Integrating, Representing and Reasoning over Human Knowledge in myExperiment

1. Integrating, Representing and Reasoning over Human Knowledge in myExperiment David De Roure

2. 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, ...

3. 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.

4. Sharing pieces of process

5. method data

6. 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

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

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

9. Not Facebook for scientists! Facebook for scientists! mySpace for scientists!

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

11. “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 • A probe into researcher behaviour • Open source (BSD) Ruby on Rails app • REST and SPARQL interfaces, Linked Data compliant • Basis or inspiration for other projects: BioCatalogue, MethodBox and SysmoDB myExperiment currently has 4739 members, 234 groups, 1252 workflows, 337 files and 126 packs

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

14. Paul’s Research Object Paul’s Pack Workflow 16 QTL Results produces Included in Published in Included in Feeds into Logs produces Included in Included in Metadata Slides Paper produces Published in Common pathways Results Workflow 13

15. Taverna Plugins Bringing myExperiment to the Taverna user

16. Google Gadgets Bringing myExperiment to the iGoogle user

17. Facebook

18. Windows 7

19. Vocabulary of Interlinked Datasets Finding myExperiment by searching for Linked Data sources with Workflow in their descriptions http://kwijibo.talis.com/voiD/

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

22. Francois Belleau

23. A Bioinformatics Experiment Scott Marshall Marco Roos “…to discover proteins that interact with transmembrane proteins, particularly those that can be related to neuro-degenerative diseases in which amyloids play a significant role” • Taverna provenance exposed as RDF • myExperiment RDF document for a protein discovery workflow • Mocked-up BioCatalogue document using myExperiment RDF data as example • Provisional RDF documents obtained from the ConceptWiki (conceptwiki.org) development server • An RDF document for an example protein, obtained from the RDF interface of the UniProt web site

24. A Computational Musicology experiment Kevin Page Ben Fields “How Country is my Country?” A researcher explaining their “workflow”... • Use SPARQL to generate a collection of signal • Publish that collection • Our local signal repository has copies of the actual signal, and publishes sub-graphs of linked data asserting what those signals are of (using the URI for that track/record etc.) • The workflow performing the feature extraction combines (2)and (3) when fetching the signal for feature extraction and classification, and persists the URI for the signal artefact (track/record etc.) • The results are published (e.g. of genre classification) and reference that URI

26. Studies using myExperiment content

27. Evolution of our research environment 1st Generation Current practices of early adoptors of tools. Characterised by researchers using tools within their particular problem area, with some re-use of tools, data and methods within the discipline. Traditional publishing is supplemented by publication of some digital artefacts like workflows and links to data. Provenance is recorded but not shared and re-used. Science is accelerated and practice beginning to shift to emphasise in silico work. 2nd Generation Projects delivering now. Some institutional embedding. Key characteristic is re-use - of the increasing pool of tools, data and methods across areas/disciplines. Contain some freestanding, recombinant, reproducible research objects. Provenance analytics plays a role. New scientific practices are established and opportunities arise for completely new scientific investigations. Some expert curation. 3rd Generation The solutions we'll be delivering in 5 years Characterised by global reuse of tools, data and methods across any discipline, and surfacing the right levels of complexity for the researcher. Routine use. Key characteristic is radical sharing . Research is significantly data driven - plundering the backlog of data, results and methods. Increasing automation and decision-support for the researcher - the VRE becomes assistive. Provenance assists design. Curation is autonomic and social.

28. Five Discussion Points • Methods as first class citizens • Co-Evolution and glimpses of the future • New digital artefacts – • Thinking outside the paper! • Thought experiment: what will we exchange instead of papers? • The Web-Particle duality • Physical and the digital • Laboratory bench, sensor networks, museum artefacts • Automation from signal to understanding • Celebrate the flux!

29. Semantic Web “The Semantic Web is about two things: It is about common formats for integration and combination of data drawn from diverse sources, where on the original Web mainly concentrated on the interchange of documents. It is also about language for recording how the data relates to real world objects. That allows a person, or a machine, to start off in one database, and then move through an unending set of databases which are connected not by wires but by being about the same thing.” http://www.w3.org/2001/sw/

30. Contact David De Roure david.deroure@oerc.ox.ac.uk Carole Goble carole.goble@manchester.ac.uk Visit wiki.myexperiment.org

31. The Team Sergejs Aleksejevs Mark Borkum Sean Bechhofer Jiten Bhagat Simon Coles Don Cruickshank Cat De Roure Paul Fisher Jeremy Frey Matt Gamble Duncan Hull Kumar Kollara Peter Li Ravi Madduri Danius Michaelides Paolo Missier David Newman Cameron Neylon Stuart Owen Kevin Page Rob Procter Marco Roos Stian SoilandShoaib Sufi MannieTagariraAndrea Wiggins Alan Williams Katy Wolstencroft Tom Eveleigh June Finch AntoonGoderisAndrew Harrison Matt Lee Yuwei Lin Kurt Mueller SavasParastatidisMeikPoschenMarcus RamsdenIan Taylor Alexander Voss David Withers Ed Zaluska

32. Funders • JISC Virtual Research Environments and Repositories programmes • EPSRC myGrid ande-Research South platform awards • Microsoft Research Technical Computing Initiative • Andrew W. Mellon Foundation

33. Publications http://wiki.myexperiment.org/index.php/Papers • De Roure, D., Goble, C. and Stevens, R. (2009) “The Design and Realisation of the myExperiment Virtual Research Environment for Social Sharing of Workflows,” Future Generation Computer Systems 25, pp. 561-567. • Goble, C.A., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., and De Roure, D.: myExperiment: a repository and social network for the sharing of bioinformatics workflows, Nucl. Acids Res., 2010. doi:10.1093/nar/gkq429 • De Roure, D. and Goble, C. (2009) "Software Design for Empowering Scientists," IEEE Software, vol. 26, no. 1, pp. 88-95, January/February 2009. • Newman, D.R., Bechhofer, S. and De Roure, D. (2009) “myExperiment: An ontology for e-Research,” Workshop on Semantic Web Applications in Scientific Discourse at 8th International Semantic Web Conference (ISWC 2009), Washington DC, October 2009. • Bechhofer, S., De Roure, D., Gamble, M., Goble, C. and Buchan, I. (2010) Research Objects: Towards Exchange and Reuse of Digital Knowledge. In: The Future of the Web for Collaborative Science (FWCS 2010), April 2010, Raleigh, NC, USA.