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European plant genome database network (PLANET)

Deliverables

PlaNet has created an integrated platform for plant genomic data. This is represented through a web portal that provides documentation and tutorials as well as search interfaces, tools and links to a network of European data providers (http://www.eu-plant-genome.net). This allows comprehensive queries across databases, flexible integration of new datasets, and powerful high-throughput analysis. Establishing connectivity on the basis of the internationally accepted BioMoby standard has enabled the novel possibility to simply and rapidly create custom analysis pipelines that use the integrated platform for comprehensive access to resources, e.g. using Taverna, a graphical bioinformatics analysis workflow design and execution tool (http://taverna.sf.net). This also integrates the plant genomics resources from the PlaNet project with international bioinformatics efforts, not only in the plant genomics field. PlaNet gives access to data from a network of seven plant research centres with more than 10 databases made available through more than 160 web services. Gene reports are displaying an integrated view on Arabidopsis thaliana genes using distributed resources.
BioMoby is a web service technology with the long-term goal to provide a simple and extensible platform offering access to all kinds of on-line databases and analytical tools in a fully automated and interoperable way. PlaNet was the first project using BioMoby as an integration technology showing that BioMoby fulfills the requirements for easy integration. The decision to use BioMoby was important to both projects and massively improved the development of BioMoby, which now is a mature system and can easily be used by other groups. Several projects followed the Planet example and use the BioMoby technology to achieve their goals. It can be expected that more groups will follow. This leads to the popping-up of hundreds of BioMoby web-services giving access to almost all kinds of analytical tools and on-line databases and all of which are extremely interoperable and can be connected to powerful workflows.
The Planet project formed a network of European plant data providers all of which hosting major European plant databases. Regular meetings led to a strong Planet community where a lot of exchange took place. Several partners are already engaged in other European project (sometimes in collaboration with former PlaNet partners). These future collaborations can also greatly benefit from the PlaNet network.
Planet actively improved the Plant Ontology (PO) by joining the developer meetings and using the existing ontologies for annotation of data. New data models were developed and registered in the Planet Moby Central registry and the Canadian BioMoby Central registry. They are available for common usage.
A common problem in computer science is to extract data from relational databases into structured flat files (e.g. XML documents). YAdumper is a Java application which organizes the database extraction based on a XML template following an external Document Type Declaration. YAdumper significantly reduces the memory requirements and the writing performance compared to other applications.
BioFloWeb is a stand-alone web application processing web services. For a given Arabidopsis Locus Code this software generates a comprehensive gene report making use of the data at the partners sites which are available through BioMoby web services. To get the gene report a user can either choose from the existing Taverna (taverna.sourceforge.net) workflows or can create his own workflow. The services are executed in parallel using the Taverna workflow execution engine and relevant results are organized according to their type before being displayed. BioFloWeb renders all bioinformatic analysis possible depending only on the existence of suitable web services. In a configuration file the way of rendering result can be changed.
Within the PlaNet project more than 160 BioMoby services were set up by the partners. Those services access data from 10 major European plant databases (mostly Arabidopsis but also Maize, Rice, Medicago) and several analysis tools like Blast, Transmembrane predictions, Interactions, etc. These services can easily be integrated into workflows allowing for complex and powerful analysis workflows.