1. Sharing the knowledge of electrophysiology data Phillip Lord, Frank Gibson and the CARMEN Consortium

2. “In the standard model, one collects data, publishes a paper or papers and then gradually loses the original dataset.” THE NEW KNOWLEDGE ECONOMY AND SCIENCE AND TECHNOLOGY POLICY Geoffrey Bowker, University of California, San Diego Geoffrey Bowker, University of California, San Diego

3. The need for clear metadata Most neurosciences data is relative simple in structure But often contextually complex Sometimes associated with behavioural features

4. Neuroscience spike data The raw data is normally a waveform But, advances in instrumentation High-throughput methods But what is the experiment for? What stimulus is the organism/tissue receiving? Which channel is which The data sets being produced are (reasonably) large (10’s of Gb, or 1Tb in three months)

5. Information Extraction How do we get extract the information? http://en.wikipedia.org/wiki/Image:Brain_090407.jpg http://en.wikipedia.org/wiki/Image:ATTtelephone-large.jpg istockphoto.com

6. Multi-Author data AuthorPMIDTypeSize 1Davierwala et al16155567Synthetic_Lethality627 2Krogan et al14759368Affinity_Capture-MS164 3Hazbun et al14690591Affinity_Capture-MS3210 4Gavin et al11805826Affinity_Capture-MS3596 5Ho et al11805837Affinity_Capture-MS733 6Ito et al11283351Two-hybrid275 From Katherine James, NCL

8. How do we represent… Laboratory Experiments In silico Analysis Derived data

10. Joseph Whitworth http://en.wikipedia.org/wiki/Image:Joseph_whitworth.jpg http://en.wikipedia.org/wiki/Image:Screw_thread_Z%C3%A1vit_M16.jpg

11. Metadata Description of results Sample How it was generated Equipment Processing steps Expensive to capture Important to validate result Lab-book

12. The need for standards! “established by consensus and approved by a recognized body, that provides, […] rules, […] for […] the optimum degree of order in a given context” BSI - http://www.bsi-global.com/en/Standards-and-Publications/About-standards/Glossary/

13. View from microarrays Content Standard – Minimal Information MAGE -- Structure MO -- Terminology From the MGED society

14. The CARMEN approach Content Standard – Minimal Information about a Neuroscience Investigation FuGE -- Structure OBI – Ontology for Biomedical Investigations

15. Minimal Information About a Neuroscience Investigation: What do I have to tell you, for you to understand what I did? Subdivided as; –Contact and context –Study subject –Recording location –Task –Stimulus –Behavioural event –Recording –Time series data Study inputs Assay inputs Assay procedures Data

16. MINI in relation to the life-science reporting requirements

17. MIAOWS Describe essential metadata for your analysis code –What does it do? Objective –What type of input does it need –What type of output does it produce –If this information is not described, your code is of most value to yourself and much less value to the community

18. The CARMEN approach Content Standard – Minimal Information about a Neuroscience Investigation FuGE -- Structure OBI – Ontology for Biomedical Investigations

19. Functional Genomics Experiment (FuGE) How do I tell you, for you to understand? Model of common components in science investigations, such as materials, data, protocols, equipment and software. Provides a framework for capturing complete laboratory workflows, enabling the integration of pre-existing data formats.

20. Model Driven Architecture -- SyMBA XML Java objects UML database

21. FuGE community of users MGED (transcriptomics) Proteomics Standards Initiative Metabolomics Standards Initiative (NMR and sample processing groups) Genomics Standards Consortium (MIGS) CARMEN, Code Analysis, Repository and Modelling for e-Neuroscience Flow Informatics and Computational Cytometry Society MIARE: Minimum Information About an RNAi Experiment

22. Functional Genomics Experiment (FuGE) How do I tell you, for you to understand? Model of common components in science investigations, such as materials, data, protocols, equipment and software. Provides a framework for capturing complete laboratory workflows, enabling the integration of pre-existing data formats.

23. The CARMEN approach Content Standard – Minimal Information about a Neuroscience Investigation FuGE -- Structure OBI – Ontology for Biomedical Investigations

24. OBI – Ontology of Biomedical Investigations OBI branches: development work Diversity communities from Nutrition to Metabolomics, from Environmental to genomics to Immunology, Imaging and Data analysis Protocol application branch Biomaterial branch Function branch Data Transformation branch Role branch Digital entity branch Molecular entities Instrument branch Adapted from Philippe Rocca-Serra, 2008

25. Summary We are generating metadata “standards” for neurosciences We are following a well-trodden path from bioinformatics We adopted FuGE and have built MINI

26. Future Work More neurosciences experimental datatypes. Minimal Information about a Service –Describe analysis software as well as lab experiments. Outreach!

27. Acknowledgements MINI: Frank Gibson, Paul G Overton, Tom V Smulders, Simon R Schultz, Stephen J Eglen, Colin D Ingram, Stefano Panzeri, Phil Bream, Evelyne Sernagor, Mark Cunningham, Christopher Adams, Christoph Echtermeyer, Jennifer Simonotto, Marcus Kaiser, Daniel C Swan, Martyn Fletcher, Phillip Lord CISBAN: Anil Wipat (PI), Allyson Lister (Research Associate), FuGE: The FuGE consortium OBI: The OBI consortium CARMEN: http://www.carmen.org.uk SyMBA: http://symba.sourceforge.net FuGE: http://fuge.sourceforge.net OBI: http://obi.sourceforge.net

28. CARMEN Consortium