Is there a sample database to look at? Neo4j can export in RDF format. Do you have a paper or tech report?
On 12/3/2020 8:35 AM, Greg Landrum wrote: > Not quite what you're asking for, but: if you're willing to use neo4j > to store the graph (which rules out SPARQL I guess) you can use the > RDKit neo4j plugin: > https://github.com/rdkit/neo4j-rdkit > <https://github.com/rdkit/neo4j-rdkit> > That gets you efficient substructure search and similarity search. > > -greg > > > On Tue, Dec 1, 2020 at 4:04 PM Steve Vestal > <steve.ves...@adventiumlabs.com > <mailto:steve.ves...@adventiumlabs.com>> wrote: > > Does anyone know of a structure database that can be queried using an > RDF query language like SPARQL? PubChemRDF can be accessed in RDF > format, but it encodes structures as SMILES strings, which cannot be > queried in this way. > > If not, can anyone suggest open source software that might be used to > construct a modest RDF dataset from an existing structure database for > the purpose of experimenting? For example, software that can > translate > SMILES strings into an annotated graph data structure of some sort? > > Thanks in advance for any suggestions. > > > > > _______________________________________________ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > <mailto:Blueobelisk-discuss@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > <https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss> >
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