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. 2010 Jul;38(Web Server issue):W683-8.
doi: 10.1093/nar/gkq297. Epub 2010 May 12.

The EMBRACE web service collection

Steve Pettifer  1 , Jon Ison, Matús Kalas, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, José M Fernández, Jose M Rodriguez; INB-Partners; David G Pisano, Christophe Blanchet, Mahmut Uludag, Peter Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B Clegg, Erik Bongcam-Rudloff, Jean Salzemann, Vincent Breton, Teresa K Attwood, Graham Cameron, Gert Vriend
Affiliations

The EMBRACE web service collection

Steve Pettifer et al. Nucleic Acids Res. 2010 Jul.

Abstract

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.

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Figures

Figure 1.
Figure 1.
An example of bioinformatics workflow, illustrating the flow of data (red ovals) through various services (blue rectangles). Without a common exchange format such as BioXSD, each edge in this graph would also require additional ‘converter' (or ‘shim’) processes to transform the data into the input formats required by the main services. This would more than double the technical complexity of the workflow for no additional scientific advantage.
Figure 2.
Figure 2.
A pie chart showing the percentage of web services reported by the EMBRACE registry as belonging to various high-level categories.
See this image and copyright information in PMC

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