Table 3.

Common network file formats (supported by HIVE).

	Description	Reference/Link
BioPAX (Biological pathway exchange)	Standardized exchange format of various network editing tools, which supports all graph attributes, such as topology, layout, visual properties, links, and also biological properties (e.g., roles, functions); hard to edit manually	Demir et al. (2010)
CSV* (Comma separated values)	Text-based exchange format of some network editing tools, which supports basic network topology without any layout information; easy to edit manually with text editors or MS Excel	–
GML (Graph modeling language)	Standardized text-based exchange format of various network editing tools, which supports all graph attributes, such as topology, layout, visual properties, links, and experiment data; hard to edit manually	http://www.fim.uni-passau.de/fileadmin/files/lehrstuhl/brandenburg/projekte/gml/gml-technical-report.pdf
SBGN (SBGN markup language, SBGN-ML)	Standardized XML-based format for the exchange of SBGN maps, which so far supports only the exchange of basic network topology without any layout information; hard to edit manually	Van Iersel et al. (2012); http://libsbgn.sourceforge.net
SIF (Simple interaction file)	Text-based exchange format of various network editing tools, which is similar to CSV and supports basic network topology without any layout information; easy to edit manually with text editors or MS Excel	Shannon et al. (2003)
SBML (Systems biology markup language)	Standardized XML-based exchange format of various tools for representing biochemical models, which supports biological properties (e.g., roles, functions) and basic network topology without any layout information; hard to edit manually	Hucka et al. (2003)