Integrating Natural Language Processing with Flybase Curation

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.

[1]  David A. Cohn,et al.  Active Learning with Statistical Models , 1996, NIPS.

[2]  William R. Hersh,et al.  A survey of current work in biomedical text mining , 2005, Briefings Bioinform..

[3]  Sri Hastuti Kurniawan,et al.  Review of Interaction design , 2003 .

[4]  Dan Tidhar,et al.  Retrieving Hierarchical Text Structure from Typeset Scientific Articles – a Prerequisite for E-Science Text Mining , 2005 .

[5]  Alexander A. Morgan,et al.  Gene name identification and normalization using a model organism database , 2004, J. Biomed. Informatics.

[6]  Ted Briscoe,et al.  The Second Release of the RASP System , 2006, ACL.

[7]  H. J. Arnold Introduction to the Practice of Statistics , 1990 .

[8]  Monica C. Jackson,et al.  Introduction to the Practice of Statistics , 2001 .

[9]  Caroline Gasperin,et al.  Semi-supervised anaphora resolution in biomedical texts , 2006, BioNLP@NAACL-HLT.

[10]  Hans-Michael Müller,et al.  Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature , 2004, PLoS biology.

[11]  Ted Briscoe,et al.  Bootstrapping the Recognition and Anaphoric Linking of Named Entities in Drosophila Articles , 2006, Pacific Symposium on Biocomputing.

[12]  L Hunter,et al.  MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. , 1999, BioTechniques.

[13]  Austin Henderson,et al.  Interaction design: beyond human-computer interaction , 2002, UBIQ.

[14]  Ralph M. Weischedel,et al.  The HOOKAH Information Extraction System , 1996, TIPSTER.

[15]  Andreas Vlachos,et al.  Bootstrapping and Evaluating Named Entity Recognition in the Biomedical Domain , 2006, BioNLP@NAACL-HLT.

[16]  Alexander A. Morgan,et al.  Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup , 2003, ISMB.

[17]  Yvonne Rogers,et al.  Interaction Design: Beyond Human-Computer Interaction , 2002 .