RT Journal Article
SR Electronic
T1 ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 011403
DO 10.1101/011403
A1 Evangelos Pafilis
A1 Sune P Frankild
A1 Julia Schnetzer
A1 Lucia Fanini
A1 Sarah Faulwetter
A1 Christina Pavloudi
A1 Aikaterini Vasileiadou
A1 Patrick Leary
A1 Jennifer Hammock
A1 Katja Schulz
A1 Cynthia Sims Parr
A1 Christos Arvanitidis
A1 Lars Juhl Jensen
YR 2014
UL http://biorxiv.org/content/early/2014/12/23/011403.abstract
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.grContact: pafilis{at}hcmr.gr; lars.juhl.jensen{at}cpr.ku.dk