Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jan;38(Database issue):D492-6.
doi: 10.1093/nar/gkp858. Epub 2009 Oct 23.

The NCBI BioSystems database

Lewis Y Geer  1 , Aron Marchler-Bauer, Renata C Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, Stephen H Bryant
Affiliations

The NCBI BioSystems database

Lewis Y Geer et al. Nucleic Acids Res. 2010 Jan.

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
A schematic representation of the integration of the BioSystems database with various NCBI resources and with resources publically available from the depositor.
Figure 2.
Figure 2.
An example BioSystems record display for the COX portion of the arachidonic acid metabolism pathway, which metabolizes lipids that are commonly found in the cell membrane into prostaglandins. The display includes a thumbnail image, links back to the depositor’s web site, and lists of the molecular identifiers and annotations associated with the pathway.
See this image and copyright information in PMC

References

    1. Bader GD, Cary MP, Sander C. Pathguide: a pathway resource list. Nucleic Acids Res. 2006;34:D504–D506. - PMC - PubMed
    1. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:D480–D484. - PMC - PubMed
    1. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009;37:D619–D622. - PMC - PubMed
    1. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: the Pathway Interaction Database. Nucleic Acids Res. 2009;37:D674–D679. - PMC - PubMed
    1. Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R, Hewett M, Lin Z, Liu Y, Liu S, Oliver DE, et al. Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J. 2001;1:167–170. - PubMed

Publication types