In his Correspondence on data sharing ('Big data: open-source format needed to aid wiki collaboration' Nature 455, 461; 2008), Tin-Lap Lee points out “there is currently no de facto standard on pathway-data format, which severely limits data portability”. Although this statement is correct, there are three particular standards in use — BioPAX (http://www.biopax.org), CellML (http://www.cellml.org) and the Systems Biology Markup Language (http://www.sbml.org) — that all serve this purpose.
These standards can provide annotations based on appropriate ontologies. In other words, they provide an indexing system that gives unambiguous representations of the entities that they describe, thereby avoiding the problem of synonyms (see M. J. Herrgård et al. Nature Biotechnol. 26, 1155–1160; 2008).
MIRIAM is a community recommendation for minimal information to be reported about models and can be used with any of the three standards (N. Le Novère et al. Nature Biotechnol. 23, 1509–1515; 2005).
I would strongly recommend that everyone with an interest in sharing models should do so using one or more of these formats.
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