eBremer

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 <1,1,0> 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.

After a few months of work, on and off, here is the first display of resource description framework (RDF) data by Nexus inside of Second Life.  This particular graph is of Tim Berners-Lee's FOAF data.  FOAF (Friend of a Friend) is an semantic ontology that describes people, their interests, and their relationships to other people.  Tim Berners-Lee (TBL) published along with James Hendler, and Ora Lassila the article "The Semantic Web" in Scientific American's May 2001 issue.  Tim Berners-Lee is also credited with the invention of the World-Wide-Web itself.  So, TBL's FOAF data seemed an appropriate selection for test data for Nexus.  There are still a few bugs in the predicate positioning code leaving some of the predicates misaligned with their subjects and objects that needs to be resolved.  The large tri-ball object in the picture is actually Nexus which is a 3D version of W3C's RDF logo seen on the right here.  The DNA molecule was generated from my Monolith project which created DNA/Protein models from the Rutger's Protein Databank inside of Second Life.  As I have mentioned previously, all functionality of Monolith will be incorporated into Nexus, but, Nexus will be able to create models on any RDF data and not be limited to just PDB data like Monolith is.  The RDF model featured above was generated by a force-based 3D-layout algorithm applied to the RDF graph of TBL's FOAF data then rendered in the 3D environment of Second Life.  The actual RDF data text/numerics/URIs are seen as hover-text above the various balls and sticks and can also be seen by clicking on the item of interest.  The visualization is vanilla at the moment, but I will be adding a variety of visual elements to the system such as color-coded subject/predicate/objects, light, texture, sound, and so forth.  Problems with "node clutter" such as in the case of highly connected nodes will also be address using node expansion and node splitting to help make the visual model easier to understand.  For Monolith functionality, rather than using a force-based algorithm to determine the positioning of the various nodes (in the case of Monolith functionality, atoms), the atomic coordinates derived from the pdb files will determine their locations, the predicates being used to represent the bonds just done semantically using a semantic conversion of PDB data (for example N13 pdb:bondedto C1).  Other features will be added such as chaining and loading other semantically linked data sources into the current graph for a combined view and layout and even a public SPARQL end-point inside of Second Life.  I've already written in a session-handling system into Nexus so I will be able to release a public version of Nexus for use in other regions of Second Life.  I had never completed a session handler for Monolith which is why it was never generally released.  For those of you scratching your heads asking, "Why do this in Second Life?", hmmm, well, a collaborative way to allow 100 people to look at the same 3D semantic model at the same time, work interactively with it together at the same time, and discuss using IM and voice as well, from 100 different locations on the planet...sorry, that's just cool!  :-) For those people reading this that are not semantically-savvy, I'm hoping it will all make more sense and be easier to understand when I have more of the visual work done.  Stay tuned...