A BioSystem record is defined as a biologically related list of gene, protein and small molecule identifiers, along with the characterization of interactions, citations and other annotations, where none of these items are mandatory. This definition is not limited to metabolic- or signaling pathways: for example, a BioSystems disease record may contain susceptibility genes, biomarkers and drugs used for treatment.
The BioSystems database is archival and each BioSystem record receives a unique identifier known as a bsid that is intended to remain constant over the lifetime of the record. Each new version of a BioSystem record is assigned a version number.
Presently, NCBI BioSystems contains pathways from KEGG (2
), Human Reactome (3
) and EcoCyc (9
) for a total of about 100 000 BioSystem records. These BioSystems records link to over 2 million protein records, nearly 900 000 gene records and several thousands PubChem records.
An example record, shown in , describes the COX portion of the human arachidonic acid metabolism pathway, which metabolizes lipids into prostaglandins that are involved in a host of regulatory mechanisms via binding to and activating G protein-coupled receptors. This pathway has an important role in pain and inflammation. Specifically, the protein encoded by human PTGS1 gene is involved in the conversion of prostaglandin PGG2 into inflammation-causing prostaglandin PGH2. Aspirin has been shown to bind to the PTGS1 gene product (prostaglandin-endoperoxide synthase 1), blocking that enzyme’s ability to produce PGH2 and thereby reducing pain and inflammation. The NCBI BioSystems record lists these genes, their associated proteins and the small molecules involved in the pathway. The BioSystems records also contain annotations such as taxonomy, description, pathway images and citations. Finally, links to and from other NCBI Entrez databases are listed, including links between BioSystems records. Links between BioSystems records are specified by the depositor and also generated computationally for BioSystems that list overlapping sets of proteins.
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 (more ...)
Currently, we distinguish between two major record types, organism-specific biosystems and conserved biosystems. Organism-specific biosystems correspond to particular instances of a biological system, such as the arachidonic acid pathway in human. Conserved biosystems are canonical biosystems that are used to group together orthologous, organism-specific biosystems. Currently, these records are derived from reference pathways in the KEGG database.