title: FACTA: a text search engine for finding associated biomedical concepts.
abstract: 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.
  
  
  BACKGROUND
  The system is available at http://www.nactem.ac.uk/software/facta/
authors.affiliation: School of Computer Science, The University of Manchester, Manchester, UK. yoshimasa.tsuruoka@manchester.ac.uk
authors.forename: Yoshimasa
authors.initials: Y
authors.lastname: Tsuruoka
authors.forename: Jun'ichi
authors.initials: J
authors.lastname: Tsujii
authors.forename: Sophia
authors.initials: S
authors.lastname: Ananiadou
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods*; D003628:Database Management Systems; D016239:MEDLINE; D012984:Software
references.citation: Bioinformatics. 2004 Dec 12;20(18):3659-61
references.pmid: 15284107
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3866-8
references.pmid: 12824439
references.citation: Genome Biol. 2008;9(6):R96
references.pmid: 18549479
references.citation: Bioinformatics. 2007 Jan 15;23(2):e237-44
references.pmid: 17237098
references.citation: Bioinformatics. 2006 Jan 1;22(1):103-5
references.pmid: 16267085
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W779-82
references.pmid: 15980584
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405
references.pmid: 18487273