Thomas J Keating Bioresearch Building

East Sahuarita, AZ, United States

Thomas J Keating Bioresearch Building

East Sahuarita, AZ, United States
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Buttigieg P.L.,Alfred Wegener Institute for Polar and Marine Research | Pafilis E.,Hellenic Center for Marine Research | Lewis S.E.,Lawrence Berkeley National Laboratory | Schildhauer M.P.,National Center for Ecological Analysis And Synthesis | And 2 more authors.
Journal of Biomedical Semantics | Year: 2016

Background: The Environment Ontology (ENVO; http://www.environmentontology.org/), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. Methods: We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. Results: Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl. Conclusions: ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, 'omics, and socioeconomic development. Through continued interactions with our users and partners, particularly those performing data archiving and sythesis, we anticipate that ENVO's growth will accelerate in 2017. As always, we invite further contributions and collaboration to advance the semantic representation of the environment, ranging from geographic features and environmental materials, across habitats and ecosystems, to everyday objects in household settings. © 2016 The Author(s).


PubMed | Lawrence Berkeley National Laboratory, Thomas J Keating Bioresearch Building, Hellenic Center for Marine Research, National Center for Ecological Analysis And Synthesis and Alfred Wegener Institute for Polar and Marine Research
Type: Journal Article | Journal: Journal of biomedical semantics | Year: 2016

The Environment Ontology (ENVO; http://www.environmentontology.org/ ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontologys initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVOs use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications.We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO.Relative to its state in 2013, ENVOs content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl .ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, omics, and socioeconomic development. Through continued interactions with our users and partners, particularly those performing data archiving and sythesis, we anticipate that ENVOs growth will accelerate in 2017. As always, we invite further contributions and collaboration to advance the semantic representation of the environment, ranging from geographic features and environmental materials, across habitats and ecosystems, to everyday objects in household settings.

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