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Research Objects (ROs) for e-Laboratories
David R NewmanW3C HCLS Scientific Discourse Concall
7th March 2011
Share Research between e-Laboratories Projects
MotivationMotivation
• Repeatable• Reproducible• Reusable• Repurpose-able• Reliable• Reference-able• Reinterpret-able• Respectable• Retrievable• Replay-able• Refreshable• Recoverablehttp://blogs.nature.com/eresearch/2010/11/replacing_the_paper_the_twelve_rs_of_the_e-research_record.html
The Twelve Rs of the e-ResearchThe Twelve Rs of the e-Research
• Publication Objects• Work Objects• Live Objects• Exposing Objects• View/Context Objects• Method Objects • Archived Objects
Types of Research ObjectTypes of Research Object
• Aggregation• Identity• Metadata• Lifecycle• Versioning• Management• Security• Graceful Degradation of Understanding
Principles, Features and Behaviours of ROsPrinciples, Features and Behaviours of ROs
• 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, RepurposingReuse, Recycling, Repurposing
Courtesy of David De Roure
Results
Logs
Results
Metadata PaperSlides
Workflow 16
Workflow 13
Common pathways
QTL
Paul’s PackPaul’s Pack
Courtesy of David De Roure
Results
Logs
Results
Metadata PaperSlides
Feeds into
produces
Included in
produces Published in
produces
Included in
Included in
Included in
Published in
Workflow 16
Workflow 13
Common pathways
QTLPaul’s Research
Object
Paul’s Research
Object
Courtesy of David De Roure
• Four Main Classes• Aggregation• Aggregated Resource• Resource Map• Proxy
Building Research Objects Using OAI-OREBuilding Research Objects Using OAI-ORE
OAI-ORE
Research Object Upper Model (ROUM)
Research Object Domain Schema
(RODS)
Research Object ArchitectureResearch Object Architecture
Taverna SysMoBiocatalogue Obesity e-Lab
Life Science Entities
Scientific DiscourseCuration Provenance
OPMSWANAnnotation OntologyOBI
• 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 myExperimentThe role for myExperiment
• 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 ontologyModelling ROs in myExperiment’s ontology
Pack vs Full Research ObjectPack vs Full Research Object
Representing Pack RelationshipsRepresenting Pack Relationships
• 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 RODSsmyExperiment and RODSs
• 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?What type of concepts are there in a RO?
A myExperiment Pack with RelationshipsA myExperiment Pack with Relationships
• 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 StepsNext Steps
• The myExperiment team
• Members of e-Laboratories projects at the Universities of Manchester and Southampton
• HCLS Scientific Subtask Group
A myExperiment Pack with RelationshipsA myExperiment Pack with Relationships