RightField Rich Annotation of Experimental Biology through Stealth Using Spreadsheets

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RightFieldRich Annotation of Experimental
Biology through Stealth Using Spreadsheets

• Katy Wolstencroft, Stuart Owen, Matthew
  Horridge,
• Olga Krebs, Wolfgang Mueller Carole Goble

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RightField

• A tool for embedding ranges of ontology terms
  into spreadsheets
• Speeds up annotation
• Makes annotation more efficient
• Hides the ontology complexity from the users

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Managing Biological Data
Describe experiments and results of experiments
Minimal Information Models Guidelines, Checklists,
Ontology terms
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Minimum Information Models

• CIMR Core Information for Metabolomics Reporting
• MIABE Minimal Information About a Bioactive
  Entity
• MIACA Minimal Information About a Cellular Assay
• MIAME Minimum Information About a Microarray
  Experiment
• MIAME/Env MIAME / Environmental transcriptomic
  experiment
• MIAME/Nutr MIAME / Nutrigenomics
• MIAME/Plant MIAME / Plant transcriptomics
• MIAME/Tox MIAME / Toxicogenomics
• MIAPA Minimum Information About a Phylogenetic
  Analysis
• MIAPAR Minimum Information About a Protein
  Affinity Reagent
• MIAPE Minimum Information About a Proteomics
  Experiment
• MIARE Minimum Information About a RNAi Experiment
  
• MIASE Minimum Information About a Simulation
  Experiment
• MIENS Minimum Information about an ENvironmental
  Sequence
• MIFlowCyt Minimum Information for a Flow
  Cytometry Experiment
• MIGen Minimum Information about a Genotyping
  Experiment
• MIGS Minimum Information about a Genome Sequence
• MIMIx Minimum Information about a Molecular
  Interaction Experiment
• MIMPP Minimal Information for Mouse Phenotyping
  Procedures

http//www.mibbi.org/index.php/MIBBI_portal
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Data MIBBI Model Ontologies Standards Body
Microarray MIAMEMinimum Information about a Microarray Experiment MGED Functional Genomics Data Society
Proteomics MIAPE Minimum Information about a Proteomics Experiment PSI-MI, PSI-MS, PSI-MOD Proteomics Standards Initiative
Interaction experiments MIMIXMinimum Information about a Molecular Interaction Experiment PSI-MI Protein-Protein Interaction Proteomics Standards Initiative
Systems Biology Models MIRIAMMinimal Information Required In the Annotation of biochemical Models SBO Systems Biology Ontology BioModels.net
Systems Biology Model Simulation MIASEMinimum Information About a Simulation Experiment KISAOKinetic Simulation Algorithm Ontology BioModels.net
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SysMO Project

• SysMO Consortium

• SysMO-DB

• Systems Biology of MicroOrganisms
• Pan-European consortium
• gt 100 research groups
• gt 320 scientists
• 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

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Experiments in SysMO
Investigation
Study
Assay
Construction
Validation
http//isatab.sourceforge.net/
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Experiments in SysMO
Metabolomics
Proteomics
Metabolomics
Mass Spec
Fluxomics
Transcriptomics
Construction
Validation
http//isatab.sourceforge.net/
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Fitting in with Laboratory practices

• Excel, excel, excel.....
• Embedding semantics into the tools already in use
• Scientists can continue to do what they have
  always done

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RightField
Excel Workbook
Terms Embedded into Excel Workbook
Ontology
Portion of ontology terms
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RightField Application
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Loading Ontologies
Published ontologies
Multiple versions
You can also load local ontologies from file or
URL
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Loading Ontologies
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Marking-up Columns or Rows
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The End Result
Ontology terms for marked-up cells in drop-down
boxes
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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

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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
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RightField Technologies
Java Platform Independent
OWL API Loading ontologies and reasoning
Apache POI HSSF libraries Loading and saving of
Excel Spreadsheets
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Ontology Languages
RDFS - RDF Schema
OWL - Web Ontology Language
OBO - Open Biomedical Ontologies
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Current Work
Populate
RDF Graph
Extract
Store / Reuse
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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
• Populous extension to RightField for building
  ontologies from simple spreadsheet like templates
• Helps biologists with ontology design patterns
• http//www.e-lico.eu/?qpopulous
• BioBanking in the Netherlands (Scott Marshall)
• Oil and Gas industry
• Egyptology specimen classification

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