Biosystems retiring March 2022 — use PubChem Pathways

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.

2 thoughts on “Biosystems retiring March 2022 — use PubChem Pathways

  1. 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.

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