Ontologies most used in agricultureMake your data interpretable and interoperable with ontologies.
ONTOLOGIES FROM GENETICS TO SOCIO-ECONOMICS
In this webpage, you will find a list of the most used ontologies in agriculture including the ontologies developed by the Ontologies Community of Practice of the CGIAR Platform for Big Data in Agriculture and its partners. It is recommended to use the following ontologies to annotate agrifood data. The schema organizes ontologies along the agri-food pathway from gene to plant, food and socio-economy. The schema is interactive with direct links to ontologies’ website. It is a snapshot of the current ontologies environment and may evolve in the future. It has been adapted from a schema made by Erick Antezana, Senior Data Management Scientist at Bayer Crop Science. The webpage also offers a list of generic ontologies and thesauri and ontologies repositories.
(For citation please use: Aubert, Céline, & Arnaud, Elizabeth. (2021). ONTOLOGIES MOST USED IN AGRICULTURE: Make your data interpretable and interoperable with ontologies. (Version 1). Zenodo. https://doi.org/10.5281/zenodo.6609666)
Features and attributes of biological sequence.
Molecular entities focused on ‘small’ chemical compounds.
Molecular functions, biological processes, cellular components.
Tissues and enzymes
Tissues, cell types and enzyme sources.
Ontology of anatomical structures.
Plant anatomy, morphology, growth and development.
Organisms’ classification and nomenclature.
Mycological nomenclatural novelties.
Environmental features and habitats.
Growth conditions used
in plant experiments.
Agronomic practices, techniques and inputs.
Fisheries and aquaculture
Fisheries and aquaculture (under development).
Species-specific phenotypic plant traits.
Phenotypic traits in plants.
Phenotypes of livestock in their environment.
Food and nutrition
Food, fodder and food processes.
Nutritional attributes contributing to human diet.
Ontology for agricultural household surveys.
- 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) provides a single point of access to the latest ontology versions.
- FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.
Generic ontologies and thesauri
Controlled vocabulary for agriculture, forestry, horticulture, soil science, entomology, mycology, parasitology, veterinary medicine, nutrition, rural studies.
CG Core Metadata Schema
Minimum set of elements applicable for data and publication annotation and curation across CGIAR.
Comparative Data Analysis Ontology (CDAO)
Formalization of concepts and relations relevant to evolutionary comparative analysis.
EMBRACE Data and Methods Ontology (EDAM)
Comprehensive ontology for bioscientific data analysis and data management.
Represents places through their names using an ontological approach to promote semantic coherence.
Covers all countries and contains over eleven million placenames.
National Agricultural Library’s Agricultural Thesaurus and Glossary (NAL)
Online vocabulary tools English and Spanish to select controlled vocabulary terms for subject indexing of AGRICOLA, PubAg and other databases.
Research Organization Registry (ROR)
Registry of open, sustainable, usable, and unique identifiers for every research organization in the world.
Units of Measurement Ontology (UO)
Ontology of units of measurements.
Variation Ontology (VariO)
Ontology for standardized, systematic description of effects, consequences and mechanisms of variations.
Open-source software and an ontology for representing scholarship.