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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: Thu, 17 Jan 2013 10:45:09 -0800
Message-ID: <81fa97265f51cb517f2b1dcf173573c5@mail.gmail.com>
To: "Lin MD, Simon" <LINMD.SIMON@mcrf.mfldclin.edu>, Kingsley Idehen <kidehen@openlinksw.com>
Cc: public-semweb-lifesci@w3.org
hi simon,

my lab group here at ISB has a web application called pubcrawl [1] which
looks through medline abstracts driven by a protein-protein interaction
database and results from analysis of TCGA data that we use in conjunction
with our regulome explorer [2].

the developer who wrote the app looked at RDF but settled on neo4j because
it seemed to scale better.  she didn't do any thorough testing between the
two, just played with both and found she liked a general graph engine
better.

we too are involved with cray, so it will be interesting to see what they
do with pubcrawl [3].

michael

[1] https://www.systemsbiology.org/pubcrawl
[2] http://explorer.cancerregulome.org/
[3]
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&cad=r
ja&ved=0CD0QFjAA&url=http%3A%2F%2Fwww.yarcdata.com%2Fdocs%2FSB-rapid-recov
ery.pdf&ei=b0X4ULTdKonUiwLe-IDYAQ&usg=AFQjCNEYpPBbBxvnQGVWmxls8nsRXSrWpw

Michael Miller
Software Engineer
Institute for Systems Biology

> -----Original Message-----
> From: Lin MD, Simon [mailto:LINMD.SIMON@mcrf.mfldclin.edu]
> Sent: Thursday, January 17, 2013 10:06 AM
> To: Kingsley Idehen; public-semweb-lifesci@w3.org
> Subject: RE: Facebook's new Graph Search: An endorsement of the RDF
> approach to healthcare data?
>
> Kingsley,
>
> I tried the link you send. With 55 Billion+ live triples, the response
time is very
> much impressive.
>
> However, I must say that I am lost on viewing the results -- the
presentation
> is not designed to anybody outside of the RDF community!
>
> By the way, how you compare your approach to neo4j? I am planning for a
> research prototype that needs ontology-driven query of millions of nodes
for
> treatment comparisons. Your inputs are appreciated!
>
> Simon
>
> ==================================================
> Simon Lin, MD | Director, Biomedical Informatics Research Center |
> Marshfield Clinic Research Foundation | 1000 N Oak Ave, Marshfield, WI
> 54449 | 715-221-7299 | Lin.Simon@mcrf.mfldclin.edu |
> www.marshfieldclinic.org/birc
>
>
> -----Original Message-----
> From: Kingsley Idehen [mailto:kidehen@openlinksw.com]
> Sent: Thursday, January 17, 2013 8:38 AM
> To: public-semweb-lifesci@w3.org
> Subject: Re: Facebook's new Graph Search: An endorsement of the RDF
> approach to healthcare data?
>
> On 1/16/13 8:12 PM, Rafael Richards wrote:
> > Yesterday Facebook announced a new feature called Graph Search.  This
> > Graph includes 1 billion people,  240 billion photos, and over 1
> > trillion connections.
> >
> > Graph search is privacy aware:  every piece of content has its own
> > specified audience. Most content is not public; you can only search
> > for content that has been shared with you.
> >
> > http://readwrite.com/2013/01/15/facebook-graph-search
> > https://newsroom.fb.com/News/562/Introducing-Graph-Search-Beta
> > https://newsroom.fb.com/Photos-and-B-Roll/4321/Graph-Search-
> Announcment
> >
> >
> > RDF data stores are also currently capable of  loading a trillion
> > triples ("connections"), and we have hardware such as the Cray
> > purpose built for graph analytics.
> >
> > http://www.franz.com/about/press_room/trillion-triples.lhtml
> > http://www.cray.com/Products/BigData/uRiKA.aspx
> > http://investors.cray.com/phoenix.zhtml?ID=1766098&c=98390&p=irol-
> newsArticle
> >
> >
> > There is also work done on a natural language query interface for RDF
> > using Cyc as the foundation ontology.
> >
> http://www.w3.org/2001/sw/sweo/public/UseCases/ClevelandClinic/#figur
> e3
> >
> > While not a "success story" of RDF per se,  Graph Search (if anyone
> > knows what its actual technology is)  may be at least an endorsement
> > of the RDF-like approach to managing, repurposing, and securing data.
> >
> > Is there any reason to believe that an RDF-based system could not
also:
> > 1. Enable similar storage and query as Graph Search?
> > 2. Provide similar data-atomic granular control of privacy of
> > (personal or healthcare) data similar to that of Graph Search?
> >
> >
> > Rafael
> >
> >
> > _____________________
> > Rafael Richards MD MS
> Rafael,
>
> Also note that there is a live 55 Billion+ triples instance of the LOD
> Cloud cache that showcases what's always been possible re. Linked Data,
> RDF, and machine readable Entity Relationship Semantics.
>
> Links:
>
> 1. http://lod2.openlinksw.com -- live instance
> 2. http://bit.ly/11ezuCz -- detailed instance report covering loading
> and some simple analytics
> 3. http://bit.ly/W8MYMj -- Uniprot citations overview
> 4. http://bit.ly/13HGvwX -- Bio2RDF entities associated with Genetic
> Dissorders
> 5. http://bit.ly/101tE55 -- Biopax data sources by collective attributes
.
>
>
>
> --
>
> 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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Received on Thursday, 17 January 2013 18:45:38 GMT

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