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

• DOI: 10.1093/bioinformatics/btv045
• Publication Date: 2015-01-26T01:18:20Z
• Authors: Evangelos Pafilis; Sune P. 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
• Keywords: Encyclopedia; Identification

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 taxa and habitats are now being consolidated centralized resources. However, structured annotations needed facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, fast dictionary-based tagger capable identifying Environment Ontology (ENVO) terms text. We evaluate the accuracy on new manually curated corpus 600 Encyclopedia Life (EOL) species pages. use associate with by tagging EOL text content monthly, integrate results into disseminate them broad audience users. Availability implementation: software available under open-source BSD CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr Contact: [e-mail] or [e-mail] Supplementary information: data Bioinformatics online.