FACTA: A text search engine for finding associated biomedical concepts

Yoshimasa Tsuruoka; Jun'ichi Tsujii; Sophia Ananiadou

doi:10.1093/bioinformatics/btn469

FACTA: A text search engine for finding associated biomedical concepts

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou

Research output: Contribution to journal › Article › peer-review

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. © 2008 The Author(s).

Original language	English
Pages (from-to)	2559-2560
Number of pages	1
Journal	Bioinformatics
Volume	24
Issue number	21
DOIs	https://doi.org/10.1093/bioinformatics/btn469
Publication status	Published - Nov 2008

Keywords

MEDLINE

Access to Document

10.1093/bioinformatics/btn469

Cite this

@article{acf90ade6c5a47208ac125f3d307cd10,

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. {\textcopyright} 2008 The Author(s).",

keywords = "MEDLINE",

author = "Yoshimasa Tsuruoka and Jun'ichi Tsujii and Sophia Ananiadou",

year = "2008",

month = nov,

doi = "10.1093/bioinformatics/btn469",

language = "English",

volume = "24",

pages = "2559--2560",

journal = "Bioinformatics",

issn = "1460-2059",

publisher = "Oxford University Press",

number = "21",

}

TY - JOUR

T1 - FACTA: A text search engine for finding associated biomedical concepts

AU - Tsuruoka, Yoshimasa

AU - Tsujii, Jun'ichi

AU - Ananiadou, Sophia

PY - 2008/11

Y1 - 2008/11

N2 - 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. © 2008 The Author(s).

AB - 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. © 2008 The Author(s).

KW - MEDLINE

U2 - 10.1093/bioinformatics/btn469

DO - 10.1093/bioinformatics/btn469

M3 - Article

SN - 1460-2059

VL - 24

SP - 2559

EP - 2560

JO - Bioinformatics

JF - Bioinformatics

IS - 21

ER -

FACTA: A text search engine for finding associated biomedical concepts

Abstract

Keywords

Access to Document

Fingerprint

Cite this