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Standards and infrastructure for managing experimental metadata

Susanna-Assunta Sansone¹ and Philippe Rocca-Serra¹

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

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Date:

Received 22 April 2009 18:19 UTC; Posted 22 April 2009

Subjects:

Genetics & Genomics, Bioinformatics

Tags:

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

Abstract:

See also related poster

Today’s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as ‘omics’). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.

Standards initiatives normally cater to particular domains. However, several synergistic standards activities foster cross-domain harmonization of the three kinds of reporting standard (minimum information checklists, ontologies and file formats). Some 29 groups participate in the MIBBI project, which offers a one-stop shop for those exploring the range of extant ‘minimum information’ checklists, and which fosters integrative development¹. More than 60 groups participate in the OBO Foundry ², which coordinates the orthogonal development of ontologies such as OBI for describing experimental (meta)data. And several groups participate in the development of ISA-Tab, a tabular framework for presenting experimental metadata³ (analogous to FuGE, a generic data model to underpin various XML file formats⁴).

We have developed an infrastructure that leverages the aforementioned synergistic reporting standards 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.

View the public instance of our ISA-based infrastructure, 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. 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

4. 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:

Sansone, Susanna-Assunta and Rocca-Serra, Philippe. Standards and infrastructure for managing experimental metadata. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3145.1> (2009)

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