The NCBI BioSystems Database will be retired in March 2022. This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content.
NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource that offers a fresh, extended, and more modern interface. See the PubChem blog for more details on PubChem Pathways.
Table 1 presents a snapshot of the richer and more extensive data coverage in PubChem Pathways.
| Source database | BioSystems | PubChem Pathways (as of 8/10/21) |
|---|---|---|
| BioCyc | 15,259 records | 15,037 records |
| PlantCyc | 64,851 records | |
| Reactome | 20,478 records | 26,407 records |
| Plant Reactome | 18,910 records | |
| NCI Pathway Interaction DB | 188 records | 745 records |
| Wiki Pathways | 1,478 records | 1,823 records |
| Lipid Maps | 14 records | 15 records |
| PharmGKB | 147 records | |
| PathBank | 110,315 records | |
| COVID-19 Disease Map | 20 records | |
| INOH | 511 records | |
| GO | 44,525 records | |
| KEGG | 902,026 records |
Table 1: Coverage for BioSystems records in PubChem Pathways. In anticipation of retiring BioSystems, we will begin directing relevant queries to PubChem Pathways to provide users with a richer dataset and enhanced user experience.
Requests to NCBI BioSystems will be directed to PubChem Pathways in order to make the transition as seamless as possible. The static content of NCBI BioSystems will remain available on the BioSystems FTP site but will not be updated.
We thank everyone for their support of BioSystems through the years. Please contact us with any comments, concerns, or if you need help with the use of BioSystems data.
Says “PubChem pathways are searchable within PubChem Search.” but that link just goes to general pubchem and I do not see ability to choose between structure and pathway. Do you mean that pathway will be within each chem page? That needs to be explicitly stated.
If you search with the name of a pathway, for instance ‘glycolysis’, you’ll get a full set of results with a tab containing the pathways https://pubchem.ncbi.nlm.nih.gov/#query=glycolysis
https://pubchem.ncbi.nlm.nih.gov/#query=glycolysis&tab=pathway