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

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Wed, 23 Jan 2013 14:08:25 -0500
Message-ID: <51003529.3090701@openlinksw.com>
To: public-semweb-lifesci@w3.org
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

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..

Kingsley
>
> 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
>>
>>
>>
>>
>
>


-- 

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 19:08:49 GMT

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