Research Objects (ROs)  for e-Laboratories  David R Newman W3C HCLS Scientific Discourse Concall  7th March2011
<ul><li>Share Research between e-Laboratories Projects </li></ul>Motivation
<ul><li>Repeatable </li></ul><ul><li>Reproducible </li></ul><ul><li>Reusable </li></ul><ul><li>Repurpose-able </li></ul><u...
<ul><li>Publication Objects </li></ul><ul><li>Work Objects </li></ul><ul><li>Live Objects </li></ul><ul><li>Exposing Objec...
<ul><li>Aggregation </li></ul><ul><li>Identity </li></ul><ul><li>Metadata </li></ul><ul><li>Lifecycle </li></ul><ul><li>Ve...
<ul><li>Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis  in cattle <...
Results Logs Results Metadata Paper Slides Workflow 16 Workflow 13 Common pathways QTL Paul’s Pack Courtesy of David De Ro...
Results Logs Results Metadata Paper Slides Feeds into produces Included in produces Published in produces Included in Incl...
<ul><li>Four Main Classes </li></ul><ul><ul><li>Aggregation </li></ul></ul><ul><ul><li>Aggregated Resource </li></ul></ul>...
OAI-ORE Research Object Upper Model (ROUM) Life Science Entities  Taverna  SysMo  Obesity  e-Lab  Gene Ontology  OBI OBI O...
<ul><li>An environment for building Research Objects </li></ul><ul><li>A central store for Research Objects </li></ul><ul>...
<ul><li>myExperiment Pack is a very basic RO </li></ul><ul><ul><li>Pack is a sub-class of OAI-ORE’s Aggregation </li></ul>...
Pack vs Full Research Object
Representing Pack Relationships
<ul><li>Relationship predicates defined in Vocabularies </li></ul><ul><ul><li>Vocabularies are a sub-class of SKOS Concept...
<ul><li>Sharing </li></ul><ul><li>Usage </li></ul><ul><li>Curation </li></ul><ul><li>Provenance </li></ul><ul><li>Lifecyle...
A myExperiment Pack with Relationships
<ul><li>Provide a UI for building and viewing relationships for ROs </li></ul><ul><li>Finalise the ROUM specification </li...
<ul><li>The myExperiment team </li></ul><ul><li>Members of e-Laboratories projects at the Universities of Manchester and S...
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Research Objects for e-Laboratories

  1. 1. Research Objects (ROs) for e-Laboratories David R Newman W3C HCLS Scientific Discourse Concall 7th March2011
  2. 2. <ul><li>Share Research between e-Laboratories Projects </li></ul>Motivation
  3. 3. <ul><li>Repeatable </li></ul><ul><li>Reproducible </li></ul><ul><li>Reusable </li></ul><ul><li>Repurpose-able </li></ul><ul><li>Reliable </li></ul><ul><li>Reference-able </li></ul><ul><li>Reinterpret-able </li></ul><ul><li>Respectable </li></ul><ul><li>Retrievable </li></ul><ul><li>Replay-able </li></ul><ul><li>Refreshable </li></ul><ul><li>Recoverable </li></ul>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. 4. <ul><li>Publication Objects </li></ul><ul><li>Work Objects </li></ul><ul><li>Live Objects </li></ul><ul><li>Exposing Objects </li></ul><ul><li>View/Context Objects </li></ul><ul><li>Method Objects </li></ul><ul><li>Archived Objects </li></ul>Types of Research Object
  5. 5. <ul><li>Aggregation </li></ul><ul><li>Identity </li></ul><ul><li>Metadata </li></ul><ul><li>Lifecycle </li></ul><ul><li>Versioning </li></ul><ul><li>Management </li></ul><ul><li>Security </li></ul><ul><li>Graceful Degradation of Understanding </li></ul>Principles, Features and Behaviours of ROs
  6. 6. <ul><li>Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis in cattle </li></ul><ul><li>Paul meets Jo. Jo is investigating Whipworm in mouse. </li></ul><ul><li>Jo reuses one of Paul’s workflow without change . </li></ul><ul><li>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. </li></ul><ul><li>Previously a manual two year study by Jo had failed to do this. </li></ul>Reuse, Recycling, Repurposing Courtesy of David De Roure
  7. 7. Results Logs Results Metadata Paper Slides Workflow 16 Workflow 13 Common pathways QTL Paul’s Pack Courtesy of David De Roure
  8. 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. 9. <ul><li>Four Main Classes </li></ul><ul><ul><li>Aggregation </li></ul></ul><ul><ul><li>Aggregated Resource </li></ul></ul><ul><ul><li>Resource Map </li></ul></ul><ul><ul><li>Proxy </li></ul></ul>Building Research Objects Using OAI-ORE
  10. 10. OAI-ORE Research Object Upper Model (ROUM) Life Science Entities Taverna SysMo Obesity e-Lab Gene Ontology OBI OBI Ontology Research Object Domain Schema (RODS) Scientific Discourse SWAN Ontology Biocatalogue Research Object Architecture
  11. 11. <ul><li>An environment for building Research Objects </li></ul><ul><li>A central store for Research Objects </li></ul><ul><li>Provide visualizations of Research Objects </li></ul><ul><li>A publisher of the ROUM and some higher level RODSs </li></ul><ul><li>A development environment for RODSs </li></ul><ul><li>Sandbox for development of Research Object model </li></ul>The role for myExperiment
  12. 12. <ul><li>myExperiment Pack is a very basic RO </li></ul><ul><ul><li>Pack is a sub-class of OAI-ORE’s Aggregation </li></ul></ul><ul><ul><ul><li>Items it contains are referenced using OAI-ORE’s aggregrates property. </li></ul></ul></ul><ul><ul><li>Pack currently has two types of item </li></ul></ul><ul><ul><ul><li>myExperiment Contributions (Local) </li></ul></ul></ul><ul><ul><ul><li>Links to things outside myExperiment (Remote) </li></ul></ul></ul><ul><ul><li>These items are encapsulated as entries so they can be described in context of the Pack </li></ul></ul><ul><ul><ul><li>LocalPackEntry and RemotePackEntry are sub-classes of OAI-ORE’s Proxy class </li></ul></ul></ul>Modelling ROs in myExperiment’s ontology
  13. 13. Pack vs Full Research Object
  14. 14. Representing Pack Relationships
  15. 15. <ul><li>Relationship predicates defined in Vocabularies </li></ul><ul><ul><li>Vocabularies are a sub-class of SKOS Concept Schemes </li></ul></ul><ul><ul><li>RODSs will consist of one of more Vocabularies </li></ul></ul><ul><ul><li>RODSs may also have vocabularies for the properties needed by items, entries or even the packs themselves </li></ul></ul><ul><ul><li>These RODSs should reuse existing properties / concepts where possible </li></ul></ul>myExperiment and RODSs
  16. 16. <ul><li>Sharing </li></ul><ul><li>Usage </li></ul><ul><li>Curation </li></ul><ul><li>Provenance </li></ul><ul><li>Lifecyle </li></ul><ul><li>Scientific Discourse </li></ul><ul><li>Etc. </li></ul>What type of concepts are there in a RO?
  17. 17. A myExperiment Pack with Relationships
  18. 18. <ul><li>Provide a UI for building and viewing relationships for ROs </li></ul><ul><li>Finalise the ROUM specification </li></ul><ul><li>Start defining project / use case specific RODSs </li></ul><ul><li>Evaluate how Research Objects align with: </li></ul><ul><ul><li>Nano-publications </li></ul></ul><ul><ul><li>Annotation Ontology </li></ul></ul><ul><ul><li>KEfED </li></ul></ul><ul><ul><li>Other Scientific Discourse efforts </li></ul></ul>Next Steps
  19. 19. <ul><li>The myExperiment team </li></ul><ul><li>Members of e-Laboratories projects at the Universities of Manchester and Southampton </li></ul><ul><li>HCLS Scientific Subtask Group </li></ul>A myExperiment Pack with Relationships
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