ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

Evangelos Pafilis; Sune Pletscher-Frankild; Julia Schnetzer; Lucia Fanini; Sarah Faulwetter; Christina Pavloudi; Katerina Vasileiadou; Patrick Leary; Jennifer Hammock; Katja Schulz; Cynthia Sims Parr; Christos Arvanitidis; Lars Juhl Jensen

doi:10.1093/bioinformatics/btv045

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

Evangelos Pafilis, Sune Pletscher-Frankild, Julia Schnetzer, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Katerina Vasileiadou, Patrick Leary, Jennifer Hammock, Katja Schulz, Cynthia Sims Parr, Christos Arvanitidis, Lars Juhl Jensen

Disease Systems Biology Program

11 Citations (Scopus)

Abstract

Summary: The 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.

Original language	English
Journal	Bioinformatics
Volume	31
Issue number	11
Pages (from-to)	1872-1874
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btv045
Publication status	Published - 1 Jun 2015

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Pafilis, E., Pletscher-Frankild, S., Schnetzer, J., Fanini, L., Faulwetter, S., Pavloudi, C., Vasileiadou, K., Leary, P., Hammock, J., Schulz, K., Parr, C. S., Arvanitidis, C., & Jensen, L. J. (2015). ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics, 31(11), 1872-1874. https://doi.org/10.1093/bioinformatics/btv045

Pafilis, E, Pletscher-Frankild, S, Schnetzer, J, Fanini, L, Faulwetter, S, Pavloudi, C, Vasileiadou, K, Leary, P, Hammock, J, Schulz, K, Parr, CS, Arvanitidis, C & Jensen, LJ 2015, 'ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life', Bioinformatics, vol. 31, no. 11, pp. 1872-1874. https://doi.org/10.1093/bioinformatics/btv045

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title = "ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life",

abstract = "Summary: The 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.",

author = "Evangelos Pafilis and Sune Pletscher-Frankild and Julia Schnetzer and Lucia Fanini and Sarah Faulwetter and Christina Pavloudi and Katerina Vasileiadou and Patrick Leary and Jennifer Hammock and Katja Schulz and Parr, {Cynthia Sims} and Christos Arvanitidis and Jensen, {Lars Juhl}",

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AU - Pafilis, Evangelos

AU - Pletscher-Frankild, Sune

AU - Schnetzer, Julia

AU - Fanini, Lucia

AU - Faulwetter, Sarah

AU - Pavloudi, Christina

AU - Vasileiadou, Katerina

AU - Leary, Patrick

AU - Hammock, Jennifer

AU - Schulz, Katja

AU - Parr, Cynthia Sims

AU - Arvanitidis, Christos

AU - Jensen, Lars Juhl

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N2 - Summary: The 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.

AB - Summary: The 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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JO - Bioinformatics

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ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

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