You should have a lookat rdf and json-ld. More and more bio databases are supporting these serialisations of their data. Quite a few even allow sparql access (s

You should have a lookat rdf and json-ld. More and more bio databases are supporting these serialisations of their data. Quite a few even allow sparql access (sql over http for semantic graphs) e.g. rd.ebi.ac.uk and beta.sparql.uniprot.org among others. there is also work to make data stored in existing databases and files available by sparql without transforming the data first.