Skip Navigation


Bioinformatics Advance Access originally published online on September 4, 2008
Bioinformatics 2008 24(21):2559-2560; doi:10.1093/bioinformatics/btn469
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
24/21/2559    most recent
btn469v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Tsuruoka, Y.
Right arrow Articles by Ananiadou, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tsuruoka, Y.
Right arrow Articles by Ananiadou, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

FACTA: a text search engine for finding associated biomedical concepts

Yoshimasa Tsuruoka 1,2,*, Jun'ichi Tsujii 1,2,3 and Sophia Ananiadou 1,2

1School of Computer Science, The University of Manchester, 2National Centre for Text Mining (NaCTeM), Manchester, UK and 3Department of Computer Science, The University of Tokyo, Japan

*To whom correspondence should be addressed.


  Abstract

Summary: FACTA is a text search engine for MEDLINE abstracts, which is designed particularly to help users browse biomedical concepts (e.g. genes/proteins, diseases, enzymes and chemical compounds) appearing in the documents retrieved by the query. The concepts are presented to the user in a tabular format and ranked based on the co-occurrence statistics. Unlike existing systems that provide similar functionality, FACTA pre-indexes not only the words but also the concepts mentioned in the documents, which enables the user to issue a flexible query (e.g. free keywords or Boolean combinations of keywords/concepts) and receive the results immediately even when the number of the documents that match the query is very large. The user can also view snippets from MEDLINE to get textual evidence of associations between the query terms and the concepts. The concept IDs and their names/synonyms for building the indexes were collected from several biomedical databases and thesauri, such as UniProt, BioThesaurus, UMLS, KEGG and DrugBank.

Availability: The system is available at http://www.nactem.ac.uk/software/facta/

Contact: yoshimasa.tsuruoka{at}manchester.ac.uk

Associate Editor: Jonathan Wren

Received on June 13, 2008; revised on August 9, 2008; accepted on August 29, 2008

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.