I looked around and experimented a bit, and it seems pretty
straight-forward to use Apache Jena and Open Babel to insert an RDF
graph representation of structure into chebi.owl that is constructed
from the existing SMILES strings.
Can someone suggest a widely-used existing vocabulary for concepts
(rdf:types, owl:classes) and associated properties that are reasonably
synonymous with primary things obtained from an OBMol object such as
OBBond, OBAtom, etc.? I would prefer an OWL-DL over an OWL-FULL
vocabulary, and OWL-FULL over an RDFS vocabulary, but being widely-used
is a more important criteria.
On 12/4/2020 9:45 AM, christian.pil...@web.de wrote:
Dear all,
currently, our "work horse" is a database of 50k chemical reactions
extracted from US patents. Chemical structures are assigned by our
neo4j/RDKit-plugin as node attributes and can be queried by
(sub-)structure queries through the neo4j query language CYPHER.
Please find attached a short PDF outlining the opportunities of the
plugin. Let me know if you find it useful. We recently updated to the
latest releases of RDkit (2020.09.01) and neo4j (4.2.1) - testing is
intended to be fiinalized over the upcoming weekend. I'm happy to
provide afore mentioned sample database and - if needed - detailed
instructions how to upload it into a neo4j instance.
Viele Grüße,
Christian
*Gesendet:* Donnerstag, 03. Dezember 2020 um 18:15 Uhr
*Von:* "Greg Landrum" <greg.land...@gmail.com>
*An:* "Steve Vestal" <steve.ves...@adventiumlabs.com>,
christian.pil...@web.de
*Cc:* "BlueObelisk-Discuss" <blueobelisk-discuss@lists.sourceforge.net>
*Betreff:* Re: [BlueObelisk-discuss] Structure database that can be
queried by SPARQL?
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
<mailto: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
<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.
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