Repositories and Linked Open Data: the view from myExperiment

1. Repositories and Linked Open Data: the view from myExperiment David De Roure

2. Overview http://www.myexperiment.org/packs/131 • Motivation: the primacy of method • myExperiment and Other Animals • Design and implementation • The future of research

3. Virtual Learning Environment Reprints Peer-Reviewed Journal & Conference Papers Technical Reports LocalWeb Preprints & Metadata Repositories Certified Experimental Results & Analyses The social process of Science 1.0 Undergraduate Students 2.0 Next Generation Researchers Digital Libraries scientists Graduate Students experimentation Data, Metadata, Provenance, Scripts, Workflows, Services,Ontologies, Blogs, ...

4. E. Science laboris • Workflows are the new rock and roll • Machinery for coordinating the execution of (scientific) services and linking together (scientific) resources • The era of Service Oriented Applications • Repetitive and mundane boring stuff made easier Carole Goble

5. Taverna Taverna Workflows • Access to distributed and local resources • Automation of data flow • Iteration over data sets • Interactive • Agile software development • Experimental protocols • Declarative mashups • But... • Can be hard to build • Can “decay” as services change

6. Reuse, Recycling, Repurposing • Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis in cattle • Paul meets Jo. Jo is investigating Whipworm in mouse. • Jo reuses one of Paul’s workflow without change. • Jo identifies the biological pathways involved in sex dependence in the mouse model, believed to be involved in the ability of mice to expel the parasite. • Previously a manual two year study by Jo had failed to do this.

7. Kepler Ptolemy II Triana BPEL Trident Meandre Taverna

8. Sharing pieces of process

9. method data

10. Carole Goble “e-Science is me-Science: What do Scientists want?”, EGEE 2006 “There are these great collaboration tools that 12-year-olds are using. It’s all back to front.” Robert Stevens

11. “A biologist would rather share their toothbrush than their gene name” Mike Ashburner and others Professor in Dept of Genetics, University of Cambridge, UK

12. “Data mining: my data’s mine and your data’s mine”

13. Overview • Motivation: the primacy of method • myExperiment and Other Animals • Design and implementation • The future of research

14. Not Facebook for scientists! Facebook for scientists! mySpace for scientists!

15. The experiment that is Web 2 Social Scientists Social Network Developers Open Repositories Researchers

16. “Facebook for Scientists” ...but different to Facebook! • A repository of research methods • A community social network of people and things • A Social Virtual Research Environment • Open source (BSD) Ruby on Rails app • REST and SPARQL interfaces, Linked Data compliant • Basis or inspiration for multiple projects including BioCatalogue, MethodBox and SysmoDB myExperiment currently has 4060 members, 231 groups, 1175 workflows, 326 files and 119 packs

19. myExperiment Features • User Profiles • Groups • Friends • Sharing • Tags • Workflows • Developer interface • Credits and Attributions • Fine control over privacy • Packs • Multiple instances • Enactment Distinctives

20. Workflow 16 QTL Logs Results A Pack Metadata Slides Paper Common pathways Results Workflow 13

21. Taverna Plugins Bringing myExperiment to the Taverna user

22. Google Gadgets Bringing myExperiment to the iGoogle user

23. Facebook

24. Windows 7

25. http://www.openarchives.org/ore/terms/aggregates http://eprints.ecs.soton.ac.uk/id/eprint/20817

26. EPrints

27. ECS id

29. Overview • Motivation: the primacy of method • myExperiment and Other Animals • Design and implementation • The future of research

30. Web 2.0 patterns The Long Tail Data is the Next “Intel Inside” Users add value Network effects by default Some Rights Reserved The Perpetual Beta Cooperate, don’t Control Software above the level of the single device http://oreilly.com/web2/archive/what-is-web-20.html

32. Six Principles of Software Design to Empower Scientists Keep your Friends Close Embed Keep Sight of the Bigger Picture Favours will be in your Favour Know your users Expect and Anticipate Change • Fit in, Don’t Force Change • Jam today and more jam tomorrow • Just in Time and Just Enough • Act Local, think Global • Enable Users to Add Value • Design for Network Effects De Roure, D. and Goble, C. "Software Design for Empowering Scientists," IEEE Software, vol. 26, no. 1, pp. 88-95, January/February 2009 http://eprints.ecs.soton.ac.uk/15032/

33. For Developers XML ORE FOAF SIOC facebook iGoogle android APIconfig HTML SearchAPI Managed REST API Search Engine SPARQL endpoint tags ratings reviews profiles groups workflows credits EPrints DSpace Fedora S3 SRB friendships packs files ` RDF Store mySQL Enactor API Enactor

34. SPARQL endpoint rdf.myexperiment.org Transform tags ratings reviews profiles groups workflows credits SPARQL endpoint friendships packs files RDF Store mySQL Modularised myExperiment Ontology myExperiment data model (evolving!) DC, FOAF, SIOC(Semantically-Interlinked Online Communities)

35. David Newman

36. myExperiment modularised ontology http://eprints.ecs.soton.ac.uk/17787/ David Newman

37. Exporting packs

38. Linked Open Data

39. Levels of (social) compliance? • 303s • 303s + RDF • 303s + RDF + SPARQL • Being on the diagram! http://www.w3.org/DesignIssues/LinkedData.html

40. Hugh Glaser

44. David Newman

45. David Newman

46. The hidden costs of linked data • Usability • We had a perfectly good scheme before and now we change it for something more complicated! • Performance • All those 303s! • Rumoured that on some sites developers append .xml to save round trips

47. Non Information Resource Usability Hacks Used to share this... www.myexperiment.org/packs/112 Still do, but browser now shows this... www.myexperiment.org/packs/112.html * * actually this works, sssh!

48. Jiten Bhagat BioCatalogue

49. myExperiment NIR

50. Overview • Motivation: the primacy of method • myExperiment and Other Animals • Design and implementation • The future of research