together in the repo and use the wiki and issue trackers
  • EA question: What is the projected release date for the CG repos?
    • Can give them a link to the "master" (similar to the "head" in SVN)
    • CM: Should avoid giving urls to a particular version, but could give them a purl that always resolves to the latest version, could be part of the OBO library or elsewhere. Could have a release process where the files are put onto a web-visible file server somewhere.
  • Perhaps we could set this up so that the files are served from the CO directly for the users
    • MAL: It is already set up for the CO, but would just have to be pointed at the Github repo
  • EA: There is a developer at the IBP who is ready to start working on this: Brandon Took

Setting up the Purls (CM):

  • For the ontologies in the OBO library, we can use the OBO purls, but the rest can be linked somewhere else.


Action Items:

  • Move the rest of the files from the SVN folder (JE)
  • Remove the other test repo "planteome-ref-ontologies" (JE). LC transferred the only comment (from CM) to the plant-trait-ontology repo.
  • JE will also work on getting the TO development browser (http://palea.cgrb.oregonstate.edu/amigo/TO_dev) set up to read from the OBO file on the GitHub, rather than the one on the SVN.

3. Updates on hiring:

  • At OSU- have been interviewing candidates, PJ may be able to make a decision later this week or early next week.
  • No report from NYBG- DWS not on the call
  • No report from Aberystwyth- JD and GG not on the call

4. Updates from Elizabeth- visit to CIMMYT

TBA

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

Tabled for next meeting

6. Discussion of format and schedule for future meetings

7. Other items?

  • Next meeting Tuesday May 26, 2015 8:00 AM (GMT-7:00) Pacific Time
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