ArticleBioinformatics (Oxford, England)2015
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.
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Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- CCMRI: a classification and curated database of climate change-related microbiome studies.Scientific reports · 2026Article
- Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations.Computational and structural biotechnology journal · 2025Article
- Pancreatic cancer symptom trajectories from Danish registry data and free text in electronic health records.eLife · 2023Article
- PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types.Microorganisms · 2022Article
- The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.Journal of biomedical semantics · 2016Article
- The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.Journal of biomedical semantics · 2016Article
- Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.Database : the journal of biological databases and curation · 2016Article
- EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.Database : the journal of biological databases and curation · 2016Article
- Crowdsourcing and curation: perspectives from biology and natural language processing.Database : the journal of biological databases and curation · 2016Article
- Overview of the interactive task in BioCreative V.Database : the journal of biological databases and curation · 2016Article
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Authors and funding
13 authors.
Evangelos PafilisInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Sune P FrankildInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Julia SchnetzerInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Lucia FaniniInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Sarah FaulwetterInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Christina PavloudiInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Katerina VasileiadouInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Patrick LearyInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Jennifer HammockInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Katja SchulzInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Cynthia Sims ParrInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Christos ArvanitidisInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Lars Juhl JensenInstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledThe association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. AVAILABILITY AND IMPLEMENTATION: The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr.
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BiodiversityBiological OntologiesSoftwareAnimalsData MiningEcosystemInternet
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