Literature DB >> 17990496

Integrating natural language processing with FlyBase curation.

Nikiforos Karamanis1, Ian Lewin, Ruth Seal, Rachel Drysdale, Edward Briscoe.   

Abstract

Applying Natural Language Processing techniques to biomedical text as a potential aid to curation has become the focus of intensive research. However, developing integrated systems which address the curators' real-world needs has been studied less rigorously. This paper addresses this question and presents generic tools developed to assist FlyBase curators. We discuss how they have been integrated into the curation workflow and present initial evidence about their effectiveness.

Mesh:

Year:  2007        PMID: 17990496

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN: 2335-6928


  14 in total

Review 1.  Frontiers of biomedical text mining: current progress.

Authors:  Pierre Zweigenbaum; Dina Demner-Fushman; Hong Yu; Kevin B Cohen
Journal:  Brief Bioinform       Date:  2007-10-30       Impact factor: 11.622

2.  Intrinsic evaluation of text mining tools may not predict performance on realistic tasks.

Authors:  J Gregory Caporaso; Nita Deshpande; J Lynn Fink; Philip E Bourne; K Bretonnel Cohen; Lawrence Hunter
Journal:  Pac Symp Biocomput       Date:  2008

3.  Fine-grained indexing of the biomedical literature: MeSH subheading attachment for a MEDLINE indexing tool.

Authors:  Aurélie Névéol; Sonya E Shooshan; James G Mork; Alan R Aronson
Journal:  AMIA Annu Symp Proc       Date:  2007-10-11

4.  An interactive and user-centered computer system to predict physician's disease judgments in discharge summaries.

Authors:  Jonathan P DeShazo; Anne M Turner
Journal:  J Biomed Inform       Date:  2009-09-03       Impact factor: 6.317

5.  A text-mining system for extracting metabolic reactions from full-text articles.

Authors:  Jan Czarnecki; Irene Nobeli; Adrian M Smith; Adrian J Shepherd
Journal:  BMC Bioinformatics       Date:  2012-07-23       Impact factor: 3.169

6.  Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts.

Authors:  Chih-Hsuan Wei; Bethany R Harris; Donghui Li; Tanya Z Berardini; Eva Huala; Hung-Yu Kao; Zhiyong Lu
Journal:  Database (Oxford)       Date:  2012-11-17       Impact factor: 3.451

7.  Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.

Authors:  Zhiyong Lu; Lynette Hirschman
Journal:  Database (Oxford)       Date:  2012-11-17       Impact factor: 3.451

8.  BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature.

Authors:  Moushumi Sen Sarma; David Arcoleo; Radhika S Khetani; Brant Chee; Xu Ling; Xin He; Jing Jiang; Qiaozhu Mei; ChengXiang Zhai; Bruce Schatz
Journal:  Nucleic Acids Res       Date:  2011-05-09       Impact factor: 16.971

9.  Literature retrieval and mining in bioinformatics: state of the art and challenges.

Authors:  Andrea Manconi; Eloisa Vargiu; Giuliano Armano; Luciano Milanesi
Journal:  Adv Bioinformatics       Date:  2012-06-21

10.  Using ODIN for a PharmGKB revalidation experiment.

Authors:  Fabio Rinaldi; Simon Clematide; Yael Garten; Michelle Whirl-Carrillo; Li Gong; Joan M Hebert; Katrin Sangkuhl; Caroline F Thorn; Teri E Klein; Russ B Altman
Journal:  Database (Oxford)       Date:  2012-04-23       Impact factor: 3.451

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