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Table 1 Standards for systems biology, grouped by type

From: Trends in modeling Biomedical Complex Systems

Minimum Information (see also the MIBBI initiative [58])

MIAME

Microarray Experiment

http://www.mged.org/Workgroups/MIAME/miame_2.0.html

MIAPE

Proteomics Experiment

http://www.psidev.info/

MIRIAM

Annotation of biochemical Models

http://biomodels.net/miriam/

MIACA

Cellular Assay (MIACA)

http://miaca.sourceforge.net/

Ontologies (see also the OBO Foundry [43])

GO

Gene Ontology

http://www.geneontology.org/

MO

Microarray Ontology

http://mged.sourceforge.net/ontologies/MGEDontology.php

PW

Pathway ontology

http://rgd.mcw.edu/tools/ontology/ont_search.cgi

PSI-MI

Protein-protein interaction

http://www.psidev.info/

SBO

Systems Biology

http://www.ebi.ac.uk/sbo/

FuGO

Functional Genomics Investigation

http://fugo.sourceforge.net/ontologyInfo/ontology.php

XML Languages

MAGE-ML

Microarray Gene Expression ML

http://www.mged.org/Workgroups/MAGE/mage-ml.html

HUP-ML

Human Proteome ML

http://www1.biz.biglobe.ne.jp/~jhupo/HUP-ML/hup-ml.html

mzXML

Mass spectrometry data ML

http://sashimi.sourceforge.net/software.html

SBML

Systems Biology ML

http://www.sbml.org/Documents/

CSML

Cell System ML

http://csml.org/

CellML

Cell ML

http://www.cellml.org/about/about

BioPAX

Biological Pathways Exchange

http://www.biopax.org/