research objects for e-laboratories

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