SyMBA (http://symba.sf.net) is a data archive and integrator based on Version 1 of the Functional Genomics Experiment (FuGE, http://fuge.sf.net) Object Model (FuGE-OM), and which archives, stores, and retrieves raw high-throughput data. Until now, few published systems have successfully integrated multiple omics data types and information about experiments in a single database. SyMBA includes a database back-end, expert and standard interfaces, and a Life Science Identifier (LSID) Resolution and Assigning service to identify objects and provide programmatic access to the database. Having a central data repository prevents deletion, loss, or accidental modification of primary data, while giving convenient access to the data for publication and analysis. It also provides a central location for storage of metadata for the high-throughput data sets, and will facilitate subsequent data integration strategies.
We encourage the use, installation and development of SyMBA by other groups. Please let us know if you are interested in using or evaluating SyMBA for use at your own Centre. Contact us: symba-devel at lists.sourceforge.net
8. “This transition will require...standardized methods” Nature 455, 47-50 Release of September 2 2008: http://uniprot.org
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10. “ This takes a degree of intellectual and practical commitment to what can seem like tedious bookkeeping.” Nature 455, 1 Nature Biotechnology 25, 1127 - 1133
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12. “ Researchers need to be obliged to document and manage their data with as much professionalism as they devote to their experiments.” ( Nature 455, 1) CC-NC-2.0
22. Semantics: providing agreed-upon definitions for the information PD: http://commons.wikimedia.org/wiki/Image:Duke_Ellington_-_Hurricane_Ballroom_-_trio.jpg
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24. the final processed (normalised) data for the set of hybridisations in the experiment
28. the essential laboratory and data processing protocols adapted from mibbi.org (image) and text from http://www.mged.org/Workgroups/MIAME/miame.html
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30. standardizes and structures experimental metadata for a range of omics experiments
31. models experimental objects such as samples, protocols, instruments, and software
32. provides extension points for the creation of individual community standards PD: http://commons.wikimedia.org/wiki/Image:Syntax_tree.svg
36. Why Use SyMBA? CC-SA-2.0, Tom Murphy VII, commons.wikimedia.org
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38. CISBAN has a way to allow researchers to provide this metadata at the same time as they archive and backup their data: SyMBA
39. The Big Data special was only 2 weeks ago, but SyMBA has been in development for > 2 years! CC BY-SA 3.0: http://commons.wikimedia.org/wiki/File:DNA_microarray.svg
71. CC-BY-2.5 is under the Creative Commons Attribution – 2.5 Generic license. Details here: http://creativecommons.org/licenses/by/2.5
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73. I have strived to keep attribution for all images used. Please let me know if I have gotten anything wrong. Please note all other portions of this presentation are copyright by Allyson Lister and her employers under the CC BY-SA 3.0. See http://creativecommons.org/licenses/by-sa/3.0