XGMML (the eXtensible Graph Markup and
Modeling Language) is an
XML
Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. ...
application based on
GML which is used for graph description. Technically, while GML is not related to
XML
Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. ...
nor
SGML
The Standard Generalized Markup Language (SGML; ISO 8879:1986) is a standard for defining generalized markup languages for documents. ISO 8879 Annex A.1 states that generalized markup is "based on two postulates":
* Declarative: Markup should d ...
, XGMML is an XML application that is so designed that there's a 1:1 relation towards GML for trivial conversion between the two formats.
Applications supporting XGMML
*
Cytoscape
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available f ...
, an
open source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...
bioinformatics software The list of bioinformatics software tools can be split up according to the license used:
* List of proprietary bioinformatics software
*List of open-source bioinformatics software
Alternatively, here is a categorization according to the respective ...
platform for visualizing molecular interaction networks, loads and saves networks and node/edge attributes in XGMML
*
Biomax BioXM Knowledge Management Environment, a customizable knowledge management system for life sciences, supports export of
semantic network
A semantic network, or frame network is a knowledge base that represents semantic relations between concepts in a network. This is often used as a form of knowledge representation. It is a directed or undirected graph consisting of vertices ...
graphs as XGMML files
*
JNets, a network visualization and analysis tool.
See also
*
LOGML, a markup language enabling data mining for web server logs. LOGML is derived from XGMML.
External links
XGMML Reference(archived copy, original link offline)
XML markup languages
Computer file formats
Graph description languages
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