PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana.

Prefix

pathbank

Keywords

animal genetics bioinformatics biology catalytic activity cell biology chemical structure cheminformatics database management disease drug drug interaction drug metabolism drug name drug target endocrinology enzymatic reaction enzyme gene gene name genetic disorder genetics glucose metabolic process human genetics image/movie interaction/pathway medical informatics metabolite metabolomics microbiology molecular biology molecular microbiology ontology pathway pathway diagram plant genetics polypeptide region protein protein interactions protein name protein structure protein-protein interaction proteomics reaction data receptor regulation of gene expression signaling systems biology transcriptomics xenobiotic metabolic process

License

ODbL-1.0

Links

Homepage OBO OWL OBO JSON

Publications

https://bioregistry.io/pubmed:37962386

https://bioregistry.io/pubmed:31602464

Pattern for Local Unique Identifiers

Local unique identifiers in PathBank should match this regular expression:
^(SMP|PW)\d+$

Example Local Unique Identifier

SMP0000219   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from PathBank should match this regular expression:
^pathbank:(SMP|PW)\d+$

Example CURIE

pathbank:SMP0000219

Contact

David S. Wishart   0000-0002-3207-2434   DavidWishartLab

Contributor

creator Charles Tapley Hoyt   0000-0003-4423-4370   cthoyt

Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 3 mappings to external registries with 3 unique external prefixes.

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier SMP0000219 is used to demonstrate the providers available for PathBank. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.