BioSystems is a new NCBI database of biological systems. It contains a tremendous variety of information regarding groups of molecules that interact in many types of biological systems. Biological systems, or BioSystems, are broadly defined to include not only the more traditional signaling pathways, but also diseases, and more. Many associated components are described, including genes, proteins, small molecules, biomarkers and drugs. You can use this database to find all the molecules in a specific pathway, to find pathways in which a specific molecule is involved, or to find structures for associate protein components, for example. BioSystems can be searched with very simple keyword or ID queries, or you can utilize some of the many types of advanced searches offered. Because BioSystems is part of NCBIs Entrez system of databases you have access to a tremendous variety of tools to customize your searches and results, and to find more information. The links to related data are extensive, and allow you to further your explorations by linking to the biological systems associated literature, molecular and chemical data.

You will learn:

  • to perform basic searches and to understand your results
  • to link out to a variety of related information in many different fields
  • about some Entrez tools that you can use to customize your searches and results
  • how to access and customize full-size pathway images
  • some advanced searching techniques, including Boolean queries and batch searching


This tutorial is a part of the tutorial group Interaction resources. You might find the other tutorials in the group interesting:

Pathway Interaction Database: A resource of pathway and network data and displays

MINT: Molecular Interaction Database

Cytoscape: An open-source software platform used for visualization and analysis of molecular interaction and network data

BiologicalNetworks: Analyze and visualize molecular interaction networks

Reactome Legacy: Older version of the current Reactome knowledgebase of biological processes.

Reactome: Knowledgebase of biological processes

GeneMANIA: GeneMANIA: Fast Gene Function Predictions

GenMAPP: A freely available open source software application for visualizing microarray data in the context of biological pathways.

VisANT: A web-based or downloadable software platform used for visualization and analysis of networks and interaction pathways

InterPro: A comprehensive protein signature resource

IntAct protein interaction database: IntAct is an open source database and analysis resource for protein interaction data

KEGG: KEGG, The Kyoto Encyclopedia of Genes and Genomes


Pathways and Interactions : Tools that are involved with protein interactions and pathway features. Some tools are primarily repositories and some offer analysis options.

NCBI : This category includes resources maintained at the National Center for Biotechnology Information (NCBI).


Tip of the Week: NCBI's FLink: Today I'd like to introduce you to FLink, which is a tool that NCBI released earlier this year, and we recently came across  during our 'regularly scheduled' update to our NCBI BioSystems tutorial. Al...

Tip of the Week: PathCase for pathway data: We spend a lot of time exploring genomic data, variations, and annotations. But of course a linear perspective on the genes and sequences is not the only way to examine the data. Understanding the pat...

New Online Tutorials for NCBI resources BioSystems and DCODE: Comprehensive tutorials on the publicly available NCBI resources BioSystems and DCODE enable researchers to quickly and effectively use these invaluable resources. Seattle, WA (PRWEB) February 23, 2010...

Tip of the Week: NCBI's New BioSystems Resource: At the Biocuration meeting that I attended back in April, Jim Ostell of NCBI announced that they would soon be releasing a new resource on biological networks. A few weeks ago a friend  alerted me tha...


Recent BioMed Central research articles citing this resource

Stevens Adam et al., Can network biology unravel the aetiology of congenital hyperinsulinism?. Orphanet Journal of Rare Diseases (2013) doi:10.1186/1750-1172-8-21

Iourov Y Ivan et al., Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies. Molecular Cytogenetics (2012) doi:10.1186/1755-8166-5-46

Cui Guangyu et al., Prediction of protein-protein interactions between viruses and human by an SVM model Advanced intelligent computing theories and their applications in bioinformatics. Proceedings of the 2011 International Conference on Intelligent Computing (ICIC 2011) The 2011 International Conference on Intelligent Computing (ICIC 2011). BMC Bioinformatics (2012) doi:10.1186/1471-2105-13-S7-S5

Gruszka Damian et al., The barley EST DNA Replication and Repair Database (bEST-DRRD) as a tool for the identification of the genes involved in DNA replication and repair. BMC Plant Biology (2012) doi:10.1186/1471-2229-12-88

ZarinKamar Nazanin et al., The Pax gene eyegone facilitates repression of eye development in Tribolium. EvoDevo (2011) doi:10.1186/2041-9139-2-8