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

Research output: Contribution to journalJournal articleResearchpeer-review

  • 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
  • Jensen, Lars Juhl

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.

Original languageEnglish
Issue number11
Pages (from-to)1872-1874
Publication statusPublished - 2015

ID: 137983100