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Natural language processing in aid of FlyBase curators.


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Authors

Karamanis, Nikiforos 
Lewin, Ian 
McQuilton, Peter 

Abstract

BACKGROUND: Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. RESULTS: PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. CONCLUSION: We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully.

Description

Keywords

Algorithms, Artificial Intelligence, Database Management Systems, Databases, Bibliographic, Information Storage and Retrieval, Natural Language Processing, Periodicals as Topic, Software, Vocabulary, Controlled

Journal Title

BMC Bioinformatics

Conference Name

Journal ISSN

1471-2105
1471-2105

Volume Title

Publisher

Springer Science and Business Media LLC
Sponsorship
Medical Research Council (G0500293)
BBSRC (BBS/B/16291)