Ontologies

Community of Practice

Welcome
Engage
News
Resources
Events

Welcome
Engage
News
Resources
Events

Welcome!

Community members gathered at the 2018 PhenoHarmonIS workshop, the biennial event hosted by the Ontologies Community of Practice.

The Ontologies Community of Practice brings together researchers, modelers, information specialists, data managers, and ontology experts from the CGIAR research network, academia, and the private sector, thus creating a critical mass of expertise to tackle the major issues related to semantics for FAIR data in agri-food science.

The CoP provides the ideal forum for co-learning and knowledge exchange on ontologies and for guiding consistent data annotation, as well as the deployment of quality ontologies in databases and repositories. The CoP stimulates exchanges between domain experts and experts in ontology design, knowledge modeling, ontology-driven applications, and semantic web technologies

The CoP is led by the Alliance of Bioversity International and CIAT and was launched by the CGIAR Platform for Big Data in Agriculture.

This webpage presents the different working groups of the CoP, lists the tools developed by CoP members, and displays the latest news. For further details on the CoP’s goals and achievements, read the paper published in Patterns.

Ontologies are important to all data-driven research, and this CoP serves as an intermediary to assess common goals, needs, and opportunities across the CoPs and working groups of the Platform.

The Ontologies CoP harnesses in-house and external expertise in the development of ontologies and supports the other BIG DATA CoPs toward finding adequate ontologies for data description. The Ontologies CoP has the objective of establishing best practices and guidelines in the selection of ontologies of reference and developing and curating ontologies in the agri-food domain.

The Ontologies CoP works to include data generated by the latest technologies and to expand beyond crops to data on fisheries and aquaculture, livestock, socio-economics, water management, and agroecology. The Ontologies CoP’s thematic working groups currently develop ontologies such as the Crop Ontology (CO), the Agronomy Ontology (AgrO), and the Socio-Economic Ontology (SEOnt).

Get in touch

CoP Lead

Elizabeth Arnaud | Email
Elizabeth leads the Ontologies CoP and is a scientist at the Alliance of Bioversity International and CIAT in Montpellier, France

CoP Communication

Céline Aubert | Email
The International Food Policy Research Institute, France

Read the Ontologies CoP paper

Visit the Ontologies CoP YouTube channel

Engage with the Community

BE INFORMED

Tune in to the latest CoP updates by subscribing to our newsletter.

ENGAGE

Interact with community members through our LinkedIn Group.

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CONTRIBUTE

Share your expertise in our working groups.

See our Working Groups

Working groups

Plant Phenotypes Ontologies

The Plant Phenotypes Ontologies WG develops and maintains the community-built Crop Ontology (CO) compiling traits and variables per crop species. CO fosters the standardization of data including data recorded on phenotyping platforms, collected during food processing, generated from consumers’ surveys and used to describe ecological interventions.

This work enriches the species-agnostic reference ontologies of the Planteome project:

The Alliance of Bioversity International and CIAT leads the working group in collaboration with CGIAR centers, Boyce Thompson Institute, members of ELIXIR-EXCELERATE, Phenome Projects, and the Jaiswal Lab of the Oregon State University.

See Ontologies Development Leaders

See Ontologies Development Partners

See CGIAR Crop Ontology Curators

Guillaume Bauchet
Breeding Bioinformatician, Boyce Thompson Institute
Banana ontology

Jing Yu
Genome Database Curator, Washington State University
Cotton ontology

Vilma Rocio Hualla Mamani
Data Management Specialist, International Potato Center
Sweet potato and potato ontologies

Abhishek Rathore
Principal Scientist and Theme Leader, International Crops Research Institute for the Semi-Arid Tropics
Chickpea, finger millet, groundnut, pearl millet, pigeonpea, and sorghum crop ontologies

Roma Rani Das
Statistician, International Crops Research Institute for the Semi-Arid Tropics
Chickpea, finger millet, groundnut, pearl millet, pigeonpea, and sorghum crop ontologies

Praveen Reddy Teegala
Programmer-cum-Systems Analyst, International Crops Research Institute for the Semi-Arid Tropics
Chickpea, finger millet, groundnut, pearl millet, pigeonpea, and sorghum crop ontologies

Afolabi Agbona
Data Manager, IITA
Cassava and yam ontologies

Noel Madalla
Bioversity International
Banana ontology

Rosemary Shrestha
Data Coordinator, CIMMYT
Wheat and maize ontologies

Marie Angélique Laporte
Associate Scientist, Bioversity International
Global Curator

Julian Pietragalla
Regional Deployment Manager, Latin America, Integrated Breeding Platform
Global Curator

Fish Ontology

The Fish Ontology Working Group aims to enable easy aggregation and analysis of data. This will be done by describing the fisheries terminologies that enhance data quality, thus ensuring that fisheries-related datasets can be integrated and used in more efficient ways.

The Fish Ontology Working Group was formed in April 2019 and is currently led by WorldFish with the support of Bioversity International.

Agronomy Ontology

AgrO, the Agronomy Ontology, provides semantically described agronomic terms to facilitate the standards-annotated collection, storage and use of agronomic data, enabling easy aggregation and analysis. AgrO is being built using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO. A key use case for AgrO is the Agronomy Field Information Management System (AgroFIMS) that enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO. This effort involves multiple centers and is lead by IFPRI and the Alliance of Bioversity International and CIAT.

Socio-Economic Ontology (SEONT)

A socio-economic ontology of controlled vocabularies, classifications, and concordances that allow standardization of key indicators. The key is that SEONT is a ‘living’ ontology, since the high variety of socio-economic data implies that it will need to evolve continuously.

The ontology has been developed by CGIAR researchers from the International Food Policy Research Institute (IFPRI), Bioversity International, and the International Maize and Wheat Improvement Centre (CIMMYT). The working group on the socio-economic ontology works in close collaboration with the SED CoP led by Gideon Kruseman. The working group is led by Soonho Kim of IFPRI.

Interested in contributing to the development of these ontologies?

Community News

Webinar - An introductory journey to the Virtual Knowledge Graph approach to data access and data integration

Resources

Tools & Publications

Ontology registries

Agroportal offers a reference ontology repository for agronomy.
Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis.
Ontology Look up Service of the European Bioinformatics Institute (EBI-EMBL)

Ontologies developed/curated by the CoP

Agronomy Ontology provides standardized terms to describe agronomic practices, techniques, and variables used in agronomic experiments.
Crop Ontology Curation Tool enables you to browse the Crop Ontology, search for specific terms and access the definition, as well as additional information.
Planteome provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes.

View tools

Fairsharing is a curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.
Obo-Foundry has the objective to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate.
Wheat Data Interoperability Guidelines provides a common framework for describing, representing, linking and publishing wheat data with respect to open standards.

Documents

2017 Work Plan – Detailed description of expected outcomes and deliverables for 2017
2018 Work Plan – Detailed description of expected outcomes and deliverables for 2018
2019 Work Plan – Detailed description of expected outcomes and deliverables for 2019
2020 Work Plan – Detailed description of expected outcomes and deliverables for 2020
2021 Work Plan – Detailed description of expected outcomes and deliverables for 2021
Crop Ontology leaflet
Dimensions to consider when identifying an ontology for data