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

From: Andrea Splendiani <andrea.splendiani@deri.org>
Date: Sat, 19 Jan 2013 12:24:18 +0000
Cc: Kingsley Idehen <kidehen@openlinksw.com>, public-semweb-lifesci@w3.org
Message-Id: <D0709B22-2A0A-43CE-9B58-62530E2457F4@deri.org>
To: Michael Miller <Michael.Miller@systemsbiology.org>
Hi,

RDF/Triplestores and Neo4J can both be used as technologies to represent graph structures (like p-p interactions). Neo4J may offer a slightly more natural representation of edge attributes for some, but otherwise they both can "hold graphs".
Than they are different tools.
If you go for queries, I think RDF/Triplestores have a edge. They are naturally the technology to use if you want to make queries that span different web-distributed resources. But even to query your own dataset, SPARQL is pretty rich, and I guess more likely optimized for triplestore than as a front-end to Neo4J (though that'ps a guess).
However, if you are into graph analysis, you may want to do lots of simple calls to the graph (I'm thinking about some path analysis). Here sparql is too heavy. It can be that some triplestore offer some native interfaces to graphs, but I think Neo4J has an advantage in this case (it's more focused, less overhead).

Another thing to consider, last time I had a look at Neo4J I think it was limited to 4B nodes, on a single instance machine.

best,
Abdrea


Il giorno 18/gen/2013, alle ore 18:14, Michael Miller <Michael.Miller@systemsbiology.org> ha scritto:

> 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&cd=2&cad=r
> ja&ved=0CEYQFjAB&url=http%3A%2F%2Fwww.lirmm.fr%2F~croitoru%2Frdfs.pdf&ei=L
> Xr4UKmTPJDZigK22oDgDg&usg=AFQjCNGMzLXob8zCs0-j_85uFtR_a6Y26Q
> 
>> -----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
>> 
>> 
>> 
>> 
> 
Received on Monday, 21 January 2013 09:24:22 GMT

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