RT Journal Article
SR Electronic
T1 Tagger: BeCalm API for rapid named entity recognition
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 115022
DO 10.1101/115022
A1 Lars Juhl Jensen
YR 2017
UL http://biorxiv.org/content/early/2017/03/08/115022.abstract
AB Most BioCreative tasks to date have focused on assessing the quality of text-mining annotations in terms of precision of recall. Interoperability, speed, and stability are, however, other important factors to consider for practical applications of text mining. The new BioCreative/BeCalm TIPS task focuses purely on these. To participate in this task, I implemented a BeCalm API within the real-time tagging server also used by the Reflect and EXTRACT tools. In addition to retrieval of patent abstracts, PubMed abstracts, and Pub-Med Central open-access articles as required in the TIPS task, the BeCalm API implementation facilitates retrieval of documents from other sources specified as custom request parameters. As in earlier tests, the tagger proved to be both highly efficient and stable, being able to consistently process requests of 5000 abstracts in less than half a minute including retrieval of the document text.