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

[Kingsley Idehen]

On 1/23/13 12:48 PM, Michael Miller wrote:

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

Kingsley

None of the above (unless I've overlooked something) include Virtuoso. Do understand that Virtuoso is engineered for massive scalability with historical DBMS challenges in mind etc..

Michael Miller
Software Engineer
Institute for Systems Biology

-----Original Message-----
From: Kingsley Idehen [mailto:kide...@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:kide...@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

--

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

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