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Rinaldi, Fabio; Clematide, Simon; Garten, Yael; Whirl-Carrillo, Michelle; Gong, Li; Hebert, Joan M; Sangkuhl, Katrin; Thorn, Caroline F; Klein, Teri E; Altman, Russ B (2012). Using ODIN for a PharmGKB re-validation experiment. Database: The Journal Of Biological Databases And Curation, 2012:bas021.

Abstract

The need for efficient text-mining tools that support curation of the biomedical literature is ever increasing. In this article, we describe an experiment aimed at verifying whether a text-mining tool capable of extracting meaningful relationships among domain entities can be successfully integrated into the curation workflow of a major biological database. We evaluate in particular (i) the usability of the system's interface, as perceived by users, and (ii) the correlation of the ranking of interactions, as provided by the text-mining system, with the choices of the curators.

The need for efficient text-mining tools that support curation of the biomedical literature is ever increasing. In this article, we describe an experiment aimed at verifying whether a text-mining tool capable of extracting meaningful relationships among domain entities can be successfully integrated into the curation workflow of a major biological database. We evaluate in particular (i) the usability of the system's interface, as perceived by users, and (ii) the correlation of the ranking of interactions, as provided by the text-mining system, with the choices of the curators.

Citations

7 citations in Web of Science®
7 citations in Scopus®
Google Scholar™

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Downloads

58 downloads since deposited on 07 May 2012
15 downloads since 12 months
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:06 Faculty of Arts > Institute of Computational Linguistics
Dewey Decimal Classification:000 Computer science, knowledge & systems
410 Linguistics
Language:English
Date:2012
Deposited On:07 May 2012 09:03
Last Modified:05 Apr 2016 15:47
Publisher:Oxford University Press
ISSN:1758-0463
Funders:Swiss National Science Foundation (grant 100014-118396/1), Novartis Pharma AG, NIBR-IT, Text Mining Services, National Institute of Health/National Institute of General Medical Sciences (R24 GM61374), National Library of Medicine (contract HHSN276201000025C)
Publisher DOI:10.1093/database/bas021
Permanent URL: http://doi.org/10.5167/uzh-62071

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Licence: Creative Commons: Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)

TrendTerms

TrendTerms displays relevant terms of the abstract of this publication and related documents on a map. The terms and their relations were extracted from ZORA using word statistics. Their timelines are taken from ZORA as well. The bubble size of a term is proportional to the number of documents where the term occurs. Red, orange, yellow and green colors are used for terms that occur in the current document; red indicates high interlinkedness of a term with other terms, orange, yellow and green decreasing interlinkedness. Blue is used for terms that have a relation with the terms in this document, but occur in other documents.
You can navigate and zoom the map. Mouse-hovering a term displays its timeline, clicking it yields the associated documents.

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