User:Vincent Rouilly/Data Exchange Standards For Synthetic Biology

Data Exchange Standards For Synthetic Biology

For many years, the Molecular Biology and Systems Biology communities are working on data exchange standards to stimulate communication and scientific discoveries. The Synthetic Biology community might find useful to evaluate and re-use these standards when applicable.

Vincent 08:32, 5 January 2010 (EST):Feel free to add links, it is a work in progress.

Experimental measurements

• Fluorescent microscopy: OME: Open Microscopy Environment
• Flow cytometry: FuGEFlow: data model and markup language for flow cytometry
• Microarrays: Minimum Information About a Microarray Experiment
• RT-PCR: MIQE: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
• Minimum Info Required Initiative: MIBBI: Minimum Information for Biological and Biomedical Investigations
• Fluorescent measure:
  • ANSI:Fluorescence Calibration and Quantitative Measurement of Fluorescence Intensity; Approved Guideline
  • NIST, BioAssay Methods

Biological Entity Description

• DNA sequences formats
  • FASTA
  • GenBank
  • DAS: Distributed Annotation System
  • BioSQL, sequence storage in relational database.

Computational Biology

• SBML: Systems Biology Markup Language
• CellML
• MIRIAM:Minimal Information Required In the Annotation of Models

Reviews and Publications

1. Quackenbush J. Data standards for 'omic' science. Nat Biotechnol. 2004 May;22(5):613-4. DOI:10.1038/nbt0504-613 |
2. Strömbäck L, Hall D, and Lambrix P. A review of standards for data exchange within systems biology. Proteomics. 2007 Mar;7(6):857-67. DOI:10.1002/pmic.200600438 |
3. Strömbäck L, Jakoniene V, Tan H, and Lambrix P. Representing, storing and accessing molecular interaction data: a review of models and tools. Brief Bioinform. 2006 Dec;7(4):331-8. DOI:10.1093/bib/bbl039 |
4. Schilling M, Pfeifer AC, Bohl S, and Klingmüller U. Standardizing experimental protocols. Curr Opin Biotechnol. 2008 Aug;19(4):354-9. DOI:10.1016/j.copbio.2008.06.007 |
5. Martens L, Palazzi LM, and Hermjakob H. Data standards and controlled vocabularies for proteomics. Methods Mol Biol. 2008;484:279-86. DOI:10.1007/978-1-59745-398-1_18 |
6. Orchard S and Kerrien S. Molecular interactions and data standardisation. Methods Mol Biol. 2010;604:309-18. DOI:10.1007/978-1-60761-444-9_21 |
7. Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus HJ, and Binz PA. Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands. Proteomics. 2009 Feb;9(3):499-501. DOI:10.1002/pmic.200800838 |