Bio2RDF presentation at Combine 2012
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This document discusses how semantic web technologies like RDF and SPARQL can help navigate complex bioinformatics databases. It describes a three step method for building a semantic mashup: 1) transform data from sources into RDF, 2) load the RDF into a triplestore, and 3) explore and query the dataset. As an example, it details how Bio2RDF transformed various database cross-reference resources into RDF and loaded them into Virtuoso to answer questions about namespace usage.
Bio2RDF presentation at Combine 2012
- 1. Bio2RDF's namespace SPARQL endpoint François Belleau Centre de Biologie Computationnelle du CRCHUQ
- 2. You know them? How can we help to navigate in the huge Bioinformatics databases cloud ?
- 3. 2005 BioPAX.gif next to Semantic Web image vision of Tim Berner Lee
- 4. Linked Data in 2007
- 5. Bio2RDF contribution in 2009
- 6. 2011 Linked Data cloud
- 7. Databases of databases names ● PathGuide ● Bioformatics.ca Links Directory ● Annual NAR Database issue ● Go, Uniprot, Genbank cross-reference list ● LSRN initiative ● MIRIAM EBI project ● BioPAX dataprovider community ● Bio2RDF Linked Data space
- 8. Two interesting questions ● Which namespace are the most popular for identifying database ? ● How far is the BioPAX community to adopt MIRIAM new namespace standard ?
- 9. Which namespaces are the most popular to identify a database ?
- 10. Namespaces collection used by the BioPAX data provider community.
- 11. How far is the BioPAX community to adopt MIRIAM new namespace standard ?
- 12. How we did this ? To answer a complex question we first need to build the database that will potentially answer it: a semantic mashup.
- 13. A mashup, in web development, is a web page, or web application, that uses and combines data, presentation or functionality from two or more sources to create new services. The term implies easy, fast integration, frequently using open Application programming interfaces (API) and data sources to produce enriched results that were not necessarily the original reason for producing the raw source data. http://en.wikipedia.org/wiki/Mashup_(web_application_hybrid)
- 14. Building a mashup is a lot easier when using Semantic Web technologies like RDF and SPARQL design for data interoperability.
- 15. A three steps method ● Get the data form the data provider and transform it into RDF, we use Talend open source Eclipse base ETL software. ● Load the data in a triplestore many software are available (Virtuoso, Sesame, Jena, store, Mulgara, etc.) to load your mashup ● Explore the new dataset using specialised user interface (RelFinder, Virtuoso facet browser) ● Design your SPARQL query and get the answer
- 16. Data provider xref resource ● http://www.ebi.ac.uk/miriam/main/ (XML format) ● Bio2RDF DNS zone description file (text) ● http://lsrn.org/ (RDF/XML) ● http://www.geneontology.org/doc/GO.xrf_abbs (key/value format) ● http://www.uniprot.org/docs/dbxref (key/value format) ● http://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ (HTML) ● 12 BioPAX providers (Reactome, Biomodels, Biocyc, Panther, INOH, etc)
- 17. Lesson #1 Produce RDF triples with a profesionnal ETL tool.
- 18. Talend ETL opensource free software http://www.talend.com/index.php
- 19. Talend workflows to convert HTML Genbank page to triples and MIRAM XML
- 20. Lesson #2 Publish with a SPARQL endpoint. (to get a free 5 stars cup)
- 21. Load RDF triples into a triplestore (we use Openlink Virtuoso) http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/
- 22. Full text search http://namespace.bio2rdf.org/fct/
- 23. Discover entity name and browse the triplestore
- 24. Lesson #3 Consume as you like. HTTP GET to obtain RDF from URI, SPARQL endpoint, SOAP services returning RDF, semantic web new software...
- 25. The needed SPARQL query to draw the previous graph using ManyEyes service http://namespace.bio2rdf.org/sparql
- 26. Use a SOAP service http://namespace.bio2rdf.org/bio2rdf/services.wsdl
- 27. Discover your relations graphicly with RelFinder http://www.visualdataweb.org/relfinder.php
- 28. Conclusion ● Building a mashup is easy with the actual software, we still need the RDF data. ● One SPARQL query in the proper triplestore (Bio2RDF's namespace mashup) could answer our two initial questions. ● Why not consider publish your own SPARQL endpoint to make semantic hacker's life easier ?
- 29. Acknowledgements ● Bio2RDF is a community project available at http://bio2rdf.org ● The community can be joined at https://groups.google.com/forum/?fromgroups#!forum/bio2rdf ● This work was done under the supervision of Dr Arnaud Droit, assistant professor and director of the Centre de Biologie Computationnelle du CRCHUQ at Laval University, where a mirror of Bio2RDF is hosted. ● Michel Dumontier, from the Dumontier Lab at Carleton University, is also hosting Bio2RDF server and actually leads the project ● Thanks to all the people member of the Bio2RDF community, and especially Marc-Alexandre Nolin and Peter Ansell, initial developers.
- 30. Come in Montreal July 2013 with your SPARQL endpoint an get a FREE cup! http://www.unbsj.ca/sase/csas/data/semantic-trilogy-2013/