The pathway information present in NetSlim can be downloaded in a variety of standard data exchange formats. These include Biological Pathway Exchange (BioPAX), Proteomics Standards Initiative - Molecular Interactions (PSI-MI), Systems Biology Markup Language (SBML)  and GenMAPP Pathway Markup Language (GPML). The files downloaded in these formats can be used with various pathway visualization and analysis software that are compatible with these file formats.
Various commonly used data exchange formats and the software that support them are given below:

  
   
1. PSI-MI: PSI-MI is a community standard data exchange format used to represent biomolecular interactions. (http://www.psidev.info/)
Cytoscape (www.cytoscape.org), ViSANT (http://visant.bu.edu)
2. BioPAX:  BioPAX is a standard language that is used to integrate, exchange, visualize and analyze pathway data. (http://www.biopax.org/)
 Cytoscape, ViSANT, Ingenuity Pathway Analysis (www.ingenuity.com), Genespring (www.agilent.com/chem/genespring), ChiBE (http://www.bilkent.edu.tr/~bcbi/chibe.html)
3. SBML: SBML is a machine-readable  format used to represent biochemical reaction networks. It can be used to model signal transduction pathways and metabolic networks. (http://sbml.org/Main_Page)
Cytoscape, Ingenuity Pathway Analysis
 
 

For example, the TGF beta pathway data in NetSlim can be saved in SBML format by clicking on the 'Download'  tab and selecting the 'SBML' option. This SBML file can be imported in Cytoscape by selecting the File>Import>Network (Multiple File Types) option and selecting the corresponding file. Other standard data exchange formats can also be imported using this option. This generates the corresponding TGF beta network in cytoscape which can be used for analysis purposes including overlaying gene expression datasets.
Apart from these standard formats, the user also has the option to download the NetSlim information in GenMAPP Pathway Markup Language (GenMAPP) format. This format can be used with the GenMAPP software.  Also, collaborative efforts between GenMAPP and BioPAX developers and Cytoscape consortium are underway to build a new software framework that can implement GenMAPP-style visualization and analysis methods.		  
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