RightField The Semantic Annotation of Experimental Data using Spreadsheets, The 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 Models Guidelines, Checklists, vocabularies Managing Biological Data Necessary for publication, submission to public databases and sharing

Describe experiments and results of experiments Minimal Information Models Guidelines, Checklists, Managing Biological Data MIACAMIACA Minimal Information About a Cellular Assay MIAMEMIAME Minimum Information About a Microarray Experiment MIAPEMIAPE Minimum Information About a Proteomics Experiment MIAREMIARE Minimum Information About a RNAi Experiment MIASEMIASE Minimum Information About a Simulation Experiment MIBBI >30

Describe experiments and results of experiments Ontologies and Vocabularies for Annotation Managing Biological Data Gene Ontology ChEBI MGED SBO BioPortal >270 biomedical ontologies

Data MIBBI ModelOntologies 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 InvestigationStudyAssay Construction Validation SOP

SOP Data Templates and Vocabularies Construction Validation SOP 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 workbook Saved in plain Excel Informaticians/ontologists End Users

RightField Application

Loading Ontologies Published ontologies Multiple versions You can also load local ontologies from file or URL

Loading Ontologies

Excel workbook loaded into RightField with multiple worksheets

Class hierarchies of loaded 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 Label The human readable term label Term IRI The (unique) term identifier Ontology IRI Ontology Version The ontology that defines the term The version of the ontology Physical Location The (web) location of the ontology

RightField Technologies OWL API Loading ontologies and reasoning Apache POI HSSF libraries Loading and saving of Excel Spreadsheets Java Platform 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 Extract RDF 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 Simon Jupp, Robert Stevens, University of Manchester

Availability Open source

Acknowledgements Stuart OwenKaty WolstencroftCarole Goble Wolfgang MuellerOlga Krebs Matthew Horridge