MetNet connectivity options

In order to server as a data provider, MetNet pursues several strategies:

• Support of community standards. All pathways are available for download in SBML-format. Since MetNet contains more information than SBML is able to represent by default, custom <annotation> are embedded at various levels in the alternate BioPax-format.
  Checking out your shopping basket means a custom SBML-file is generated with your relevant combination of entities/interactions/pathways.
• Linkout pages are intented for third-parties to provide links to us. An example is http://www.plant-metabolomics.org, where for each metabolites a link is provided to MetNet to generate a list of pathways in which a metabolite participates.
• SOAP webservices are the most comprehensive way to interact with MetNet. All abovementioned features are available through SOAP, in addition to additional automation functions such as "give me a list of updated function since my visit on YYYY/MM/DD". In order to target as many platforms as possible, simple datastructures are returned (for more advanced biological webservice features, see BioMoby), resulting in each occasion in a list of identifiers for either interactions or pathways. Seperate linkout-scripts can then be used to retrieve complete SBML-data for identified features. The webservices therefore serve as a querying mechanism rather than a data retrieval system.

In the future, the following extensions are planned: SBW integration, BioMoby services, in addition to exposure of more MetNet features through SOAP, such as AtGeneSearch or PubMed Assistant.