W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > January 2013

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

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Fri, 18 Jan 2013 10:14:51 -0800
Message-ID: <f075fcb89492ecc7c63cda2b59d5ef23@mail.gmail.com>
To: Kingsley Idehen <kidehen@openlinksw.com>, public-semweb-lifesci@w3.org
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 Friday, 18 January 2013 18:15:18 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:01:17 GMT