1. RightField Rich Annotation of Experimental Biology through Stealth 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 Speeds up annotation Makes annotation more efficient Hides the ontology complexity from the users

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

4. CIMRCIMR Core Information for Metabolomics Reporting MIABEMIABE Minimal Information About a Bioactive Entity MIACAMIACA Minimal Information About a Cellular Assay MIAMEMIAME Minimum Information About a Microarray Experiment MIAME/EnvMIAME/Env MIAME / Environmental transcriptomic experiment MIAME/NutrMIAME/Nutr MIAME / Nutrigenomics MIAME/PlantMIAME/Plant MIAME / Plant transcriptomics MIAME/ToxMIAME/Tox MIAME / Toxicogenomics MIAPAMIAPA Minimum Information About a Phylogenetic Analysis MIAPARMIAPAR Minimum Information About a Protein Affinity Reagent MIAPEMIAPE Minimum Information About a Proteomics Experiment MIAREMIARE Minimum Information About a RNAi Experiment MIASEMIASE Minimum Information About a Simulation Experiment MIENSMIENS Minimum Information about an ENvironmental Sequence MIFlowCytMIFlowCyt Minimum Information for a Flow Cytometry Experiment MIGenMIGen Minimum Information about a Genotyping Experiment MIGSMIGS Minimum Information about a Genome Sequence MIMIxMIMIx Minimum Information about a Molecular Interaction Experiment MIMPPMIMPP Minimal Information for Mouse Phenotyping Procedures MINIMINI Minimum Information about a Neuroscience Investigation MINIMESSMINIMESS Minimal Metagenome Sequence Analysis Standard MINSEQEMINSEQE Minimum Information about a high-throughput SeQuencing Experiment MIPFEMIPFE Minimal Information for Protein Functional Evaluation MIQASMIQAS Minimal Information for QTLs and Association Studies MIqPCRMIqPCR Minimum Information about a quantitative Polymerase Chain Reaction experiment MIRIAMMIRIAM Minimal Information Required In the Annotation of biochemical Models MISFISHIEMISFISHIE Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments STRENDASTRENDA Standards for Reporting Enzymology Data TBCTBC Tox Biology Checklist BioPAX : Biological Pathways Exchange http://www.biopax.org/http://www.biopax.org/ FuGE Functional Genomics Experiment MGED: Microarray Experimental Conditions http://www.mibbi.org/index.php/MIBBI_portal Minimum Information Models

5. Data MIBBI ModelOntologiesStandards Body Microarray MIAME:Minimum 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 MIMIX:Minimum Information about a Molecular Interaction Experiment PSI-MI Protein-Protein Interaction Proteomics Standards Initiative Systems Biology Models MIRIAM:Minimal Information Required In the Annotation of biochemical Models SBO: Systems Biology Ontology BioModels.net Systems Biology Model Simulation MIASE:Minimum Information About a Simulation Experiment KISAO:Kinetic Simulation Algorithm Ontology BioModels.net

6. SysMO Project SysMO Consortium Systems Biology of MicroOrganisms Pan-European consortium > 100 research groups > 320 scientists 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

7. SOP Experiments in SysMO InvestigationStudyAssay Construction Validation SOP http://isatab.sourceforge.net/

8. SOP Experiments in SysMO Construction Validation SOP http://isatab.sourceforge.net/ Metabolomics Mass Spec Transcriptomics Proteomics Fluxomics

9. 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

10. RightField Excel Workbook Ontology “Portion” of ontology terms Terms Embedded into Excel Workbook

11. RightField Application

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

14. Loading Ontologies

15. Excel workbook loaded into RightField with multiple worksheets

16. Class hierarchies of loaded ontologies

17. Term lists for selected cells Methods for specifying ontology terms Selected parent term from the ontology

18. Excel workbook with marked-up cells

19. Marking-up Columns or Rows

20. Ontology terms for marked- up cells in drop-down boxes The End Result

21. 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

22. 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

23. RightField Technologies OWL API Loading ontologies and reasoning Apache POI HSSF libraries Loading and saving of Excel Spreadsheets Java Platform Independent

24. Ontology Languages RDFS - RDF Schema OBO - Open Biomedical Ontologies OWL - Web Ontology Language

25. Populate Store / Reuse Extract Current Work RDF Graph

26. 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/?q=populous BioBanking in the Netherlands (Scott Marshall) Oil and Gas industry Egyptology specimen classification

27. Availability

28. Acknowledgements Stuart OwenKaty WolstencroftCarole Goble Wolfgang MuellerOlga Krebs Matthew Horridge