Nexus

3D RDF Model of RxNorm data

The following is a 3D RDF Model of RxNorm data of drugs (example here) that contain lithium carbonate as an ingredient.  The red balls are the drug products and the greens (difficult to see them in this view, easier to view in 3D) are the various ways lithium carbonate is listed in the RxNorm database.  Predicates rxnorm:ingredient_of and rxnorm:hac_ingredient are colored yellow.  The RxNorm data was converted/maintained by my colleague Dr. Janos Hajagos at Stony Brook University.  He participates in the W3C Linked Open Drug Data group.  The original RxNorm data can be found at:

http://www.nlm.nih.gov/research/umls/rxnorm/

and the RDF version can be found at our SPARQL endpoint/Triple Store (based on Virtuoso) at:

http://link.informatics.stonybrook.edu/sparql/

The data set for this model was constructed with the following RDF query:

prefix rxnorm: <http://link.informatics.stonybrook.edu/rxnorm/>
construct {
  ?aui ?auip ?auio .
  ?auiingred ?auiingredp ?auiingredo . }
where {
<http://link.informatics.stonybrook.edu/rxnorm/RXAUI/2072077> rxnorm:hasRXCUI ?cui .
?aui rxnorm:hasRXCUI ?cui .
?aui ?auip ?auio .
?aui <http://link.informatics.stonybrook.edu/rxnorm/REL#ingredient_of> ?auiingred .
?auiingred ?auiingredp ?auiingredo
}

Nexus to this point, used FOAF data for testing.  I did this model to test with something a bit different.  This model is also a bit more complex and it will help with visualizations in the future as additional visual functions are added, as well as, modifications to the layout engine.

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Color 3D RDF FOAF Graphs in Second Life

Added a new command for coloring of the 3D RDF graphs.  It uses the syntax:

color <r,g,b> spo where { pattern }

where:

<r,g,b> is a rgb color vector.  <1,1,0> would be yellow.

spo is either spo, sp, so, po, s, p, o to have the command operate on one of the combinations of subject, predicate, and/or object of the triple.

where { pattern } is borrowed right out of SPARQL's syntax.  Nexus actually uses it's own ontology that is used to describe the visual features of the 3D graph such as {nex:color, nex:alpha, nex:xyz, etc}  All graph data can then be streamed out and include the Nexus ontology for persistence of a visualization session for later viewing or sharing.  In these three graphs, the @timberners_lee and @jahendler FOAF graph data that I have been using as test data are colored by issuing the following two commands:

color <1,0,0> spo where { ?s ?p ?o . filter ( ?p=foaf:knows ) }
color <0,1,0> spo where { ?s ?p ?o . filter ( ?p=rdf:type ) }

The first command colors all foaf:know triples red and the second command colors all triples that are rdf:type green.  The default color for everything is blue <0,0,1>  In the lower right image, the lone green ball is actually foaf:Person.  No, data that can be loaded can be any RDF not just FOAF.  This model is currently on display at the Stony Brook SOM region.  Yes, this is in Second Life, so, bring your friends and look at it together and use IM and voice to discuss it collaboratively while your there.  The region supports up to 100 concurrent users.

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