I'm going to bring in Christian to answer the questions about the RDKit/Neo4J integration. Christian defined the use cases we implementing, as done all the testing, and coordinated the development work.
-greg On Thu, Dec 3, 2020 at 3:54 PM Steve Vestal <steve.ves...@adventiumlabs.com> wrote: > 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 > 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> 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 >> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss >> >
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