The environment ontology: contextualising biological and biomedical entities

By P. Buttigieg, N. Morrison, Barry Smith, C. Mungall, Suzanna Lewis. Journal of Biomedical Semantics, 2013

338 citations recorded by the source corpus.

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO; http://www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, content, structure, adoption, and governance approach. The ontology is available from http://purl.obolibrary.org/obo/envo.owl - an OBO format version is also available by switching the file suffix to “obo”.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3fe20db321fc0ed2c0bfd354ab2418856b67547a

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Citations in the corpus

DNA Sequencing as a Tool to Monitor Marine Ecological Status (2017, methodology): “Efforts that promote community collaboration and participation to produce standard practices include theMIxS standard from the Genomic Standards Consortium (GSC) (Yilmaz et al., 2011; ten Hoopen et al., 2015), the Environmental Ontology (Buttigieg et al., 2013, 2016), and data standards of the Globa”
The MG-RAST metagenomics database and portal in 2015 (2015, methodology): “Because of the everchanging nature of the controlled vocabularies used (13), users can now specify an EnvO version (Environmental Ontology Project that affords a community-driven ontology for the representation of environments) to be used for each study independently.”
Finding Our Way through Phenotypes (2015, background): “include the Environment Ontology (EnvO) [60] and the Exposure Science Ontology (ExO) [61], which provide controlled, structured vocabularies designed to enable representation of the relationships between organisms and biological samples to their environment.”
Genomes OnLine Database (GOLD) v.8: overview and updates (2020, methodology): “GOLD follows the Minimum Information about any (x) Sequence (MIxS) standards (12) established by The Genomic Standards Consortium (GSC) (13) and also works in close collaboration with The Environment Ontology (ENVO) community (14).”