ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life
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ENVIRONMENTS and EOL : identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. / Pafilis, Evangelos; Pletscher-Frankild, Sune; Schnetzer, Julia; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, Christina; Vasileiadou, Katerina; Leary, Patrick; Hammock, Jennifer; Schulz, Katja; Parr, Cynthia Sims; Arvanitidis, Christos; Jensen, Lars Juhl.
In: Bioinformatics, Vol. 31, No. 11, 2015, p. 1872-1874.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - ENVIRONMENTS and EOL
T2 - identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life
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
N1 - © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
PY - 2015
Y1 - 2015
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 CONTACT: pafilis@hcmr.gr or lars.juhl.jensen@cpr.ku.dk Supplementary information: Supplementary data are available at Bioinformatics online.
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 CONTACT: pafilis@hcmr.gr or lars.juhl.jensen@cpr.ku.dk Supplementary information: Supplementary data are available at Bioinformatics online.
U2 - 10.1093/bioinformatics/btv045
DO - 10.1093/bioinformatics/btv045
M3 - Journal article
C2 - 25619994
VL - 31
SP - 1872
EP - 1874
JO - Computer Applications in the Biosciences
JF - Computer Applications in the Biosciences
SN - 1471-2105
IS - 11
ER -
ID: 137983100