MetNet Online: a novel integrated resource for plant systems biology

Abstract

Background: Plants are important as foods, pharmaceuticals, biorenewable chemicals, fuel resources, bioremediation tools and general tools for recombinant technology. The study of plant biological pathways is advanced by easy access to integrated data sources. Today, various plant data sources are scattered throughout the web, making it increasingly complicated to build comprehensive datasets.

Results: MetNet Online is a web-based portal that provides access to a regulatory and metabolic plant pathway database. The database and portal integrate Arabidopsis, soybean (Glycine max) and grapevine (Vitis vinifera) data. Pathways are enriched with known or predicted information on sub cellular location. MetNet Online enables pathways, interactions and entities to be browsed or searched by multiple categories such as sub cellular compartment, pathway ontology, and GO term. In addition to this, the "My MetNet" feature allows registered users to bookmark content and track, import and export customized lists of entities. Users can also construct custom networks using existing pathways and/or interactions as building blocks.

Conclusion: The site can be reached at http://www.metnetonline.org. Extensive video tutorials on how to use the site are available through http://www.metnetonline.org/tutorial/.

Figure 1

The order of the data integration for MetNetDB, with respect to Arabidopsis: AraCyc is the backbone of the whole database, then AGRIS is used to extend the networks. Other databases are integrated without any special order requirement. External data usually does not need any special transformation because the data can be easily added into to the database as a new field/label of a gene, a protein or a molecule. So the data integration from the external data source to MetNetDB is straightforward in most cases.

Figure 2

The MetNet Online portal start page. In order to rapidly familiarize novice users, a “pathway of the day” display and a “gene of day” display encourage self-guided exploration.

Figure 3

Different browsing options. Pathways can be browsed by the subcellular location where (part of) the pathway occurs. Hovering over a pathway in the right-side panel bring up a thumbnail of the pathway. The pathway can then be browsed in textual mode (enumerated list of interactions and entities that make up the pathway) and visual mode.

Figure 4

A custom ethylene-related network. The network was generated dynamically by selecting all pathways in which ethylene (ethane) was found.