NCBI BioSystems Database
About the BioSystems Database

Thumbnail image showing the types of data you can obtain for a metabolic pathway in the NCBI BioSystems database, including genes, proteins, small molecules, and related biosystems.  Click on the image to open the live BioSystems record for human arachidonic acid metabolism and explore the links to the gene, protein, chemical, and literature databases. A biosystem, or biological system, is a group of molecules that interact in a biological system. One type of biosystem is a biological pathway, which can consist of interacting genes, proteins, and small molecules. Another type of biosystem is a disease, which can involve components such as genes, biomarkers, and drugs.

A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. The NCBI BioSystems Database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data.

The NCBI BioSystems record for arachidonic acid metabolism, for example, displays the name and description of the biosystem along with a thumbnail image of the pathway diagram that links to the full size illustration on the source database's web site. In addition, the BioSystems record lists and categorizes the genes, proteins, and small molecules involved in the biological system, along with related biosystems and citations, and allows instant retrieval of the those data sets through a wide range of Links. Integrating the data in this way makes it possible to search across all the pathways to answer broad questions such as the "how to" examples shown below. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems.

The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). The BioSystems database includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. Detailed diagrams and annotations for individual biosystems are then available on the web sites of the source databases.

How to use the BioSystems database: examples back to top

List the genes, proteins, and small molecules that are involved in a biological pathway


Find the pathways in which a given gene or protein is involved


Find the pathways in which a specific small molecule is involved


Retrieve 3D structures for proteins involved in a biosystem


Find related biosystems that are linked to each other because they share an identical protein sequence or have another relationship


Large scale data processing:  input a list of proteins and retrieve ranked list of biosystems (using FLink icon FLink)


Start with a gene expression study and retrieve a ranked list of biosystems in which the up- or down-regulated genes are involved (using FLink icon FLink)

BioSystem Record: Components and Features

Thumbnail image showing portions of the NCBI BioSystems record bsid82991, for human arachidonic acid.  Click on image to read more about biosystem record components and features in the help document.

Explore large scale data associations with FLink icon FLink:

Use FLink to input lists of gene, protein sequence, or small molecule identifiers and retrieve ranked lists of pathways from the BioSystems database. Click on this image to learn more about FLink.

Revised 19 September 2016