Bio2RDF
Bio2RDF uses Semantic Web methods to convert many separate biological databases into a common format called RDF, which expresses data as subject-predicate-object statements known as triples. Once everything shares that format, you can query across datasets that were never designed to work together.
Queries run through a SPARQL endpoint, SPARQL being the standard query language for this kind of knowledge graph. The combined graph reaches roughly 11 billion triples spanning 35 datasets, among them DrugBank, PubMed, and MeSH.
Licensing varies by the underlying source dataset, so there is no single blanket licence covering the whole collection. Check the terms of each dataset you rely on before building a commercial product on it.
Related sources
ChEBI
A dictionary of small chemical compound molecular entities, with structure files and ontology files available for download. Particularly useful as a controlled vocabulary for chemical entity linking, where you match a mention in text to a standard identifier.
ChEMBL
A manually curated database of bioactive molecules with drug-like properties, bringing together chemical, bioactivity, and genomic data to support drug discovery. Holds close to 2.5M compound records on nearly 2M unique chemical structures, extracted mainly from the medicinal chemistry literature.
Crystallography Open Database
A collection of over 350,000 crystal structure files covering organic, inorganic, and metal-organic compounds, released into the public domain under CC0.
Materials Project
A database of computed properties for known and predicted materials, produced through high-throughput density functional theory calculations (a physics method for modelling how electrons behave in a material). Free API access with registration.