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 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 done
  • 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
  • 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.
  • IBP team publishes the xls files on their site, need a single source for the latest trait dictionaries [1]
    • Resource platform, one page per crop, currently covers ten crops, e.g. cassava
    • Breeders can download the Excel format from this page, would be good to have the latest format there
    • Could store as a TSV file and converted to an Excel for the user consumption??
  • 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 Purls (CM): For the ontologies registered in the OBO library (PO, EO, EO), we can use the OBO purls, but the rest can be linked somewhere else.
    • Will depend upon what the existing users need
    • CG ontologies are named CO_XXX: for historical reasons, underscore may cause issues in the conversion from OBO to OWL- maybe remove the separator? (except for Rice phenotypes, which are GCP_XXX:)
  • Need to consider the long term goals- Will the ontologies be combined into one file which can be split into separate views?
  • Currently the entry point for the breeders and data mangers is the individual crop. One possibility is an entry point of the trait concept and be able to see the variation across crops
  • Breeders are the most interested in their respective crop species- it can be split into separate views or the ind ontologies can be combined into a unified Uber-Crop Ontology
  • Having 20-30 separate id spaces will complicate the integration into the Planteome AmiGO instance
  • One option may be a 'combined view' with a common id space that can be extracted for each crop species.
  • AmiGO users would be redirected back to the the CO page, using the universal resolver
  • Currently about 20 ontologies and more are being added, mapped to SoyBase and SGN etc

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. Done

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- Probably need to set up a meeting with them soon

4. Updates from Elizabeth- visit to CIMMYT

  • Main focus was on the IBP, and to align Leo's efforts with the Field Book needs
    • Modifications to the best practices and rules for the Trait Dictionary
    • Outcome: TD- add columns for the names of standard variables, with the property, method and scale combined
    • The standard variables will be used directly by the BMS to create the field books
    • Future improvement of the TD will the the addition of additional columns for the decomposition of the trait in entity and attribute (quality), this will facilitate the mapping to the reference ontologies. will these be ontology terms?

e.g. seed germination % = 'seed germination' and % will be scale of the method

  • Will the TDs still have a column for a mapping to the TO term? Currently added as a xref. May not be needed as the EQ can be inferred by the reasoner.
  • Breeders may not be comfortable selecting the TO term, so it most likely would not be filled in anyway
  • Have a lot of the logical definitions in the TO, and could be a mapping file between the two with the equivalence axioms
  • Will probably need to be at the level of curation, bridging file such as we have for the TO
  • Workplan- LV and Julio (?)- plan is to focus on adding the varibales to the 10 crops in the IBP (end June) followed by the addition of the EQ columns
  • Also met with Rosemary and Kate: Objective: To understand the curation process on wheat and maize data

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

  • All Hand's meeting on Thursday May 21st - Elizabeth will be gone next week-
  • Next Ontology meeting Tuesday May 26, 2015 8:00 AM (GMT-7:00) Pacific Time
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