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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:
; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1618945
Alternate Identifier(s):
OSTI ID: 1377498
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
Journal of Biomedical Semantics
Additional Journal Information:
Journal Name: Journal of Biomedical Semantics Journal Volume: 7 Journal Issue: 1; Journal ID: ISSN 2041-1480
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
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 Kingdom: 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 Kingdom. https://doi.org/10.1186/s13326-016-0097-6
Buttigieg, Pier Luigi, Pafilis, Evangelos, Lewis, Suzanna E., Schildhauer, Mark P., Walls, Ramona L., and Mungall, Christopher J. 2016. "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation". United Kingdom. https://doi.org/10.1186/s13326-016-0097-6.
@article{osti_1618945,
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},
url = {https://www.osti.gov/biblio/1618945}, journal = {Journal of Biomedical Semantics},
issn = {2041-1480},
number = 1,
volume = 7,
place = {United Kingdom},
year = {Fri Sep 23 00:00:00 EDT 2016},
month = {Fri Sep 23 00:00:00 EDT 2016}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1186/s13326-016-0097-6

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Cited by: 99 works
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Works referenced in this record:

Swarm: robust and fast clustering method for amplicon-based studies
journal, January 2014


Uberon, an integrative multi-species anatomy ontology
journal, January 2012


Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data
journal, October 2013


Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets
journal, November 2014


Species Distribution Models: Ecological Explanation and Prediction Across Space and Time
journal, December 2009


TreeBASE2: Rise of the Machines
journal, June 2010


eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment
journal, March 2015


Clarifying Concepts and Terms in Biodiversity Informatics
journal, May 2013


Emerging semantics to link phenotype and environment
journal, January 2015


Resistance and resilience of the forest soil microbiome to logging-associated compaction
journal, September 2013


Open science resources for the discovery and analysis of Tara Oceans data
journal, May 2015


Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes
journal, May 2013


TermGenie – a web-application for pattern-based ontology class generation
journal, January 2014


Putting people in the map: anthropogenic biomes of the world
journal, October 2008


Value, but high costs in post-deposition data curation
journal, January 2016


The environment ontology: contextualising biological and biomedical entities
journal, January 2013


Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
journal, October 2014


envo-habitats v0.0.1
software, December 2015


Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities
journal, October 2015


The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
journal, November 2007


The Genomic Standards Consortium
journal, June 2011


Darwin Core: An Evolving Community-Developed Biodiversity Data Standard
journal, January 2012


A decadal view of biodiversity informatics: challenges and priorities
journal, January 2013


MIREOT: The minimum information to reference an external ontology term
journal, January 2011


The ocean sampling day consortium
journal, June 2015


Bacterial diversity along a 2600 km river continuum: River bacterioplankton diversity
journal, June 2015


Mind the Gap: House Structure and the Risk of Malaria in Uganda
journal, January 2015


ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life
journal, January 2015


Effects of Air Pollution on Ecosystems and Biological Diversity in the Eastern United States
journal, April 2009


Human Occupancy as a Source of Indoor Airborne Bacteria
journal, April 2012


Cross-product extensions of the Gene Ontology
journal, February 2011


OBO-Edit an ontology editor for biologists
journal, June 2007


PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
journal, November 2013


Microbiota of the indoor environment: a meta-analysis
journal, October 2015


Microbial Biogeography of Public Restroom Surfaces
journal, November 2011


The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth
journal, April 2014


Limits to robustness and reproducibility in the demarcation of operational taxonomic units: Robustness and reproducibility in OTU demarcation
journal, September 2014


The FAIR Guiding Principles for scientific data management and stewardship
journal, March 2016


Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale
journal, April 2014


Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics
journal, August 2014


Sustainable development agenda: 2030
journal, September 2015


MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment
journal, October 2013


Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)
journal, January 2014


DISEASES: Text mining and data integration of disease–gene associations
journal, March 2015


The Airborne Metagenome in an Indoor Urban Environment
journal, April 2008


Meeting report: advancing practical applications of biodiversity ontologies
journal, December 2014


Malaria in Uganda: Challenges to control on the long road to elimination. II. The path forward
journal, March 2012


DISEASES: Text mining and data integration of disease???gene associations
preprint, August 2014


Works referencing / citing this record:

Building an information infrastructure of spectroscopic profiling data for food-drug quality and safety management
journal, November 2019


Ontology Summit 2018 Communiqué: Contexts in context
journal, July 2018


Evolving and Sustaining Ocean Best Practices and Standards for the Next Decade
journal, June 2019


Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences
journal, January 2017


Using a hydro-reference ontology to provide improved computer-interpretable semantics for the groundwater markup language (GWML2)
journal, February 2018


Documenting provenance in noncomputational workflows: Research process models based on geobiology fieldwork in Yellowstone National Park
journal, July 2018

  • Thomer, Andrea K.; Wickett, Karen M.; Baker, Karen S.
  • Journal of the Association for Information Science and Technology, Vol. 69, Issue 10
  • https://doi.org/10.1002/asi.24039

Integrative concepts and practices of health in transdisciplinary social ecology
journal, November 2019


A communal catalogue reveals Earth’s multiscale microbial diversity
journal, November 2017


FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
journal, December 2018


Towards global data products of Essential Biodiversity Variables on species traits
journal, September 2018


Towards a new online species-information system for legumes
journal, January 2019


Temporal and spatial dynamics in microbial community composition within a temperate stream network: Microbial community assembly in streams
journal, September 2018


Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale: Building global EBVs
journal, August 2017


An Ontology-based Approach to Plant Disease Identification System
conference, January 2018

  • Jearanaiwongkul, Watanee; Anutariya, Chutiporn; Andres, Frederic
  • Proceedings of the 10th International Conference on Advances in Information Technology - IAIT 2018
  • https://doi.org/10.1145/3291280.3291786

Phenotype annotation with the ontology of microbial phenotypes (OMP)
journal, July 2019


Latent environment allocation of microbial community data
journal, June 2018


DNA Sequencing as a Tool to Monitor Marine Ecological Status
journal, May 2017


Ocean Data Product Integration Through Innovation-The Next Level of Data Interoperability
journal, February 2019


Curating Scientific Information in Knowledge Infrastructures
journal, January 2018