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

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

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 t...

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Bibliographic Details
Published in:Bioinformatics 2015-06, Vol.31 (11), p.1872-1874
Main Authors: Pafilis, Evangelos, Frankild, Sune P, Schnetzer, Julia, Fanini, Lucia, Faulwetter, Sarah, Pavloudi, Christina, Vasileiadou, Katerina, Leary, Patrick, Hammock, Jennifer, Schulz, Katja, Parr, Cynthia Sims, Arvanitidis, Christos, Jensen, Lars Juhl
Format: Article
Language:eng
Subjects:
Animals
Annotations
Applications Notes
Biodiversity
Bioinformatics
Biological Ontologies
Computer programs
Data Mining - methods
Ecosystem
Encyclopaedias
Internet
Knowledge representation
Licenses
Software
Source code
Texts
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Description
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. 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.
ISSN:1367-4803
1367-4811
1460-2059