The NCBI BioSystems database

By Lewis Y. Geer, Aron Marchler-Bauer, Renata C. Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, Stephen H. Bryant. Nucleic Acids Res., 2009

865 citations recorded by the source corpus.

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/61076194ec631a89daa30edbcc90bc7be37804cc

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Citations in the corpus

WikiPathways: building research communities on biological pathways (2011, background): “The WikiPathways content is already accessible from several external resources, such as NCBI BioSystems (7) and BioGPS (8).”
Reactome: a database of reactions, pathways and biological processes (2010, neutral): “) that interact in biological systems (28).”
Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life (2014, methodology): “The proteomes were assigned to their taxonomic lineage based on the National Center for Biotechnology Information (NCBI) [36], where the lowest taxonomic level, which we refer to as “species”, could be the genus, family or species.”
Gene: a gene-centered information resource at NCBI (2014, background): “Its content is from NCBI’s BioSystems (16) database, which centralizes information about pathways from multiple sources, including KEGG (17) and Reactome (18).”
PubChem structure–activity relationship (SAR) clusters (2015, background): “The UID indicates AID, GI, and BSID for assay-centric (panel a), protein-centric (panel b), and pathway-centric clusters (panel c), respectively. encoded in molecular fingerprints by using feature atoms that represent six functional group types.”
PubChem in 2021: new data content and improved web interfaces (2020, neutral): “For instance, the following URL directs to the pathway page for the human glycolysis pathway from PathBank (ID: SMP0000040): https://pubchem.ncbi.nlm.nih.gov/pathway/PathBank: Pathways resource supersedes the NCBI BioSystems database (60), which is no longer being updated.”
WikiPathways: capturing the full diversity of pathway knowledge (2015, background): “Biosystems (13)), other BioPAX-formatted pathways (PathwayCommons (14)), microRNA target information (miRWalk2.”
PubChem 2019 update: improved access to chemical data (2018, background): “Genomes (KEGG) (21), BioSystems (22), Molecular Modeling Database (MMDB) (23).”
NCBI GEO: archive for functional genomics data sets—update (2012, background): “The ‘ﬁnd pathways’ feature on GEO proﬁles (http:// www.ncbi.nlm.nih.gov/geoproﬁles/) retrievals allows users to map genes to a frequency weighted list of pathways in NCBI’s BioSystems database (11) helping to characterize lists of genes.”