Presenting linked data for life sciences at the GMOD (Genetic Model Organism Databases) Europe 2009.

1. Open Genomic Data Web Dr Jun Zhao Image Bioinformatics Research Group Department of Zoology University of Oxford 6 August 2009 GMOD Meeting Europe

2. Web of Data: “ may more accurately be described as a web of things in the world, described by data on the Web.”

3. Linked Data Design Issues

4. Resource Description Framework (RDF) rdf:type chado:pub fbgn:FBgn11367 so:Gene fbgn:FBgn11367 pubmed:PMID12

5. Resource Description Framework (RDF) rdf:type chado:pub fbgn:FBgn11367 so:Gene

6. SPARQL queries PREFIX chado: <http://purl.org/net/chado/schema> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX xs: <http://www.w3.org/2001/XML_Schema#> SELECT ?flybaseID WHERE { ?feature rdf:type chado:Feature ; chado:name “schuy”^^xs:string ; chado:uniquename ?flybaseID . } SELECT ?feature.uniquename AS flybaseID FROM feature WHERE feature.name = “schuy” SPARQL SQL

7. SPARQL protocol GET /query/flybase?query=[URL encoded query] HTTP/1.1 Host: openflydata.org Accept: application/sparql-results+json POST /query/flybase HTTP/1.1 Host: openflydata.org Accept: application/sparql-results+json Content-Type: application/x-www-form-urlencoded Content-Length: 456 query=[URL encoded query] HTTP GET HTTP POST

11. Connect TCM with Western Medicine

13. In a quantitative way

15. But not quantitative

17. Searches have to be repeated, different search interfaces, different use of terminology

18. Limited (if any) programmatic access to data … hard work to answer questions that span data sources

20. Search gene expression by gene batch [ go ]

21. Search gene expression by tissue expression profile [ go ]

22. System architecture SPARQL endpoint Web browser FlyUI application FlyUI widget HTTP Client side SPARQL server (SPARQLite, Tomcat, Apache)‏ RDF cache (Jena TDB) ‏ FlyBase BDGP FlyTED FlyAtlas AffyMetrix Server side

26. Generating N3 from spreadsheet table

29. Pre-generated lower-case gene names and loaded into the FlyBase RDF DB

30. Tried with OpenLink Virtuoso, still ~10 seconds for a case-insensitive search

32. Demonstrate the value of Linked Data

33. Demonstrate a novel technique for creating interlinks between datasets on a large scale

34. A joint effort of the BioRDF and LODD (Linked Open Drug Data) task forces of the World Wide Web Consortium (W3C) Health Care Life Science Interest Group TCM-LODD: Background

41. Support for unanticipated queries

43. Expressive query protocol is a double-edged sword

44. Performance is good for some queries, not for others…

48. http://esw.w3.org/topic/HCLSIG/AlternativeMedicineUseCase/ Further information

50. Anja Jentzsch, Matthias Samwald, Kei-Hoi Cheung and others from W3C HCLSIG

51. Dr Helen White-Cooper and her research group

52. BBSRC for funding building the FlyTED database

53. BDGP, FlyAtlas and FlyBase for making the data available

54. JISC, for funding the FlyWeb project

55. The Jena team, esp. Andy Seaborne

56. OpenLink Virtuoso

57. Thank you! jun.zhao @ zoo.ox.ac.uk