The EMBRACE web service collection

Steve Pettifer; Jon Ison; Matúš Kalaš; Dave Thorne; Philip McDermott; Inge Jonassen; Ali Liaquat; José M. Fernández; Jose M. Rodriguez; 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

doi:10.1093/nar/gkq297

The EMBRACE web service collection

Steve Pettifer^*, Jon Ison, Matúš Kalaš, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, José M. Fernández, Jose M. Rodriguez, David G. Pisano, Christophe Blanchet, Mahmut Uludag, Peter Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B. Clegg, Erik Bongcam-RudloffJean Salzemann, Vincent Breton, Teresa K. Attwood, Graham Cameron, Gert Vriend

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

38 Scopus citations

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.

Original language	English (US)
Article number	gkq297
Pages (from-to)	W683-W688
Journal	NUCLEIC ACIDS RESEARCH
Volume	38
Issue number	SUPPL. 2
DOIs	https://doi.org/10.1093/nar/gkq297
State	Published - May 12 2010
Externally published	Yes

Bibliographical note

Funding Information:
The authors gratefully acknowledge the contributions of Fred Marcus, Stephan Hohman, Rita Casadio, Matthew Woodwark, Jacques van Helden and Kay Hofmann for providing constant encouragement and stimulating discussions. European Commission within its FP6 Programme, under the thematic area ‘life sciences, genomics and biotechnology for health’ (contract number LHSG-CT-2004-512092 to EMBRACE project).

ASJC Scopus subject areas

Genetics

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Pettifer, S., Ison, J., Kalaš, M., Thorne, D., McDermott, P., Jonassen, I., Liaquat, A., Fernández, J. M., Rodriguez, J. M., Pisano, D. G., Blanchet, C., Uludag, M., Rice, P., Bartaseviciute, E., Rapacki, K., Hekkelman, M., Sand, O., Stockinger, H., Clegg, A. B., ... Vriend, G. (2010). The EMBRACE web service collection. NUCLEIC ACIDS RESEARCH, 38(SUPPL. 2), W683-W688. Article gkq297. https://doi.org/10.1093/nar/gkq297

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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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Pettifer, S, Ison, J, Kalaš, M, Thorne, D, McDermott, P, Jonassen, I, Liaquat, A, Fernández, JM, Rodriguez, JM, Pisano, DG, Blanchet, C, Uludag, M, Rice, P, Bartaseviciute, E, Rapacki, K, Hekkelman, M, Sand, O, Stockinger, H, Clegg, AB, Bongcam-Rudloff, E, Salzemann, J, Breton, V, Attwood, TK, Cameron, G & Vriend, G 2010, 'The EMBRACE web service collection', NUCLEIC ACIDS RESEARCH, vol. 38, no. SUPPL. 2, gkq297, pp. W683-W688. https://doi.org/10.1093/nar/gkq297

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AU - Liaquat, Ali

AU - Fernández, José M.

AU - Rodriguez, Jose M.

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AU - Uludag, Mahmut

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AU - Bartaseviciute, Edita

AU - Rapacki, Kristoffer

AU - Hekkelman, Maarten

AU - Sand, Olivier

AU - Stockinger, Heinz

AU - Clegg, Andrew B.

AU - Bongcam-Rudloff, Erik

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AU - Breton, Vincent

AU - Attwood, Teresa K.

AU - Cameron, Graham

AU - Vriend, Gert

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The EMBRACE web service collection

Abstract

Bibliographical note

ASJC Scopus subject areas

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