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RightField The Semantic Annotation of Experimental Data using Spreadsheets,

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Title: RightField The Semantic Annotation of Experimental Data using Spreadsheets,


1
RightFieldThe Semantic Annotation of
Experimental Data using Spreadsheets,
  • Katy Wolstencroft, Stuart Owen, Matthew
    Horridge,
  • Olga Krebs, Wolfgang Mueller Carole Goble

2
RightField
  • A tool for embedding ranges of ontology terms
    into spreadsheets to allow the users of those
    spreadsheets to add semantic annotations from
    simple drop-down lists

3
RightField
  • A tool for embedding ranges of ontology terms
    into spreadsheets to allow the users of those
    spreadsheets to add semantic annotations from
    simple drop-down lists
  • Why?
  • Makes annotation quicker and more efficient
  • Standardises annotation
  • Hides the ontology complexity from the users

4
Managing Biological Data
Describe experiments and results of experiments
Minimal Information Models Guidelines, Checklists
, vocabularies
Necessary for publication, submission to public
databases and sharing
5
Managing Biological Data
Describe experiments and results of experiments
Minimal Information Models Guidelines, Checklists,
  • MIACA Minimal Information About a Cellular Assay
  • MIAME Minimum Information About a Microarray
    Experiment
  • MIAPE Minimum Information About a Proteomics
    Experiment
  • MIARE Minimum Information About a RNAi Experiment
  • MIASE Minimum Information About a Simulation
    Experiment
  • MIBBI gt30

6
Managing Biological Data
Describe experiments and results of experiments
Ontologies and Vocabularies for Annotation
Gene Ontology ChEBI MGED SBO BioPortal gt270
biomedical ontologies
7
Data MIBBI Model Ontologies
Microarray MIAMEMinimum Information about a Microarray Experiment MGED
Proteomics MIAPE Minimum Information about a Proteomics Experiment PSI-MI, PSI-MS, PSI-MOD
Interaction experiments MIMIXMinimum Information about a Molecular Interaction Experiment PSI-MI Protein-Protein Interaction
Systems Biology Models MIRIAMMinimal Information Required In the Annotation of biochemical Models SBO Systems Biology Ontology
Systems Biology Model Simulation MIASEMinimum Information About a Simulation Experiment KISAOKinetic Simulation Algorithm Ontology
8
SysMO Systems Biology of Micro-Organisms
  • SysMO Consortium
  • SysMO-DB
  • Pan-European consortium
  • gt 100 research groups
  • gt 320 scientists
  • Distributed, interdisciplinary projects
  • Expected to pool data and results and disseminate
  • Microbiologists, molecular biologists,
    biochemists, mathematicians....not many
    informaticians
  • SysMO-SEEK a platform for systems biology data
    sharing
  • Web based environment for sharing in the
    consortium and disseminating to the community
  • Used in other consortia
  • Virtual Liver, EraSysBio, UNICELLSYS and
    more....

9
Associating Experiments
Investigation
Study
Assay
Construction
Validation
http//isatab.sourceforge.net/
10
Data Templates and Vocabularies
Metabolomics
Proteomics
Metabolomics
Mass Spec
Fluxomics
Transcriptomics
Construction
Validation
11
Fitting in with Laboratory practices
  • Scientists can continue to do what they have
    always done
  • Embedding semantics into the tools already in use
  • Excel, excel, excel.....

12
The End Result
Ontology terms for marked-up cells in drop-down
boxes
13
How it Works
Marked-up workbook Saved in plain Excel
Excel Workbook
RightField Client
Terms Embedded into Excel Workbook
Ontology
Portion of ontology terms
End Users
Informaticians/ontologists
14
RightField Application
15
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16
Loading Ontologies
Published ontologies
Multiple versions
You can also load local ontologies from file or
URL
17
Loading Ontologies
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22
Marking-up Columns or Rows
23
The User View
Ontology terms for marked-up cells in drop-down
boxes
24
Ontology Information
  • Ontologies encapsulated
  • Scientists can work offline
  • Ensures same versions of ontologies used for a
    series of experiments
  • No special macros or plugins required, just Excel
    or Open Office
  • Versions and URIs captured in hidden worksheets
  • Provenance
  • Comparisons between sheets
  • Linking back to the vocabularies

25
Provenance
The human readable term label
Term Label
The (unique) term identifier
Term IRI
The ontology that defines the term
Ontology IRI
The version of the ontology
Ontology Version
The (web) location of the ontology
Physical Location
26
RightField Technologies
Java Platform Independent
OWL API Loading ontologies and reasoning
Apache POI HSSF libraries Loading and saving of
Excel Spreadsheets
27
Ontology Languages
RDFS - RDF Schema
OWL - Web Ontology Language
OBO - Open Biomedical Ontologies
28
RightField in Use
  • SysMO Systems Biology of MicroOrganisms
  • E-Lico - a virtual laboratory for
    interdisciplinary collaborative research in data
    mining and data-intensive sciences. Case Studies
    in kidney research
  • BioBanking in the Netherlands
  • Outside Biology
  • Oil and Gas industry
  • Egyptology specimen classification

29
Using RightField Spreadsheets
Populate
RDF Graph
Extract
Store / Reuse
30
Future Developments
  • Auto-complete
  • Validation of annotation
  • Populating ontology content - Populous

31
Populous
http//www.e-lico.eu/populous
  • Generic tool for populating ontology templates
  • Supports validation at the point of data entry
  • Expressive Pattern language for OWL Ontology
    generation
  • Helps biologists with ontology design patterns

Simon Jupp, Robert Stevens, University of
Manchester
32
Availability
  • Open source
  • http//www.rightfield.org.uk

33
Acknowledgements
Stuart Owen
Katy Wolstencroft
Carole Goble
Wolfgang Mueller
Olga Krebs
Matthew Horridge
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