Bio2RDF-ISMB2008

How to use Bio2RDF with a Virtuoso server.

ISMB2008 Technology track

François Belleau, Marc-Alexande Nolin, Philippe Rigault

● Centre de Recherche du CHUL, Université Laval● Département d'informatique et de génie logiciel, Université Laval

ISMB2005

Toronto, July 21, ISMB2008 CHUL research center - Laval University 3

Outline Introduction

− The data integration problem in bioinformatics− What is Bio2RDF Atlas− Semantic web 101− Bio2RDF approach

How to − install Virtuoso and Bio2RDF− load N3 databases into the graph− to query the graph with SPARQL and text search

Future works


How to solve the data integration problem in

bioinformatics ?


Vaugondy, Louis XV geograph, view of the world in the 18th century


The 2005 data integration problem in bioinformatics


Solution :Use the Semantic Web model

for data integration.


Linked data map around DBpedia RDF version of Wikipedia

http://wiki.dbpedia.org/Interlinking

http://wiki.dbpedia.org/Interlinking

Joanne Luciano's vision @ ISMB2005


Bio2RDF's 30 data sources loadedinto the Atlas graph about Human and mouse


We Drag and Drop databases converted to RDF into a triplestore


2008 Bio2RDF linked data map of Knowledge


Bio2RDF Semantic Web Atlas in numbers

● 30 different datasources, 30 different namespaces− go, geneid, uniprot, pubmed, pdb, reactome, omim, etc.

● 195 namespaces referencing non-rdfized datasource− cog, genethon, tigr, cath, goa, etc.

● 8 millions topics● 65 millions triples● 973 Mo, size of N3 format compressed data

− http://bio2rdf.org/download/bio2rdf-atlas-080414.n3.gz

http://bio2rdf.org/download/bio2rdf-atlas-080414.n3.gz


All this knowledge with a 32 Go fileand the Virtuoso server ...


Our approach● Adopt W3C standards

− HTTP, RDF, OWL, SPARQL● Apply the semantic web model to data

integration in bioinformatics;− Follow Tim's 4 rules about linked data.

● Use existing software − PiggyBank, Sesame, Virtuoso


Semantic Web 101


W3C standard : RDFEverything is express in triple.

<subject> <predicate> <object>


W3C standard : SPARQLA sort of SQL for RDF

SELECT ?type, count(*)WHERE {

?s1 ?p1 ?o1 . ?o1 bif:contains "paget" .?s2 ?p2 ?s1 . ?s2 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . }

ORDER BY DESC (count(*))


Tim Berners-Lee 4 linked data rules● Rule #1: Use URIs as names for things.

− Hexokinase is GO:0004396● Rule #2 : Use HTTP URIs so that people can look up those

names.− Derefencable URL http://bio2rdf.org/go:0004396

● Rule #3 When someone looks up a URI, provide useful information.

− http://bio2rdf.org/go:0004396 returns the RDF graph describing this topic

● Rule #4 :Include links to other URIs so that they can discover more things.

− go:0004396 refers to pubmed:6341351


How it works ?


The semantic mashup effect

OR = 0M eSH

OR = 1GeneID

OR = 0,5PubM ed

mean OR = 0,5


The semantic mashup effect

OR = 0M eSH

OR = 1GeneID

OR = 0,5PubM ed

mean OR = 0,16

Triplestore


How to install Bio2RDF/Virtuoso


How to install Bio2RDF in Tomcat● You need the Java JDK 6 downloaded from :

− http://java.sun.com/javase/downloads/index.jsp● Download Tomcat JSP server version 6 from :

− http://tomcat.apache.org/download-60.cgi● Install Tomcat server

− Unzip the archive− In TOMCAT_ROOT/conf/server.xml configuration file change

<Connector port="8080" for <Connector port="80"− Replace TOMCAT_ROOT/conf/tomcat-user.xml content of with :

<?xml version='1.0' encoding='utf-8'?> <tomcat-users> <role rolename="manager"/> <role rolename="admin"/> <user username="admin" password="" roles="admin,manager"/></tomcat-users>


How to install Bio2RDF in Tomcat● Define bio2rdf.org domain name locally by adding to

C:\WINDOWS\system32\drivers\etc\host :

127.0.0.1 localhost bio2rdf.org● In command mode, change directory to TOMCAT_ROOT/bin and

executre startup.bat, Tomcat server you start in a new window.● Now http://bio2rdf.org should respond.● With http://bio2rdf.org/manager/html connect using admin and an

empty password.● Undeploy path /● Deploy Bio2RDF application from the

http://bio2rdf.org/download/ROOT.war● Bio2RDF application should be installed and now http://bio2rdf.org

returns home page.

http://bio2rdf.org/

http://bio2rdf.org/

http://bio2rdf.org/


How to install Virtuoso Download the software from SourceForge

− http://sourceforge.net/projects/virtuoso Install it and start the server

− Unzip the archive− Change directory to virtuoso-opensource/database− Run ..\bin\virtuoso-t -f in command mode− http://localhost:8890/sparql should responds;− Connect to to Conductor using dba/dba at

http://localhost:8890


How to install Virtuoso Go to the virtuoso\bin folder and execute isql

− C:\Bio2RDF\Virtuoso\bin>isqlOpenLink Interactive SQL (Virtuoso), version 0.9849b.Type HELP; for help and EXIT; to exit.SQL>

Add the needed index to the triplestore − CREATE BITMAP index RDF_QUAD_POGS on

DB.DBA.RDF_QUAD (P,O,G,S);CREATE BITMAP index RDF_QUAD_PSOG on DB.DBA.RDF_QUAD (P,S,O,G);CREATE BITMAP index RDF_QUAD_SOPG on DB.DBA.RDF_QUAD (S,O,P,G);

Create the full text index and update it− DB.DBA.RDF_OBJ_FT_RULE_ADD ('', null, '');

DB.DBA.VT_INC_INDEX_DB_DBA_RDF_OBJ ();


How to load data from N3 files

http://bio2rdf.org/download


How to load data from N3 filesuse n32triplestore.pl PERL script

http://bio2rdf.org/download/n32triplestore.pl


Bio2RDF demo using Virtuoso SPARQL server


What is known about « Paget disease» ?


Popular web search engines without semantic


Integrated bioinformatics search engine


'Paget'->topic->rdf:type

SELECT ?type, count(*)WHERE {

?s1 ?p1 ?o1 . ?o1 bif:contains "paget" .?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . }



Submit the SPARQL query to Virtuoso server at http://bio2rdf.org/sparql


Results : Number of topics by type (database) about Paget disease


View results with Piggy Bank for a facet browsing experience


'Paget'->topic1<-topic2->GO->rdfs:label

SELECT ?l3, count(*)WHERE {

?s1 ?p1 ?o1 . ?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type .

?o1 bif:contains "paget" .?s2 ?p2 ?s1 .?s2 <http://bio2rdf.org/bio2rdf#xGO> ?s3 .?s3 <http://www.w3.org/2000/01/rdf-schema#label> ?l3 .}



Results : Number of GO terms by topic related to Paget disease


Bio2RDF four services● Describe a topic

− http://bio2rdf.org/go:0004396● List of reverse links to a topic

− http://bio2rdf.org/links/go:0004396● Full text search

− http://bio2rdf.org/search/hexokinase● SPARQL endpoint to query

− http://bio2rdf.org/sparql


Future works● Build a community data provider in

bioinformatics adopting the Banff Manifesto rules;

● Build next version of Bio2RDF services using a distributed network of Virtuoso servers;

● Participate to the construction of the scientific linked data web to answer real science question using SPARQL;

● Promote the adoption of semantic web in our scientific community;


In short...● Bio2RDF project has rdfized many public data

sources and normalized URI;● This model enables scalability of complexity;● You can drag and drop knowlege into Virtuoso

triplestore;● RDF is usefull if you can query it with SPARQL;● If you do SQL you can do SPARQL;● We offer 4 new public services, try them;● Download it and try it home, install your own

Bio2RDF/Virtuoso server;


Acknowlegments

Bioinformatics lab’s team at CHUL Research Center and the Bio2RDF community on Google.

Peter Ansell for his Java coding effort

Kingsley Idehen from OpenLink Software

Thanks to the essential annotators and data providerand to developers of open source project :

Sesame, Virtuoso and PiggyBank.


http://bio2rdf.orgQuery the graph with SPARQL

http://bio2rdf.org/sparql

Download our software http://sourceforge.net/projects/bio2rdf/

Download the Atlas data in N3 format http://bio2rdf.org/download

Join our group http://groups.google.ca/group/bio2rdf

Contact us at [email protected]