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Article
MetNetAPI: A flexible method to access and manipulate biological network data from MetNet
BMC Research Notes
  • Yves Sucaet, Iowa State University
  • Eve Syrkin Wurtele, Iowa State University
Document Type
Article
Publication Version
Published Version
Publication Date
11-18-2010
DOI
10.1186/1756-0500-3-312
Abstract
BackgroundConvenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. ResultsMetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. ConclusionsAn API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api.
Comments

This article is from BMC Research Notes 3 (2010): 312, doi:10.1186/1756-0500-3-312. Posted with permission.

Rights
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright Owner
Sucaet and Wurtele
Language
en
File Format
application/pdf
Citation Information
Yves Sucaet and Eve Syrkin Wurtele. "MetNetAPI: A flexible method to access and manipulate biological network data from MetNet" BMC Research Notes Vol. 3 (2010) p. 312
Available at: http://works.bepress.com/eve-wurtele/17/