![Research Objects: Beyond the Pack
• Argumentation: Convince the reader of the
validity of a position [Mesirov]
– Reproducible Results System: facilitates enactment
and publication of reproducible research.
J. Mesirov Accessible Reproducible Research Science 327(5964), p.415-416, 2010
http://dx.doi.org/10.1126/science.1179653
• Results are reinforced by reproducability [De Roure]
– Explicit representation of method.
D. De Roure and C. Goble Anchors in Shifting Sand: the
Primacy of Method in the Web of Data Web Science Conference 2010, Raleigh
NC, 2010 http://eprints.ecs.soton.ac.uk/20817/
• Verifiability as a key factor in scientific discovery.
Stodden et. al. Reproducible Research: Addressing the Need for Data and
Code Sharing in Computational Science Computing in Science and Engineering 12
(5), p.8-13, 2010 http://dx.doi.org/10.1109/MCSE.2010.113](https://image.slidesharecdn.com/socialobjects-111009103502-phpapp02/85/Scientific-Social-Objects-22-320.jpg)
Scientific Social Objects
- 1. Scientific Social Objects David De Roure, Sean Bechhofer, Carole Goble, David Newman sean.bechhofer@manchester.ac.uk @seanbechhofer http://humblyreport.wordpress.com 1st International Workshop on Social Object Networks (SocialObjects 2011), Boston, October 9th 2011. 1
- 2. E. Science laboris • Workflows are the new rock and roll! • Machinery for coordinating the execution of services and linking together resources • Scientist friendly (for some class of scientists) • Repetitive and mundane boring stuff made easier • Enable automation • Make science repeatable (and sometimes reproducible) • Encourage best practices • Shareable Carole Goble
- 3. Reuse, Recycle, Repurpose • 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. Carole Goble
- 4. 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
- 5. A sharing platform for scientists Distinctive features supporting credit and attribution A repository of research methods Open source (BSD) Ruby on Rails app A community social network of people and things REST and SPARQL interfaces, supports Linked Data A Social Virtual Research Part of product family including Environment BioCatalogue, MethodBox and A probe into researcher SysmoDB behaviour ~4700 members, 270 groups, ~2000 workflows, ~200packs
- 6. myExperiment 6
- 7. myExperiment 7
- 8. myExperiment Content • User accounts – Groups – Friendships • Various types of Contributables – Workflows, files, presentations – Versions – Compositions Workflows – services, tasks Packs – workflows, files, URIs. • Annotations – Attribution, Credit, Ratings, Tags, 8
- 10. Scenario: Finding Help 10
- 11. Scenario: Matching Tasks 11
- 12. myExperiment For Developers XML facebook iGoogle android HTML API config SPARQL endpoint Managed REST API tags ratings reviews profiles Search workflows credits groups Engine packs friendships files ` RDF Store mySQL Enactor
- 13. SPARQL endpoint SPARQL endpoint rdf.myexperiment.org Transform tags ratings reviews profiles workflows credits groups files packs friendships RDF Store Modularised myExperiment mySQL myExperiment data model Ontology (evolving!) DC, FOAF, SIOC (Seman8cally-‐Interlinked Online Communi8es)
- 14. SPARQL endpoint It is effectively a generic API whereby the user can specify exactly what information they want to send and what they expect back -- rather than providing query/ access mechanism via specific API functions. In some ways it has the versatility of querying the myExperiment database directly, but with the significant benefit of a common data model which is independent of the codebase, and through use of OWL and RDF it is immediately interoperable with available tooling. Exposing data in this way is an example of the cooperate don't control principle of Web 2.0. Use of existing vocabularies (FOAF, SIOC etc) allows for mashup/integration with other sources. Packs can also link to external resources. Links out and Links in to to the “Linked Data Cloud”. 14
- 15. Users 15
- 16. Things Community Sharing Personal Preservation 16
- 17. Friendships SELECT ?requester ?accepter WHERE { ?membership rdf:type mebase:Friendship. ?membership mebase:has-requester ?requester. ?membership mebase:has-accepter ?accepter. } 17
- 18. Groups SELECT ?group ?user WHERE { ?group rdf:type mebase:Group. ?group sioc:has_member ?user. } 18
- 19. Tagging SELECT ?wf ?user WHERE { ?wf rdf:type mecontrib:Workflow. ?t mebase:annotates ?wf; rdf:type meannot:Tagging; mebase:has-annotator ?user. } 19
- 20. Packs and Contents SELECT?pack ?contrib WHERE { ?pack rdf:type mepack:Pack. ?pack ore:aggregates ?contrib. } 20
- 21. Workflows and services SELECT?wf ?uri WHERE { ?wf mebase:has-current-version ?v. ?v mecomp:executes-dataflow ?d. ?d mecomp:has-component ?c. ?c rdf:type mecomp:WSDLProcessor. ?c mecomp:processor-uri ?uri. } 21
- 22. Research Objects: Beyond the Pack • Argumentation: Convince the reader of the validity of a position [Mesirov] – Reproducible Results System: facilitates enactment and publication of reproducible research. J. Mesirov Accessible Reproducible Research Science 327(5964), p.415-416, 2010 http://dx.doi.org/10.1126/science.1179653 • Results are reinforced by reproducability [De Roure] – Explicit representation of method. D. De Roure and C. Goble Anchors in Shifting Sand: the Primacy of Method in the Web of Data Web Science Conference 2010, Raleigh NC, 2010 http://eprints.ecs.soton.ac.uk/20817/ • Verifiability as a key factor in scientific discovery. Stodden et. al. Reproducible Research: Addressing the Need for Data and Code Sharing in Computational Science Computing in Science and Engineering 12 (5), p.8-13, 2010 http://dx.doi.org/10.1109/MCSE.2010.113
- 23. Research Objects as Social Objects 23
- 24. Research Objects as Social Objects 24
- 25. Research Objects • Aggregations intended to foster Reuse, Repurposing and Repeatability of investigations • A generalisation of the pack • Rich social interactions – Sharable – Citeable – Credit and Attribution – Provenance 2 5 25
- 26. Wf4Ever …technological infrastructure for the preservation and efficient retrieval and reuse of scientific workflows in a range of disciplines. • Architecture/implementation for workflow preservation, sharing and reuse • Research Object models • Workflow Decay, Integrity and Authenticity • Workflow Evolution and Recommendation • Provenance • Driven by Use Cases FP7 Digital Libraries and Digital Preservation iSOCO, University of Manchester, Universidad Politécnica de Madrid, University of Oxford, Poznan Supercomputing and Networking Centre, Instituto de Astrofísica de Andalucía, Leiden University Medical Centre 26
- 27. Astronomers Questions When accessing a workflow When sharing a workflow • Can I use it for my purposes (in my • What rights others have? words)? • What a good workflow is to get a • If I can expect it to run, when was good score? it was last run, by whom? – Make my workflow findable, reusable, and ready for review • What it does quickly, by one of – Instructions to authors – example input / output (and trying it) – Two types of contributions: serious – a description science, preliminary/playing around – ‘reading’ its key parts • If my workflow may have issues – what it was used for – What the system or other users think – related workflows its creator it does – contacting the creator or last user • How it relates to other things • How I need to cite the author and workflow? • Share freely or anonymously upon request? 27 http://www.flickr.com/photos/-bast-/349497988/
- 28. Other Work Jia Zhang Wei Tan, John Alexander, Ian Foster, Ravi Madduri, Recommend-As-You- Go: A Novel Approach Supporting Services-Oriented Scientific Workflow Reuse, Proceedings of the 2011 IEEE International Conference on Services Computing, 2011 http://dx.doi.org/10.1109/SCC.2011.120 Wei Tan, Jia Zhang, Ian Foster Network Analysis of Scientific Workflows: A Gateway to Reuse IEEE Computer 43(9) pp54-61 http://dx.doi.org/10.1109/MC.2010.262 • Volume of data is not enough, but additional consideration of content could help us. • Approach also being considered for recommendation in Wf4Ever. Julia Stoyanovich, Ben Taskar, and Susan Davidson Exploring Repositories of Scientific Workflows WANDS 2010 http://wands2010.doc.ic.ac.uk/ • Organising workflows into categories. Now available as “Topics” tab. 28
- 29. Wrap up • myExperiment as a platform for sharing – Contributables, Annotations, Users – APIs RDF/SPARQL endpoints – Come and play! • Workflows (and their constituent parts) as social objects • Various networks layered on those objects • Compositional nature of the objects – Workflows combining services – Packs combining objects • Research Object as a future vision for composite Scientific Social Objects 29
- 30. Thanks! • myExperimentTeam – http://www.myexperiment.org/ • Wf4Ever Team – http://www.wf4ever-project.org/ • Manchester Information Management Group – http://img.cs.manchester.ac.uk 30