Research Objects for e-Laboratories
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The document discusses research objects (ROs), which aim to make research more reproducible, reusable, and shareable. It describes the types and components of ROs, including aggregation, identity metadata, and lifecycle information. An example is given of how one researcher's workflow was reused and repurposed by another researcher to identify biological pathways. The role of myExperiment is discussed in modeling and sharing ROs according to the Open Archives Initiative Object Reuse and Exchange specification. Next steps include finalizing the Research Object Upper Model specification and defining domain-specific schemas.
Research Objects for e-Laboratories
- 1. Research Objects (ROs) for e-Laboratories David R Newman W3C HCLS Scientific Discourse Concall 7th March 2011
- 2. Share Research between e-Laboratories Projects Motivation
- 3. Repeatable Reproducible Reusable Repurpose-able Reliable Reference-able Reinterpret-able Respectable Retrievable Replay-able Refreshable Recoverable http://blogs.nature.com/eresearch/2010/11/replacing_the_paper_the_twelve_rs_of_the_e-research_record.html The Twelve Rs of the e-Research
- 4. Publication Objects Work Objects Live Objects Exposing Objects View/Context Objects Method Objects Archived Objects Types of Research Object
- 5. Aggregation Identity Metadata Lifecycle Versioning Management Security Graceful Degradation of Understanding Principles, Features and Behaviours of ROs
- 6. 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. Reuse, Recycling, Repurposing Courtesy of David De Roure
- 7. Results Logs Results Metadata Paper Slides Workflow 16 Workflow 13 Common pathways QTL Paul’s Pack Courtesy of David De Roure
- 8. Results Logs Results Metadata Paper Slides Feeds into produces Included in produces Published in produces Included in Included in Included in Published in Workflow 16 Workflow 13 Common pathways QTL Paul’s Research Object Courtesy of David De Roure
- 9. Four Main Classes Aggregation Aggregated Resource Resource Map Proxy Building Research Objects Using OAI-ORE
- 10. OAI-ORE Research Object Upper Model (ROUM) Research Object Domain Schema (RODS) Research Object Architecture Taverna SysMo Biocatalogue Obesity e-Lab Life Science Entities Scientific Discourse Curation Provenance OPM SWAN Annotation Ontology OBI
- 11. An environment for building Research Objects A central store for Research Objects Provide visualizations of Research Objects A publisher of the ROUM and some higher level RODSs A development environment for RODSs Sandbox for development of Research Object model The role for myExperiment
- 12. myExperiment Pack is a very basic RO Pack is a sub-class of OAI-ORE’s Aggregation Items it contains are referenced using OAI-ORE’s aggregrates property. Pack currently has two types of item myExperiment Contributions (Local) Links to things outside myExperiment (Remote) These items are encapsulated as entries so they can be described in context of the Pack LocalPackEntry and RemotePackEntry are sub-classes of OAI-ORE’s Proxy class Modelling ROs in myExperiment’s ontology
- 13. Pack vs Full Research Object
- 15. Relationship predicates defined in Vocabularies Vocabularies are a sub-class of SKOS Concept Schemes RODSs will consist of one of more Vocabularies RODSs may also have vocabularies for the properties needed by items, entries or even the packs themselves These RODSs should reuse existing properties / concepts where possible myExperiment and RODSs
- 16. Sharing Usage Curation Provenance Lifecycle Scientific Discourse Project Specific Taverna Biocatalogue SysMo Etc. Domain Specific Life Science Entities NIF Brain Regions, Neurons, Diseases, Behaviours, etc. Gene Ontology What type of concepts are there in a RO?
- 17. A myExperiment Pack with Relationships
- 18. Provide a UI for building and viewing relationships for ROs Finalise the ROUM specification Start defining project / use case specific RODSs Evaluate how Research Objects align with: Nano-publications Annotation Ontology KEfED Other Scientific Discourse efforts Next Steps
- 19. The myExperiment team Members of e-Laboratories projects at the Universities of Manchester and Southampton HCLS Scientific Subtask Group A myExperiment Pack with Relationships