Crop Ontology

Crop ontology, the GCP-wide use of controlled vocabulary for both genotypic and phenotypic crop data, is a point of continuous attention for the GCP. Ontology is concerning the standarized use of terms and codes ( the vocabulary ) on type of experiment, crop type, and developmental stage.
The GCP strives to inter-operability for data submission, retrieval and storage. To this end not only the vocabulary itself needs to be standarized, but also the internal relationships between the keywords need to be defined. In this way the GCP crop ontology serves to share crop information among researchers.
The GCP ontology thus provides a controlled vocabulary and formalized relationships, to enable inter-operability for the retrieval of crop data (both genotypic and phenotypic). A general and crop-specific GCP ontology is being developed by crop teams involving GCP and external scientific experts. Particular emphasis is given on plant anatomy, developmental stage, trait and phenotype ontology for the selected priority GCP crops. It provides the exact meaning of terms related to phenotypes described by crop physiologists, plant breeders and other crop scientists.The GCP crop ontology was developed to semantically characterize both new and historic crop datasets. The systematically formatting and annotating of these data sets enables improved data management, retrieval and accessibility.

A crop-development ontology has already been initiated for chickpea, maize, Musa, potato, rice and wheat traits.

A 2009 poster displays the progress made in the development of the GCP crop ontology.

The resulting omtology terms and codes are reflected in the GCP approved data templates. These GCP approved data templates are mandatory to register GCP data, and are a prerequisite to attain high quality GCP data sets. 

The GCP crop ontology is going to be integrated into a data-entry user interface or data templates wizard as picklists. This will greatly facilitate data annotation. In addition, the GCP ontology is intergrating with Plant Ontology (PO) and Gramene (Trait Ontology, TO; Environment Ontology, EO) to develop a common, internationally-shared crop trait and anatomy ontology.
The GCP ontology and platform are described on the pantheon website (http://pantheon.generationcp.org).
The CropForge software project management site (http://cropforge.org/projects/gcpontology) provides both the latest releases and previous versions of ontology flat files, which describe the terms, relationships, definitions, software tools, forums, and mailing lists for communication among collaborators.

A new, well-designed look-up service, called the GCP Ontology Browser  or Crop Ontology look-up service, is now online.
Several ontologies ( in total 46 ) for different crops as well as for a variety of experimental data, can be browsed or searched with this service. After selecting one, several or all ontologies, queries can be made using a keyword as ontology search term (including obsolete terms). The query result will display the approved definitions and IDs. A search on ID will display the definition and the origin of the ontology for this ID. The resulting OBO-formatted ontology file can be downloaded (OBO: open biomedical ontologies).


References
Shrestha, Rosemary; Mauleon, Ramil; Simon, Reinhard; Balaji, Jayashree; Channelière, Stephanie; Alercia, Adriana; Senger, Martin; Manansala, Kevin; Metz, Thomas; Davenport, Guy; Bruskiewich, Richard; McLaren, Graham; and Arnaud, Elizabeth. 2009. Development of GCP Ontology for Sharing Crop Information.
3rd International Biocuration Conference, 17 April 2009
doi:10.1038/npre.2009.3087.1

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