Title: RightField The Semantic Annotation of Experimental Data using Spreadsheets,
1RightFieldThe Semantic Annotation of
Experimental Data using Spreadsheets,
- Katy Wolstencroft, Stuart Owen, Matthew
Horridge, - Olga Krebs, Wolfgang Mueller Carole Goble
2RightField
- 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
3RightField
- 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
4Managing Biological Data
Describe experiments and results of experiments
Minimal Information Models Guidelines, Checklists
, vocabularies
Necessary for publication, submission to public
databases and sharing
5Managing 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
6Managing Biological Data
Describe experiments and results of experiments
Ontologies and Vocabularies for Annotation
Gene Ontology ChEBI MGED SBO BioPortal gt270
biomedical ontologies
7Data 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
8SysMO Systems Biology of Micro-Organisms
- 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.... -
9Associating Experiments
Investigation
Study
Assay
Construction
Validation
http//isatab.sourceforge.net/
10Data Templates and Vocabularies
Metabolomics
Proteomics
Metabolomics
Mass Spec
Fluxomics
Transcriptomics
Construction
Validation
11Fitting 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.....
12The End Result
Ontology terms for marked-up cells in drop-down
boxes
13How 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
14RightField Application
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16Loading Ontologies
Published ontologies
Multiple versions
You can also load local ontologies from file or
URL
17Loading Ontologies
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22Marking-up Columns or Rows
23The User View
Ontology terms for marked-up cells in drop-down
boxes
24Ontology 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
25Provenance
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
26RightField Technologies
Java Platform Independent
OWL API Loading ontologies and reasoning
Apache POI HSSF libraries Loading and saving of
Excel Spreadsheets
27Ontology Languages
RDFS - RDF Schema
OWL - Web Ontology Language
OBO - Open Biomedical Ontologies
28RightField 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
29Using RightField Spreadsheets
Populate
RDF Graph
Extract
Store / Reuse
30Future Developments
- Auto-complete
- Validation of annotation
- Populating ontology content - Populous
31Populous
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
32Availability
- Open source
- http//www.rightfield.org.uk
33Acknowledgements
Stuart Owen
Katy Wolstencroft
Carole Goble
Wolfgang Mueller
Olga Krebs
Matthew Horridge