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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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Schnetzer,  Julia
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Pafilis, E., Frankild, S. P., Schnetzer, J., Fanini, L., Faulwetter, S., Pavloudi, C., et al. (2015). ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics, online: btv045v1, pp. 1-2.


Cite as: http://hdl.handle.net/21.11116/0000-0001-C48F-1
Abstract
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.