Biosystems Database from NLM

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, such as KEGG, BioCyc, Reactome, and the Pathway Interaction Database 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 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 biological pathways from four sources: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, and the National Cancer Institute's Pathway Interaction Database. It is also designed to accommodate other types of biosystems such as diseases as data about them 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:

• 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

Search other databases from:

• Entrez databases from NLM

Other databases for:

• Chemical and physical properties
• Statistics and data sets
• Freely accessible databases

Other databases covering:

• Agricultural, biological, and medical sciences