Bio2RDF cloud of
Virtuoso SPARQL endpoints
Life Science
Raw Data Now
François Belleau, Marc-Alexandre Nolin,
Peter Ansell, Michel Dumontier
30th April 2009
W3C-HCLS F2F Meeting, Cambridge, MA

Agenda
Why we did Bio2RDF ?
●
How we did it ?
●
What is know about hexokinase ?
●
Where we are going ?
●

The problem
According to NAR 2009 Database
collection 1170 public databases
exists.
How can they be integrated to behave
like a global coherent resource ?

Public map of 1744 namespaces according to
BioMoby, NAR, SRS, GO, NCBI, UniProt

Bio2RDF vision in 2007
Johanne Luciano vision for
knowledge integration in 2005
W3C vision of semantic web
in 2006

Bio2RDF Mouse and Human Atlas map
in 2008 65 millions triples

Bio2RDF actual contribution
to the Linked Data cloud
Linked data cloud
in 2007
Linked data cloud
in March 2009
http://linkeddata.org/
http://esw.w3.org/topic/TaskForces/CommunityProjects/LinkingOpenData/DataSets/Statistics

Bio2RDF cloud map of
2,3 billions triples in 2009

Why do it ?
Not to replace HTML or XML by an other new
format, RDF and OWL, but to answer science
question by submiting SPARQL query over
the global knowledge base accessible through
the Internet to the Life Science SPARQL
endpoints cloud.

Solution
Bio2RDF approach to the data integration
problem in bioinformatics :
Apply the semantic web approach based
on RDF, OWL and SPARQL technologies.

How we did it ?
Bio2RDF architecture

Our design principles
http://www.w3.org/DesignIssues/LinkedData
http://bio2rdf.wiki.sourceforge.net/Banff%20Manifesto

YeastHub design in 2005
Conversion of Dataset to RDF
●
Use of Sesame Triplestore
●
SeRQL query interface
●
http://www.ncbi.nlm.nih.gov/pubmed/15961502

Bio2RDF at ISMB 2005
the begining
Thanks to Kei Cheung,
Johanne Luciano, Eric
Neumann and
Christopher Baker they
draw the lines.

Bio2RDF realtime rdfiser in 2007

Actual Architecture
Offline rdfising process
●
● Virtuoso SPARQL endpoints
network
● Namespace resolution
through DNS subdomain

Main REST services
Describe a ressource by a dereferencable URI
●
http://bio2rdf.org/ns:id
●
Global services over federated endpoints
●
http://bio2rdf.org/links/ns:id
●
http://bio2rdf.org/search/searchedTerm
●
Targeted services to a specific endpoint
●
http://bio2rdf.org/linksns/ns2/ns1:id
●
http://bio2rdf.org/searchns/ns/searchedTerm
●
other services are available.
●

Describe service implementation
http://bio2rdf.org/ns:id
●
Corresponding SPARQL query :
●
CONSTRUCT {
●
?s ?p ?o .
}
WHERE {
?s ?p ?o .
FILTER(?s = <http://bio2rdf.org/ns:id>).
}
Submited at this URL
●
http://ns.bio2rdf.org/sparql?query=...
●
Based of DNS subdomain resolution service
–

Bio2RDF JSP server software
http://sourceforge.net/projects/bio2rdf/

Peter Ansell is writing the Bio2RDF
JSP server
The software transform Bio2RDF URIs to SPARQL
●
queries in real time.
Its aim is to access normalised RDF information
●
located in multiple endpoints using the concept of
Public Namespaces and Private Record Identifiers and
distributed SPARQL queries which are matched to the
content in each endpoint.
Each of the following databases have normalisation
●
rules which normalise them back to bio2rdf.org
URI's :Dbpedia, Drugbank, LinkedCT, HCLS
KB/Neurocommons, Diseasome, Dailymed, Bioguid
DOI

Bio2RDF.war package future
Provide more pipes to perform integrated actions without
●
having to put HTTP SPARQL requests into a workflow
system when a URI resolution can perform the query in a
distributed and normalised manner more efficiently
Bring together the current distributed efforts to provide a
●
complete HTML redirection registry so that a large
percentage of Bio2RDF namespaces can be redirected
with http://bio2rdf.org/html/namespace:identifier
Form ontologies describing the query type, provider, rdf
●
normalisation rule, namespace paradigm
Integrate http://rdf.myexperiment.org/sparql and similar
●
workflow RDF endpoints so that scientific workflows can
be linked to their data cleanly

Bio2RDF.owl
http://quebec.bio2rdf.org/download/bio2rdf-2008.owl

Michel Dumontier will design
Bio2RDF.owl ontology next version

What is known about hexokinase ?

Submit your query...
To the web search engine
●
To existing public web site offering data
●
integration services;
Using Bio2RDF SPARQL endpoints
●
Submitting a SPARQL query;
●
Using facet browser interface from Virtuoso 6.0
●
server;
Dereferencing Bio2RDF search URI;
●
Using a Taverna workflow composed of SPARQL
●
queries to obtain federated results from KEGG,
Entrez Gene and GO;

The usual unsemantic way

Existing integrated search services
EBI/EB-eye
NCBI/Entrez
KEGG/DBGET GoPubmed

By submitting a SPARQL query
http://atlas.bio2rdf.org/sparql

What is know about « hexokinase »
with semantic ?
select ?t1 ?p2 count(*)
where {
?s1 ?p1 ?o1 .
FILTER( bif:contains(?o1, \"hexokinase\")) .
?s1 a ?t1 .
?s1 ?p2 ?o2 .
}
ORDER BY ?t1 ?p2

Use Virtuoso 6.0 facet browser
http://lod.openlinksw.com/

Dereferencing search URL
http://bio2rdf.org/search/hexokinase

How can we submit a complex
query over the network of SPARQL
endpoints ?

By building a mashup with Taverna
1) Write your complex SPARQL query as if a
global graph would be available
2) Identify the needed namespaces and split the
query to fetch each data source separetly
3) Build a mashup using a Taverna workflow that
instanciate a local triplestore
4) Execute your complex query locally on the
mashup

The SPARQL query needed
(dont try this home, do it on the web !)

Get the list of genes
from KEGG pathways of a specified taxon
Clear graph
●
Get KEGG pathways list for a
●
specific taxon
For each pathway get genes
●
list and import instances
Count the number of genes
●
found
http://www.myexperiment.org/workflows/747

Insert into local triplestore
GeneID genes and KEGG pathways
Get the list of genes
●
Get the list of pathways
●
Insert into local triplestore
●
each corresponding graph
http://www.myexperiment.org/workflows/748

Insert into local triplestore
the needed GO annotations
Get the GO annotations for
●
each gene

Finally, the neeeded query merging
KEGG, Entrez Gene and GO together

Bio2RDF resources

Bio2RDF's mirrors
http://quebec.bio2rdf.org/
http://qut.bio2rdf.org/

Bio2RDF SPARQL endpoints
http://www.freebase.com/view/user/bio2rdf/public/sparql

Life Science Raw Data Now
http://quebec.bio2rdf.org/download

Visit our Wiki rdfiser cookbook
http://bio2rdf.wiki.sourceforge.net/

Bio2RDF news
http://bio2rdf.blogspot.com/
http://www.slideshare.net/search/slideshow?q=bio2rdf
http://scholar.google.com/scholar?q=bio2rdf
http://groups.google.ca/group/bio2rdf

Our 2009 objectives
Get approval from data provider to distribute
●
RDF dump and publish SPARQL endpoints
(UniProt, BioCyc, Pathway Commons, Bind are
in);
Start using Virtuoso 6 cluster;
●
Design more services accessible with REST
●
protocol via our JSP package;
Recruit mirror server;
●
Develop new rdfiser program in a community
●
effort;

Thanks
Jean Morissette, Nicole Tourigny
The Bio2RDF community
●
Centre de recherche du CHUL
●
Université Laval
●
Dumontier Lab
●
QUT eResearch Center
●
Openlink Virtuoso
●