Biology subjects
Publications and source records attributed to Evangelos Pafilis.
Automatic annotation of text is an important complement to manual annotation, because the latter is highly labor intensive. We have developed a fast dictionary-based named entity recognition system, which is used for both real-time and bulk processing of text in a variety of biomedical web resources. We propose to adapt the system to make it interoperable with the PubAnnotation and Open Annotation standards.
SummaryThe 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.\n\nAvailability and implementationThe 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\n\nContactpafilis@hcmr.gr; lars.juhl.jensen@cpr.ku.dk