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

Abstract

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 relevantmore » 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.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [3]
  1. Alfred Wegener Institute for Polar and Marine Research, Bremerhaven (Germany). Alfred Wegener Inst.
  2. Hellenic Centre for Marine Research, Crete (Greece). Inst. of Marine Biology Biotechnology and Aquaculture
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmetnal Genomics and Systems Biology Division
  4. Univ. of California, Santa Barbara, CA (United States). National Center for Ecological Analysis and Synthesis
  5. CyVerse, Tucson, AZ (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1377498
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Biomedical Semantics
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2041-1480
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; environmental semantics; habitat; ecosystem; ontology; anthropogenic environment; indoor environment; sustainable development

Citation Formats

Buttigieg, Pier Luigi, Pafilis, Evangelos, Lewis, Suzanna E., Schildhauer, Mark P., Walls, Ramona L., and Mungall, Christopher J. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. United States: N. p., 2016. Web. doi:10.1186/s13326-016-0097-6.
Buttigieg, Pier Luigi, Pafilis, Evangelos, Lewis, Suzanna E., Schildhauer, Mark P., Walls, Ramona L., & Mungall, Christopher J. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. United States. doi:10.1186/s13326-016-0097-6.
Buttigieg, Pier Luigi, Pafilis, Evangelos, Lewis, Suzanna E., Schildhauer, Mark P., Walls, Ramona L., and Mungall, Christopher J. Fri . "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation". United States. doi:10.1186/s13326-016-0097-6. https://www.osti.gov/servlets/purl/1377498.
@article{osti_1377498,
title = {The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation},
author = {Buttigieg, Pier Luigi and Pafilis, Evangelos and Lewis, Suzanna E. and Schildhauer, Mark P. and Walls, Ramona L. and Mungall, Christopher J.},
abstractNote = {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.},
doi = {10.1186/s13326-016-0097-6},
journal = {Journal of Biomedical Semantics},
number = 1,
volume = 7,
place = {United States},
year = {Fri Sep 23 00:00:00 EDT 2016},
month = {Fri Sep 23 00:00:00 EDT 2016}
}

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