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ready Environment Ontology

Abbreviation: ENVO

General Information
The Environment Ontology (EnvO) provides a controlled, structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms ranging from astronomical objects, through planetary scale biomes, to nanomaterials. Further, these terms are interlinked with logical axioms describing their composition, colocalisation, and relationships to environmental and biological processes. Using ENVO terms for an environmental description allows a comprehensive description of environment that is key to machine-assisted integration, archiving and federated searching of environmental data.

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How to cite this record ENVO; Environment Ontology; DOI:; Last edited: Dec. 16, 2020, 2:35 p.m.; Last accessed: Oct 27 2021 1:25 a.m.

Publication for citation  The environment ontology: contextualising biological and biomedical entities. Buttigieg PL,Morrison N,Smith B,Mungall CJ,Lewis SE; J Biomed Semantics ; 2013; 10.1186/2041-1480-4-43;

This record is maintained by plbuttigieg  ORCID

Record updated: Dec. 16, 2020, 2:34 p.m. by The FAIRsharing Team.

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The environment ontology: contextualising biological and biomedical entities.

Buttigieg PL,Morrison N,Smith B,Mungall CJ,Lewis SE
J Biomed Semantics 2013

View Paper (PubMed) View Publication

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.

Buttigieg PL,Pafilis E,Lewis SE,Schildhauer MP,Walls RL,Mungall CJ
J Biomed Semantics 2016

View Paper (PubMed) View Publication

Emerging semantics to link phenotype and environment.

Thessen AE,Bunker DE,Buttigieg PL,Cooper LD,Dahdul WM,Domisch S,Franz NM,Jaiswal P,Lawrence-Dill CJ,Midford PE,Mungall CJ,Ramirez MJ,Specht CD,Vogt L,Vos RA,Walls RL,White JW,Zhang G,Deans AR,Huala E,Lewis SE,Mabee PM
PeerJ 2015

View Paper (PubMed) View Publication

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.

Pafilis E,Buttigieg PL,Ferrell B,Pereira E,Schnetzer J,Arvanitidis C,Jensen LJ
Database (Oxford) 2016

View Paper (PubMed) View Publication

ENVO Ontology Display

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Related Databases (8)
Genomes OnLine Database
The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.

Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.

Manually Curated Database of Rice Proteins
The Manually Curated Database of Rice Proteins (MCDRP) is a manually-curated database based on published experimental data. The database contains data for rice proteins curated from experiments drawn from research articles. The database stores information including gene name, plant type, tissue and developmental stage. The homepage for this resource could not be loaded. Please contact us if you have any information regarding the current status of this resource.

DataONE is a community driven project providing access to data across multiple member repositories, supporting enhanced search and discovery of Earth and environmental data.

OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

Metabolomic Repository Bordeaux
MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants.

MAR databases
The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center for Bioinformatics (SfB) at the UiT The Arctic University of Norway. SfB is hosting the UiT node of ELIXIR Norway. The MarRef, MarDb, MarFun and MarCat contextual databases are built by compiling data from a number of public available sequence, taxonomy and literature databases in a semi-automatic fashion.

National Microbiome Data Collaborative
The National Microbiome Data Collaborative seeks to address fundamental roadblocks in microbiome data science and gaps in transdisciplinary collaboration. The NMDC's Phase I Pilot was launched in July 2019 funded by the Department of Energy’s (DOE) Office of Science, Biological and Environmental Research program, with two strategic priorities — infrastructure and engagement. The infrastructure goal is to democratize microbiome data science by providing access to multidisciplinary, multi-omics data (e.g., metagenomics and metaproteomics) through distributed data resources, with seamless integration to platforms that support reproducible, cross- study analyses. The engagement goal is to enable community-driven shared ownership of microbiome data that supports open science across research teams, funders, publishers, and societies. Currently, no data are available, as this project is still in the development stage. Please sign up for our Quarterly newsletter via the website (starting in Sep 2020) for updates, feature releases, and ways to get involved.

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Grant Number(s)

  • 283359 (European Commission FP7)

  • 287589 (European Commission)

  • HG004838 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)