RightFieldThe Semantic Annotation of
Experimental Data using Spreadsheets,
Katy Wolstencroft, Stuart Owen, Matthew Horridge,
Olga Krebs, Wolfgang Mueller Carole Goble
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
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
Describe experiments and results of experiments
Minimal Information ModelsGuidelines,Checklists,
vocabularies
Managing Biological Data
Necessary for publication, submission to public databases and
sharing
Describe experiments and results of experiments
Minimal Information ModelsGuidelines,Checklists,
Managing Biological Data
MIACA Minimal Information About a Cellular Assay MIAME Minimum Information About a Microarray ExperimentMIAPE Minimum Information About a Proteomics Experiment MIARE Minimum Information About a RNAi Experiment MIASE Minimum Information About a Simulation Experiment
MIBBI >30
Describe experiments and results of experiments
Ontologies and Vocabularies for Annotation
Managing Biological Data
Gene OntologyChEBIMGEDSBO
BioPortal >270 biomedical ontologies
DataMIBBI Model Ontologies
Microarray MIAME:Minimum Information about a Microarray Experiment
MGED
Proteomics MIAPE: Minimum Information about a Proteomics Experiment
PSI-MI, PSI-MS, PSI-MOD
Interaction experiments
MIMIX:Minimum Information about a Molecular Interaction Experiment
PSI-MI
Protein-Protein Interaction
Systems Biology Models
MIRIAM:Minimal Information Required In the Annotation of biochemical Models
SBO: Systems Biology Ontology
Systems Biology Model Simulation
MIASE:Minimum Information About a Simulation Experiment
KISAO:Kinetic Simulation Algorithm Ontology
SysMO: Systems Biology of Micro-Organisms
SysMO Consortium Pan-European consortium > 100 research groups > 320 scientists Distributed, interdisciplinary
projects Expected to pool data and
results and disseminate Microbiologists, molecular
biologists, biochemists, mathematicians....not many informaticians
SysMO-DB 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....
SOP
Associating Experiments
Investigation Study Assay
Construction Validation
SOP
SOP
http://isatab.sourceforge.net/
SOP
Data Templates and Vocabularies
Construction Validation
SOP
SOP
Metabolomics
Metabolomics
Mass Spec
Transcriptomics
Proteomics
Fluxomics
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.....
Ontology terms for marked-up cells in drop-down boxes
The End Result
Excel Workbook
Ontology“Portion” of ontology terms
Terms Embedded into Excel Workbook
RightField Client
How it Works
Marked-up workbookSaved in plain Excel
Informaticians/ontologists
End Users
RightField Application
Loading Ontologies
Published ontologiesPublished ontologies
Multiple versionsMultiple versions
You can also load local ontologies from file or URL
Loading Ontologies
Excel workbook loaded into
RightField with multiple worksheets
Class hierarchies ofloaded ontologies
Term lists for selected cells
Methods for specifying ontology terms
Selected parent term from the ontology
Excel workbook with marked-up cells
Marking-up Columns or Rows
Ontology terms for marked-up cells in drop-down boxes
The User View
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
Provenance
Term LabelThe human readable term label
Term IRIThe (unique) term identifier
Ontology IRI
Ontology Version
The ontology that defines the term
The version of the ontology
Physical LocationThe (web) location of the ontology
RightField Technologies
OWL APILoading ontologies and reasoning
Apache POI HSSF librariesLoading and saving of Excel Spreadsheets
JavaPlatform Independent
Ontology Languages
RDFS - RDF Schema
OBO - Open Biomedical Ontologies
OWL - Web Ontology Language
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
Populate
Store / Reuse
ExtractRDF Graph
Using RightField Spreadsheets
Future Developments
Auto-complete Validation of annotation Populating ontology content - Populous
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
http://www.e-lico.eu/populous
Simon Jupp, Robert Stevens, University of Manchester
Availability
Open source http://www.rightfield.org.uk
Acknowledgements
Stuart Owen Katy Wolstencroft Carole Goble
Wolfgang Mueller Olga KrebsMatthew Horridge