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GenDrux: a biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer.

Crasto C, Luo D, Yu F, Forero A, Chen D - BMC Med Inform Decis Mak (2011)

Bottom Line: GenDrux is designed to alleviate the difficulties of manually processing the vast biomedical literature to identify disease-gene-drug relationships.The archiving process has been automated.The successful development, implementation, and evaluation of this and similar systems when created may provide clinicians with a tool for literature management, clinical decision making, thus setting the platform for personalized therapy in the future.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Research, Department of Genetics, Univ. of Alabama at Birmingham (UAB), USA.

ABSTRACT

Background: This paper describes the development of a web-based tool, GenDrux, which extracts and presents (over the Internet) information related to the disease-gene-drug nexus. This information is archived from the relevant biomedical literature using automated methods. GenDrux is designed to alleviate the difficulties of manually processing the vast biomedical literature to identify disease-gene-drug relationships. GenDrux will evolve with the literature without additional algorithmic modifications.

Results: GenDrux, a pilot system, is developed in the domain of breast cancer and can be accessed at http://www.microarray.uab.edu/drug_gene.pl. GenDrux can be queried based on drug, gene and/or disease name. From over 8,000 relevant abstracts from the biomedical literature related to breast cancer, we have archived a corpus of more than 4,000 articles that depict gene expression-drug activity relationships for breast cancer and related cancers. The archiving process has been automated.

Conclusions: The successful development, implementation, and evaluation of this and similar systems when created may provide clinicians with a tool for literature management, clinical decision making, thus setting the platform for personalized therapy in the future.

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Related in: MedlinePlus

The searching results by a disease.
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Figure 2: The searching results by a disease.

Mentions: The GenDrux Web portal can be found at http://microarray.uab.edu/drug_gene.pl. The front page of GenDrux is shown in Figure 1. A user can search the downloaded literature using one or more parameters: disease, drug name, and gene name. A negative control feature is also available, which allows a user to exclude abstracts that contain specific keywords or phrases. The results include the title, the abstract, the gene name, drug name, the date of publication, the name of the first and ranking author and the journal name, as shown in Figure 2. Each result also includes a link to the PubMed abstract, as well as link to drug.com and (Gene Ontology) GO website. For academic users or those who subscribe to the journal, this link will also lead the user (through PubMed) to the full-text of the article. The system identifies articles that contain references to genes and drugs for specific cancer. Given the nature of information retrieval from free-text (this is discussed in detail later), the system relieves the burdens of processing large amounts of text. We leave it to the clinician-user to determine the specific relationship or whether the relationship merits a diagnosis or a prescription.


GenDrux: a biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer.

Crasto C, Luo D, Yu F, Forero A, Chen D - BMC Med Inform Decis Mak (2011)

The searching results by a disease.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116456&req=5

Figure 2: The searching results by a disease.
Mentions: The GenDrux Web portal can be found at http://microarray.uab.edu/drug_gene.pl. The front page of GenDrux is shown in Figure 1. A user can search the downloaded literature using one or more parameters: disease, drug name, and gene name. A negative control feature is also available, which allows a user to exclude abstracts that contain specific keywords or phrases. The results include the title, the abstract, the gene name, drug name, the date of publication, the name of the first and ranking author and the journal name, as shown in Figure 2. Each result also includes a link to the PubMed abstract, as well as link to drug.com and (Gene Ontology) GO website. For academic users or those who subscribe to the journal, this link will also lead the user (through PubMed) to the full-text of the article. The system identifies articles that contain references to genes and drugs for specific cancer. Given the nature of information retrieval from free-text (this is discussed in detail later), the system relieves the burdens of processing large amounts of text. We leave it to the clinician-user to determine the specific relationship or whether the relationship merits a diagnosis or a prescription.

Bottom Line: GenDrux is designed to alleviate the difficulties of manually processing the vast biomedical literature to identify disease-gene-drug relationships.The archiving process has been automated.The successful development, implementation, and evaluation of this and similar systems when created may provide clinicians with a tool for literature management, clinical decision making, thus setting the platform for personalized therapy in the future.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Research, Department of Genetics, Univ. of Alabama at Birmingham (UAB), USA.

ABSTRACT

Background: This paper describes the development of a web-based tool, GenDrux, which extracts and presents (over the Internet) information related to the disease-gene-drug nexus. This information is archived from the relevant biomedical literature using automated methods. GenDrux is designed to alleviate the difficulties of manually processing the vast biomedical literature to identify disease-gene-drug relationships. GenDrux will evolve with the literature without additional algorithmic modifications.

Results: GenDrux, a pilot system, is developed in the domain of breast cancer and can be accessed at http://www.microarray.uab.edu/drug_gene.pl. GenDrux can be queried based on drug, gene and/or disease name. From over 8,000 relevant abstracts from the biomedical literature related to breast cancer, we have archived a corpus of more than 4,000 articles that depict gene expression-drug activity relationships for breast cancer and related cancers. The archiving process has been automated.

Conclusions: The successful development, implementation, and evaluation of this and similar systems when created may provide clinicians with a tool for literature management, clinical decision making, thus setting the platform for personalized therapy in the future.

Show MeSH
Related in: MedlinePlus