BioSystems


24460210	Pathway analysis for drug repositioning based on public database mining. [PMID: 24460210] Pan Y, Cheng T, Wang Y, Bryant SH. Abstract Sixteen FDA-approved drugs were investigated to elucidate their mechanisms of action (MOAs) and clinical functions by pathway analysis based on retrieved drug targets interacting with or affected by the investigated drugs. Protein and gene targets and associated pathways were obtained by data-mining of public databases including the MMDB, PubChem BioAssay, GEO DataSets, and the BioSystems databases. Entrez E-Utilities were applied, and in-house Ruby scripts were developed for data retrieval and pathway analysis to identify and evaluate relevant pathways common to the retrieved drug targets. Pathways pertinent to clinical uses or MOAs were obtained for most drugs. Interestingly, some drugs identified pathways responsible for other diseases than their current therapeutic uses, and these pathways were verified retrospectively by in vitro tests, in vivo tests, or clinical trials. The pathway enrichment analysis based on drug target information from public databases could provide a novel approach for elucidating drug MOAs and repositioning, therefore benefiting the discovery of new therapeutic treatments for diseases. J Chem Inf Model. 2014:54(2) \| 19 Citations (from Europe PMC, 2025-03-15)
19854944	The NCBI BioSystems database. [PMID: 19854944] Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH. Abstract The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets. Nucleic Acids Res. 2010:38(Database issue) \| 432 Citations (from Europe PMC, 2025-03-15)

Pathway analysis for drug repositioning based on public database mining. [PMID: 24460210]

Pan Y, Cheng T, Wang Y, Bryant SH.

Sixteen FDA-approved drugs were investigated to elucidate their mechanisms of action (MOAs) and clinical functions by pathway analysis based on retrieved drug targets interacting with or affected by the investigated drugs. Protein and gene targets and associated pathways were obtained by data-mining of public databases including the MMDB, PubChem BioAssay, GEO DataSets, and the BioSystems databases. Entrez E-Utilities were applied, and in-house Ruby scripts were developed for data retrieval and pathway analysis to identify and evaluate relevant pathways common to the retrieved drug targets. Pathways pertinent to clinical uses or MOAs were obtained for most drugs. Interestingly, some drugs identified pathways responsible for other diseases than their current therapeutic uses, and these pathways were verified retrospectively by in vitro tests, in vivo tests, or clinical trials. The pathway enrichment analysis based on drug target information from public databases could provide a novel approach for elucidating drug MOAs and repositioning, therefore benefiting the discovery of new therapeutic treatments for diseases.

J Chem Inf Model. 2014:54(2) | 19 Citations (from Europe PMC, 2025-03-15)

The NCBI BioSystems database. [PMID: 19854944]

Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH.

Abstract

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.

Nucleic Acids Res. 2010:38(Database issue) | 432 Citations (from Europe PMC, 2025-03-15)

URL:	http://www.ncbi.nlm.nih.gov/biosystems/
Full name:	NCBI BioSystems database
Description:	The NCBI BioSystems Database provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez.
Year founded:	2010
Last update:	2015-02-01
Version:	v4.0
Accessibility:	Accessible
Country/Region:	United States

Data type:	Other
Data object:	Animal Archaea Bacteria Fungi Plant Virus
Database category:	Metadata
Major species:	NA
Keywords:	pathway structural complex functional set signature module conserved biosystem organism specific biosystem

University/Institution:	National Center for Biotechnology Information
Address:	Bldg. 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
City:	Bethesda
Province/State:	MD
Country/Region:	United States
Contact name (PI/Team):	BioSystems team
Contact email (PI/Helpdesk):	biosystems.help@ncbi.nlm.nih.gov

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a catalog of worldwide biological databases

a catalog of worldwide biological databases

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Database Commons a catalog of worldwide biological databases