Ontology Working Group Meeting, Tuesday June 9th, 2015

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Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada) Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/834566681

  • Who will attend: LC, MAL, DWS, PJ, BS
  • Others?: , CM, GG
  • Regrets: JE, EA

Agenda

Summary from last meeting May 26th:

  • Report form UN meeting- BS- need links to publication
  • Updates underway to the Trait Template (Leo)
  • Discussion of the id space for Crop Ontologies
  • Discussion of the hierarchy of the CO Vocabs- not a problem if the terms have logical def'ns, just import as flat file.
  • Mapping to TO with Agreement Maker Light - see below
  • Progress on AmiGO2 browser development: http://dev.planteome.org/amigo
  • Updates on the transition to Github: https://github.com/Planteome

Other Updates, etc

  • OSU: Offer has been made to postdoc, waiting for confirmation, hopefully will start around the end of June, undergraduate student hired for summer, another one joining in August
  • NYBG: - Offer to postdoc candidate has been made, waiting for confirmation, graduate student will be joining to help with the imaging work, and a summer undergrad intern to help with the imaging
    • Also working with the AISO-Bisque team to generate images. Idea to do a use case study involving in situ analysis- leaf development or procambium development- link GO and PO to the image. Requires color recognition
    • NYBG has received a new 5 year DOE grant to work on ?? plants in Chile and California and the effects of nitrogen stress. DWS' group is doing the molecular genetic characterization and is planning to use the ontologies such as the Stress Ontology, should be able to link the expressed genes and GO terms to the stresses.

Report from Bioversity team: Marie_Angelique

  • MAL reported that the Github repository names for the CO will be changed to IBP from CGIAR- Done. New names are of the form: "IBP-wheat-traits"
  • The Xrefs to the TO term Ids in the wheat and maize ontologies have been updated to link to the TO on the Planteome site and XRef name has been changed from "Gramene Trait Ontology" to "Plant Trait Ontology". Files on Github should be updated to the newest version
  • Maize
  • Need to work on the coordination between EO, ENVO and CR (BS)

Introduce new Crop_Ontology_Pages on the wiki (MAL)

As a follow up from the discussion last week, Marie-Angelique has created an informative page on the wiki with information about the structure and format of the CO vocabularies.

  • Current structure of the Trait template (v.4)
  • Future structure of the Trait Template (v.5)

Agrovoc discussion- Part of FAO

  • Agrovoc is maintained by FAO as a SKOS Thesaurus.
  • Agrovoc covers area related to Agriculture, including food, nutrition, agriculture, fisheries, forestry, environment etc...
  • Agrovoc is mainly used by Agris (multilingual bibliographic database of FAO) to index bibliographic documents.
  • Johannes Keizer
  • GACs project info (from web)
  • GACS beta release [1]: "GACS explored the possibility of creating a global repository of concepts and terminology in the area of agriculture. This first beta is the result of the first experimental attempt, and it went very well! We now have a pool of concepts based on a mapping between AGROVOC, the CAB Thesaurus and the NAL Thesaurus."

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

Discussion Points:

  • Started building a Plant Disease Ontology by adding diseases and pathogens causal agents from the APS "Common Names of Plant Diseases" pages. Currently has branches for the causal agents, host species and plant diseases, linked by relationships
  • Adding in information from a number of additional sources now, as the APS is a bit outdated and not comprehensive e.g. NCBI, PHI-base, MaizeGDB, Rice SES, EOL
  • Disease names are based on the common name in use with the host species and disease causal agent type added. e.g. "Bacterial blight (APS)" --> rice bacterial blight disease (PDO).
  • Ideally we would like to have the disease causal agents and host plant species in a separate ontology or taxonomy that we would not be responsible for maintaining, such as NCBI, but it is too large to import into the AmiGO browser.
  • In order to create a slim we need to have a list of the names of the pathogens. One suggestion was to use the NCBI Taxon ontology, but we would need to create a slim.
  • Suggestion from MAL after the call: There is also the Uniprot Taxonomy which has URIs for taxon along with some synonyms.
  • Compare with approach in the Human Disease Ontology- flat list of diseases and the "Plant Infectious Disease Ontology"

Mappings from CO to TO: MAL

Tabled for next meeting....

Next Meeting Tuesday June 23rd

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