A community-driven ontology for the representation of environments
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README.md

Build Status DOI

The Environment Ontology

A description of the Environment Ontology (ENVO) is published in the Journal of Biomedical Semantics in an article by Buttigieg et al. and a paper describing its development until mid-2016 is avaiable here

Our latest releases are described here

More information and guides for using ENVO in annotation exercises are available at www.environmentontology.org

Please note: ENVO is not an "authority" in itself, but we do try to provide a semantic/ontological expression of existing authoritative classifications alongside project-based or individual knowledge. We aim to create a FAIR compliant space where expressions of this knowledge can co-exist and interoperate.

Aim and Scope

ENVO is a domain ontology concerned with "environments" of all kinds and aims to promote standardisation and interoperability of diverse data sets through the concise, controlled description of environment types across several levels of granularity. It is primarily concerned with environments as encountered in ecological applications, but is able to accommodate alternative needs.

ENVO currently deals with 'environmental systems' (i.e. environments) particularly 'biomes' and environments determined by a material entity that assumes the role of an 'environmental feature' (e.g. a digestive tract environment). It also handles 'environmental materials' like soil, water, and so on.

Versions

Stable release versions

ENVO's latest release version can be downloaded in OWL and OBO format from the following links: http://purl.obolibrary.org/obo/envo.owl

http://purl.obolibrary.org/obo/envo.obo

Please note that the files above include all the imported classes from ontologies referenced by ENVO. If you would like a "simple" version with only ENVO classes, please download it from: http://purl.obolibrary.org/obo/subsets/envo-basic.obo

Please note that the OBO files are now created from the OWL file. Due to limitations in the OBO format, envo.obo will not offer as much expressibility as envo.owl. Further, to open envo.obo in OBOEdit 2, please ensure that dangling axioms are allowed using the advanced view of the "Load Ontology" window.

Subsets

A subset is a trimmed down version of ENVO. We create subsets for users who want just a few terms for their work. Read more about subsets on this wiki page. Several subsets of ENVO classes are identified with the "in_subset" annotation property.

A simple TSV of the subsets (including their labels, definitions, and URIs) is available here

More subsets can be generated on request (please post such requests on our issue tracker.

Editors' version

The editors' version of ENVO, envo-edit.owl, can be downloaded here: https://github.com/EnvironmentOntology/envo/blob/master/src/envo/envo-edit.owl This version is subject to frequent change and should be used with caution.

Contact

Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

If you would like to send a more general comment or question to the EnvO mailing list, please subscribe and post a message. This open mailing list is the best place to post general questions or comments for discussion in the wider EnvO community. Please note, your posts will be stored in publicly accessible archives.

History

The repository was moved to this location from https://code.google.com/p/envo/ in March 2015. The legacy issues were automatically migrated. The PURL targets have been updated accordingly.