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BioCodeKb - Bioinformatics Knowledgebase

The NCBI BioSystems record lists the genes, their associated proteins and the small molecules involved in the pathway. The BioSystems records also have annotations such as taxonomy, description, pathway images and citations.

A biosystem, or biological system, is a group of molecules that interact in a biological system.

The NCBI BioSystems database, 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.

For analysis of data on a large scale, such as obtained via high-throughput experimentation, we anticipate the development of services that facilitate summary views of such data characterized by biosystems. For example, this might include an ordered list of the BioSystems most represented in a high-throughput biological assay.

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 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.

Many types of records are currently available in the BioSystems database such as pathway, structural complex, functional set etc. Records of pathway, structural complex, functional set and signature module are described in detail.


The NCBI BioSystems Database was developed as a complementary project to

  • serve as a centralized repository of data

  • connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system

  • facilitate computation on biosystems data

  • includes several types of records such as pathways, structural complexes, and functional sets

  • availability of LIPID maps

  • Centralize access to existing biosystems database

  • Connect biosystems records with associated literature, molecular, and chemical data

  • Facilitate computation on biosystems data

  • desiged to accomodate other record types, such as diseases, as data become available

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

  • Find the pathways in which a specific gene or protein is involved

  • Find the pathways in which a specific small molecule (e.g., salicylic acid) is involved

  • Retrieve the 3D structures for proteins involved in a biosystem

The BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. Once we are viewing a record of interest in the NCBI BioSystems Database, simply use the links menus or folder tabs to see lists of components by type.

  • The data processing pipeline categorizes and lists the genes, proteins, and small molecules that are components in a biosystem.

  • These components are accessible from the "Related information" menu that appears in the right hand margin of an individual biosystem record.

  • The components are also accessible through the folder tabs that appear near the bottom of the biosystem record.


Need to learn more about BioSystems and much more?

To learn Bioinformatics, analysis, tools, biological databases, Computational Biology, Bioinformatics Programming in Python & R through interactive video courses and tutorials, Join BioCode.

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