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RE: Facebook's new Graph Search: An endorsement of the RDF approach to healthcare data?

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 23 Jan 2013 09:48:38 -0800
Message-ID: <45eae8b2fdf1ca18fd62a1319ace6be0@mail.gmail.com>
To: Kingsley Idehen <kidehen@openlinksw.com>
Cc: public-semweb-lifesci@w3.org
hi kingsley,

thanks for the links.  i noticed on the fourth reference, neo4j was used
as an rdf store through its SAIL interface.  i found this nice benchmark
comparison of neo4j against other general graph databases [1], including
jena as an rdf store treated as a graph database.  here's also another
nice discussion of neo4j [2]

cheers,
michael

[1] http://link.springer.com/chapter/10.1007%2F978-3-642-16720-1_4?LI=true
[2] http://www.infoq.com/articles/graph-nosql-neo4j

Michael Miller
Software Engineer
Institute for Systems Biology

> -----Original Message-----
> From: Kingsley Idehen [mailto:kidehen@openlinksw.com]
> Sent: Friday, January 18, 2013 12:47 PM
> To: public-semweb-lifesci@w3.org
> Subject: Re: Facebook's new Graph Search: An endorsement of the RDF
> approach to healthcare data?
>
> On 1/18/13 1:14 PM, Michael Miller wrote:
> > hi kingsley,
> >
> > neo4j is a nosql graph database with (my knowledge is limited so
please
> > forgive if i misspeak) attributes for nodes, including type, and
> > attributes for edges.
> >
> > RDF is actually just triples, the syntax the RDF is expressed in is
the
> > notation and the data model is implicit, if i understand right, but
can be
> > captured by an ontology.  you can only really express a 'subject->
> > predicate -> (object|primitive)' as a single triple but triples can be
> > linked together by a common subject, which gives that subject multiple
> > 'attributes' or by a common object and subject which allows traversal.
> >
> > a general graph allows a subject to have multiple predicates specified
for
> > it, which is the major difference from RDF.  it also can represent a
data
> > model, ours certainly does with proteins, genes and drugs being some
of
> > the objects
> >
> > in fact i believe there is a fairly straight-forward translation
between
> > RDF and the more general graph.  tinkerpop can go from RDF to neo4j
> > amongst other graph databases [1].  there's also a great thread on
> > performance tuning for loading triples [2] into neo4j.
> >
> > i didn't find much on general graphs to RDF but there is a fair amount
of
> > information for conceptual graphs to RDF [3].
> >
> > i think what makes neo4j a better choice for us is that, for example,
when
> > a search is preformed, there will be a constraint on what type of
node(s)
> > and what type of edge(s) should be traversed.  neo4j is very good at
> > allowing  us to make indices based on the type of edge or node.
> >
> > cheers,
> > michael
> >
> > [1] http://java.dzone.com/news/rdf-data-neo4j-tinkerpop-story
> > [2]
> >
> https://groups.google.com/forum/?fromgroups#!searchin/neo4j/rdf/neo4j/
> g8bV
> > 8w3LH9E/WIgx5GP14KAJ
> > [3]
> >
> http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&c
> d=2&cad=r
> >
> ja&ved=0CEYQFjAB&url=http%3A%2F%2Fwww.lirmm.fr%2F~croitoru%2Frdf
> s.pdf&ei=L
> > Xr4UKmTPJDZigK22oDgDg&usg=AFQjCNGMzLXob8zCs0-j_85uFtR_a6Y26Q
>
> You might find the following useful:
>
> 1. http://vschart.com/compare/openlink-virtuoso/vs/neo4j-community
> 2.
> https://groups.google.com/forum/?fromgroups=#!topic/gremlin-
> users/Li5kynhJgB0
> 3. http://stackoverflow.com/questions/3537561/neo4j-vs-openlink-virtuoso
> 4. http://tinyurl.com/b3zo24l -- benchmark report that includes Neo4j .
>
> Kingsley
> >
> >> -----Original Message-----
> >> From: Kingsley Idehen [mailto:kidehen@openlinksw.com]
> >> Sent: Thursday, January 17, 2013 1:38 PM
> >> To: public-semweb-lifesci@w3.org
> >> Subject: Re: Facebook's new Graph Search: An endorsement of the RDF
> >> approach to healthcare data?
> >>
> >> On 1/17/13 1:45 PM, Michael Miller wrote:
> >>> the developer who wrote the app looked at RDF but settled on neo4j
> >> because
> >>> it seemed to scale better.
> >> RDF is a framework comprised of:
> >>
> >> 1. Data Model
> >> 2. Syntax
> >> 3. Notations.
> >>
> >> How do you compare that with an DBMS product? The comparison isn't
> like
> >> for like.
> >>
> >> --
> >>
> >> Regards,
> >>
> >> Kingsley Idehen
> >> Founder & CEO
> >> OpenLink Software
> >> Company Web: http://www.openlinksw.com
> >> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
> >> Twitter/Identi.ca handle: @kidehen
> >> Google+ Profile: https://plus.google.com/112399767740508618350/about
> >> LinkedIn Profile: http://www.linkedin.com/in/kidehen
> >>
> >>
> >>
> >>
> >
> >
>
>
> --
>
> Regards,
>
> Kingsley Idehen
> Founder & CEO
> OpenLink Software
> Company Web: http://www.openlinksw.com
> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
> Twitter/Identi.ca handle: @kidehen
> Google+ Profile: https://plus.google.com/112399767740508618350/about
> LinkedIn Profile: http://www.linkedin.com/in/kidehen
>
>
>
>
Received on Wednesday, 23 January 2013 17:49:05 GMT

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