2 votes

Standards and infrastructure for managing experimental metadata

Philippe Rocca-Serra¹, Marco Brandizi¹, Eamonn Maguire¹, Nataliya Sklyar¹, Chris Taylor¹, Manon Delahaye¹, Richard Evans¹ & Susanna-Assunta Sansone¹

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1. EBI, Cambridge, UK, http://www.ebi.ac.uk/net-project

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Document Type:

Poster

Date:

Received 22 April 2009 18:02 UTC; Posted 22 April 2009

Subjects:

Bioinformatics

Tags:

• OBO Foundry
• data management
• standards
• metadata
• mibbi
• isa-tab
• ontologies
• reporting standards
• omics
• OBI

Abstract:

See also the related presentation

We present an infrastructure that leverages synergistic reporting standards and ontologies^1,2,3,4,5 to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies.

The infrastructure’s components include: a data capture and editing tool (ISAcreator); validator (ISAvalidator); database (BioInvestigation Index); and converter (ISAconverter); and a BioConductor analysis package (R-ISApackage). The components are designed for local installation, and can work independently, or as unified system.

View the public instance running at EBI and/or download the components for your local use.

References
1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. Nature Biotechnology Aug;26(8):889-896. http://www.mibbi.org

2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. Nature Biotechnology Nov;25(11):1251-5. http://www.obofoundry.org

3. Ontology for Biomedical Investigations (OBI) http://obi-ontology.org

4. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. OMICS. Jun;12(2):143-9. http://isatab.sf.net

5. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). Nature Biotechnology Oct;25(10):1127-1133. http://fuge.sf.net

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Rocca-Serra, Philippe, Brandizi, Marco, Maguire, Eamonn, Sklyar, Nataliya, Taylor, Chris, Delahaye, Manon, Evans, Richard, and Sansone, Susanna-Assunta. Standards and infrastructure for managing experimental metadata . Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3144.1> (2009)

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