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Using ODIN for a PharmGKB re-validation experiment


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.

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.

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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:11 Jun 2017 05:21
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:https://doi.org/10.1093/database/bas021

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