Ontologies

Community of Practice

 

Welcome!

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

The Ontologies Community of Practice is led by Bioversity International and has been launched as a part of the CGIAR Platform for Big Data in Agriculture.

Given the multi-disciplinary nature of the CGIAR Big Data Platform for Agriculture , the CoP Ontologies will span the knowledge domains that are relevant to the Platform with the objective of establishing best practices, and guidelines in the selection of ontologies of reference.

It will also focus on the use and application of semantics for data harmonization at the levels of collection and storage, and for data interoperability and data discovery following the FAIR principles. This space can be used as a discussion area, share and request relevant information and contribute towards building the community as a whole.

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Ontologies are important to all data-driven research, and this group serves as an intermediary to assess common goals, needs ,and opportunities across all BIG DATA CoPs and working groups.

The CoP aims at bringing together experts in ontology design, ontology-driven applications (fieldbooks, databases, annotation tools, query tools, etc), semantic web technologies, specialists from 15 CGIAR Centers, collaborative organizations, and other BIG DATA CoPs, to create a critical mass of expertise needed to tackle major issues related to semantics for FAIR (Findable, Accessible, Interoperable, Reusable) data in agriculture. By promoting FAIR data principles, the Ontologies CoP fosters a culture that values data and enables its members to solve global grand challenges faster, better, and at greater scale.

Get in touch

CoP Lead

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

CoP Communication

Céline Aubert | Email
Bioversity International, France

Aman Sidhu | Email
Bioversity International, France

Engage with the Community

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BE INFORMED

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

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ENGAGE

Interact with community members through our LinkedIn Group.

CONTRIBUTE

Share your expertise in 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: 

Bioversity International 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. The group is lead by Bioversity International.

SociO!

A socio-economic ontology of controlled vocabularies, classifications, and concordances that allow standardization of key indicators. The key is that in SociO! 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 Socio! works in close collaboration with the SED CoP led by Gideon Kruseman. The Socio! working group is led by Soonho Kim of IFPRI.

Interested in contributing to the development of these ontologies?

Please select the topic(s) of interest

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Community News

Agricultural Ontologies in Use: New Crops and Traits in the Crop Ontology

Agricultural Ontologies in Use: New Crops and Traits in the Crop Ontology

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The Ontologies Community of Practice is engaged in the development of ontologies for agricultural research. In a series of blog ...
Agricultural Ontologies in Use: The GEMS PLATFORM

Agricultural Ontologies in Use: The GEMS PLATFORM

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The Ontologies Community of Practice is engaged in the development of ontologies for agricultural research. In a series of blog ...
Webinar summary - Semantic annotation of images in the FAIR data era

Webinar summary – Semantic annotation of images in the FAIR data era

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The Ontologies Community of Practice hosted a webinar series to debate, share, and advance our thinking on selected topics in ...
Webinar - Semantic annotation of images in the FAIR data era

Webinar – Semantic annotation of images in the FAIR data era

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CGIAR Webinar by the Platform for Big Data in Agriculture’s Community of Practice on Ontologies – Semantic Annotation of Images ...
Agricultural Ontologies in Use: the Breeding API Project

Agricultural Ontologies in Use: the Breeding API Project

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The Ontologies Community of Practice is engaged in the development of ontologies for agricultural research. In a series of blog ...
Webinar summary – Can machine learning technologies be useful to create or complete ontologies in agriculture?

Webinar summary – Can machine learning technologies be useful to create or complete ontologies in agriculture?

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The Ontologies Community of Practice launched a webinar series to debate, share, and advance our thinking on selected topics in ...
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Resources

Tools

Ontology registries

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

 

Webinars

 

Events

[WEBINAR] Semantic Annotation of Images in the FAIR Data Era

September 3, 2019 – September 3, 2019 | Online

[WEBINAR] Digital Food Systems Evidence Clearing House

September 17, 2019 – September 17, 2019 | Online

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