Difference between revisions of "User:Vincent Rouilly/Data Exchange Standards For Synthetic Biology"

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(New page: __NOTOC__ =Data Exchange Standards For Synthetic Biology= For many years, the Molecular Biology and Systems Biology communities are working on data exchange standards to stimulate communi...)
 
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==Experimental measurements==
 
==Experimental measurements==
  
===Fluoresent assays===
+
* '''Fluorescent microscopy''': [http://www.ome-xml.org/ OME: Open Microscopy Environment]
 
+
* '''Flow cytometry''': [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711079/ FuGEFlow: data model and markup language for flow cytometry]
* Fluorescent microscopy
+
* '''Microarrays''': [http://www.mged.org/Workgroups/MIAME/miame.html Minimum Information About a Microarray Experiment]
* Flow cytometry
+
* '''RT-PCR''': [http://www.rdml.org/miqe.php MIQE: Minimum Information for Publication of Quantitative Real-Time PCR Experiments]
* Microarrays  
+
* '''Minimum Info Required Initiative: [http://www.mibbi.org/index.php/Main_Page  MIBBI: Minimum Information for Biological and Biomedical Investigations]
 +
* '''Fluorescent measure''':
 +
** [http://webstore.ansi.org/RecordDetail.aspx?sku=I%2fLA24-A ANSI:Fluorescence Calibration and Quantitative Measurement of Fluorescence Intensity; Approved Guideline]
 +
** [http://www.nist.gov NIST], [http://www.nist.gov/cstl/biochemical/bioassay/index.cfm BioAssay Methods]
  
 
==Biological Entity Description==
 
==Biological Entity Description==
  
* DNA sequences
+
* [http://www.genomatix.de/online_help/help/sequence_formats.html DNA sequences formats]
 
** FASTA
 
** FASTA
 
** GenBank
 
** GenBank
** DAS
+
** [http://www.biodas.org/wiki/Main_Page DAS: Distributed Annotation System]
 +
** [http://www.biosql.org/wiki/Main_Page BioSQL], sequence storage in relational database.
  
 
==Computational Biology==
 
==Computational Biology==
  
* SBML
+
* [http://sbml.org/Main_Page SBML: Systems Biology Markup Language
* CellML
+
* [http://www.cellml.org/ CellML]
* MIRIAM
+
* [http://www.ebi.ac.uk/miriam/main/mdb?section=standard MIRIAM:Minimal Information Required In the Annotation of Models]
  
 
==Reviews and Publications==
 
==Reviews and Publications==
 
<biblio>
 
<biblio>
 +
#0 pmid=15122299
 
#1 pmid=17370264
 
#1 pmid=17370264
 
#2 pmid=17132622
 
#2 pmid=17132622

Revision as of 06:11, 5 January 2010

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

Biological Entity Description

Computational Biology

Reviews and Publications

  1. Quackenbush J. Data standards for 'omic' science. Nat Biotechnol. 2004 May;22(5):613-4. DOI:10.1038/nbt0504-613 | PubMed ID:15122299 | HubMed [0]
  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 | PubMed ID:17370264 | HubMed [1]
  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 | PubMed ID:17132622 | HubMed [2]
  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 | PubMed ID:18617004 | HubMed [3]
  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 | PubMed ID:18592186 | HubMed [4]
  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 | PubMed ID:20013380 | HubMed [5]
  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 | PubMed ID:19132688 | HubMed [6]
All Medline abstracts: PubMed | HubMed