Ontologies most used in agriculture

Make 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.

Sequences

Sequence Ontology

Features and attributes of biological sequence.​

Genes

Gene Ontology

Molecular entities focused on ‘small’ chemical compounds.​

Biochemical entities

ChEBI Ontology

Molecular functions, biological processes, cellular components.​

Proteins

Protein Ontology

Protein-related entities.

Cell

Cell Ontology

Cell types in animals.

Cell Behavior Ontology

Multi-cell computational models.

Tissues and enzymes 

BRENDA tissues and enzyme

Tissues, cell types and enzyme sources.

Anatomy

Anatomical Entity Ontology

Ontology of anatomical structures.

Plant Ontology

Plant anatomy, morphology, growth and development.

Species

NCBI Taxonomy

Organisms’ classification and nomenclature.

MycoBank

Mycological nomenclatural novelties.

EPPO

Pest-specific information.

Environment

Environment Ontology

Environmental features and habitats.

Plant Experimental Conditions Ontology

Growth conditions used
in plant experiments.

Agronomy

Agronomy Ontology

Agronomic practices, techniques and inputs.

Fisheries and aquaculture 

Small-scale fisheries & aquaculture ontology

Fisheries and aquaculture (under development).

Plant phenotype

Crop Ontology

Species-specific phenotypic plant traits.

Phenotype And Trait Ontology

Phenotypic qualities.

Trait Ontology

Phenotypic traits in plants.

Livestock phenotype

Animal Trait Ontology for Livestock

Phenotypes of livestock in their environment.

Phenotype And Trait Ontology

Phenotypic qualities.

Food and nutrition

Food Ontology

Food, fodder and food processes.

Compositional Dietary
Nutrition Ontology​

Nutritional attributes contributing to human diet.

Socio economics

SEONT

Ontology for agricultural household surveys.

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ONTOLOGY REPOSITORIES

Generic ontologies and thesauri

AGROVOC

Multilingual and controlled vocabulary designed to cover concepts and terminology under FAO’s areas of interest.

CAB Thesaurus

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.

GAZ

Represents places through their names using an ontological approach to promote semantic coherence.

Geonames

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.

VIVO Ontology

Open-source software and an ontology for representing scholarship.