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An active registry for bioinformatics web services

S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J. C. Bryne, T. Hupponen, D. Mowbray, G. Vriend
2009 Bioinformatics  
The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators.  ...  Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks.  ...  Unlike 'passive' mechanisms for recording the existence of web services, this registry actively monitors the registration and ongoing behaviour of a service, giving providers and consumers up-to-date status  ... 
doi:10.1093/bioinformatics/btp329 pmid:19460889 pmcid:PMC2722997 fatcat:flbwio7kzbdmbcct5jlitsrtqe

Tools and data services registry: a community effort to document bioinformatics resources

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau (+57 others)
2015 Nucleic Acids Research  
BINF.KU.DK Services and Software A collection of over 20 web services, databases and software packages from The Bioinformatics Centre at The University of Copenhagen.  ...  These are available as interactive web applications, HTTP Web services and downloadable software.  ...  ACKNOWLEDGEMENTS The authors would like to thank Steve Pettifer and Dave Thorne for the initial discussions and ideas founding the registry effort.  ... 
doi:10.1093/nar/gkv1116 pmid:26538599 pmcid:PMC4702812 fatcat:npzer6xh7fezlbcamfmdvv552m

The EMBRACE web service collection

S. Pettifer, J. Ison, M. Kalas, D. Thorne, P. McDermott, I. Jonassen, A. Liaquat, J. M. Fernandez, J. M. Rodriguez, I.- Partners, D. G. Pisano, C. Blanchet (+14 others)
2010 Nucleic Acids Research  
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 (  ...  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  ...  The EMBRACE web service collection Steve  ... 
doi:10.1093/nar/gkq297 pmid:20462862 pmcid:PMC2896104 fatcat:6r262hdgtner7ouoq4qodhr25a

BioSWR – Semantic Web Services Registry for Bioinformatics

Dmitry Repchevsky, Josep Ll. Gelpi, Yu Xue
2014 PLoS ONE  
The registry provides Webbased interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL  ...  BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones.  ...  Acknowledgments The authors would like to thank José María Fernández González for his invaluable help with determination of project requirements and functionality.  ... 
doi:10.1371/journal.pone.0107889 pmid:25233118 pmcid:PMC4169436 fatcat:z7frhotehfguhcadxtyf4umava

Provenance-based validation of e-science experiments

Simon Miles, Sylvia C. Wong, Weijian Fang, Paul Groth, Klaus-Peter Zauner, Luc Moreau
2007 Journal of Web Semantics  
The validation relies on reasoning over the documented provenance of experiment results and semantic descriptions of services advertised in a registry.  ...  After an experiment has been executed, it is useful for a scientist to verify that the execution was performed correctly or is compatible with some existing experimental criteria or standards.  ...  The authors would also like to thank Klaus-Peter Zauner and Stefan Artmann for providing us with the bioinformatics experiment.  ... 
doi:10.1016/j.websem.2006.11.003 fatcat:zlmder6dbnah3fddqahq4sbr7e

Provenance-Based Validation of E-Science Experiments [chapter]

Sylvia C. Wong, Simon Miles, Weijian Fang, Paul Groth, Luc Moreau
2005 Lecture Notes in Computer Science  
The validation relies on reasoning over the documented provenance of experiment results and semantic descriptions of services advertised in a registry.  ...  After an experiment has been executed, it is useful for a scientist to verify that the execution was performed correctly or is compatible with some existing experimental criteria or standards.  ...  The authors would also like to thank Klaus-Peter Zauner and Stefan Artmann for providing us with the bioinformatics experiment.  ... 
doi:10.1007/11574620_57 fatcat:zdbucxvpdzaibeko5fobpimidq

WS-BioZard: A Wizard for Composing Bioinformatics Web Services

Zhiming Wang, John A. Miller, Jessica C. Kissinger, Rui Wang, Douglas Brewer, Cristina Aurrecoechea
2008 2008 IEEE Congress on Services - Part I  
Therefore, lowering the learning curve for Web service composition to make it easier for biologists is becoming a critical need.  ...  Recently, we have seen an increasing amount of interest in the composition of biological Web services in order to process a biological task.  ...  All these activities are transparent to the end user. Third, the Web service information in the palette is dynamically populated by querying the semantic UDDI registry.  ... 
doi:10.1109/services-1.2008.69 dblp:conf/services/WangMKWBA08 fatcat:guh4nyeirrbz7motu5vsyjbsti

Integrating biological research through Web services

H.T. Gao, J.H. Hayes, H. Cai
2005 Computer  
Their work is Japan's earliest published effort using Web services in the life sciences. 9 Some organizations that have already invested in an integration technology can use Web services as an enhancement  ...  implementation in a local registry suitable for testing and for restricting user access to services.  ... 
doi:10.1109/mc.2005.97 fatcat:pf7xaxiywjhlnki44smlbmd6x4

The Distributed Annotation System for Integration of Biological Data [chapter]

Andreas Prlić, Ewan Birney, Tony Cox, Thomas A. Down, Rob Finn, Stefan Gräf, David Jackson, Andreas Kähäri, Eugene Kulesha, Roger Pettett, James Smith, Jim Stalker (+1 others)
2006 Lecture Notes in Computer Science  
Here we provide an overview of the available DAS infrastructure and present our latest developments, including a registration server that facilitates service discovery by DAS clients while automatically  ...  monitoring service availability.  ...  With appropriate client support, the registry can also communicate back in the reverse direction: DAS sources can be activated in a client by clicking on an icon in the registry web interface.  ... 
doi:10.1007/11799511_17 fatcat:lrt64qjjufflreorzlwomljw4i

MOWServ: a web client for integration of bioinformatic resources

Sergio Ram�rez, Antonio Mu�oz-M�rida, Johan Karlsson, Maximiliano Garc�a, Antonio J. P�rez-Pulido, M. Gonzalo Claros, Oswaldo Trelles
2010 Nucleic Acids Research  
The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF.  ...  MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools.  ...  ACKNOWLEDGEMENTS The authors would like to thank all the other nodes in the INB infrastructure for their close involvement in the development of the services and integration procedures.  ... 
doi:10.1093/nar/gkq497 pmid:20525794 pmcid:PMC2896175 fatcat:4fijmcqk2bblvad62mbd6vxqwy

XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

Johannes Wagener, Ola Spjuth, Egon L Willighagen, Jarl ES Wikberg
2009 BMC Bioinformatics  
of an external registry, 2) asynchronous invocation eliminates the need for ad-hoc solutions like polling, and 3) input and output types defined in the service allows for generation of clients on the  ...  HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics  ...  ) for their help and maintenance of the servers dedicated for cloud computing in life science, and S.  ... 
doi:10.1186/1471-2105-10-279 pmid:19732427 pmcid:PMC2755485 fatcat:4uer2klj6rbnvkf2xb5ihus76m

Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt [chapter]

Phillip Lord, Sean Bechhofer, Mark D. Wilkinson, Gary Schiltz, Damian Gessler, Duncan Hull, Carole Goble, Lincoln Stein
2004 Lecture Notes in Computer Science  
We have seen an increasing amount of interest in the application of Semantic Web technologies to Web services.  ...  with these projects have implications for the development of Semantic Web services as a whole.  ...  The MOBY-Services project wishes to thank Dr. William Crosby, Mr. Matthew Links, Mr.  ... 
doi:10.1007/978-3-540-30475-3_25 fatcat:jplow662lzavhjxfp2kajy2ide

BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case

M. Wilkinson
2005 Plant Physiology  
That is to say, interoperability between bioinformatics Web Services can be largely achieved simply by specifying the data structures being passed between the services (syntax) even without rich specification  ...  of the integrative biology problem; in particular, that Web Service interoperability in the domain of bioinformatics is, unexpectedly, largely a syntactic rather than a semantic problem.  ...  MOBY Central and Feta are sufficiently similar in their functionalities that an initiative is now under way to merge these into a single unified Web Service discovery engine for bioinformatics.  ... 
doi:10.1104/pp.104.059170 pmid:15888673 fatcat:wlmqu4vpfzcffk7rg3bjzt3ita - Compact Identifier Services in the Cloud

Manuel Bernal Llinares, Javier Ferrer Gomez, Nick Juty, Carole Goble, Sarala M Wimalaratne, Henning Hermjakob, Zhiyong Lu
2020 Bioinformatics  
We have developed a new front end for accessing the registry data and APIs to simplify integration of CID services with third party applications.  ...  Motivation Since its launch in 2010, has become an important tool for the annotation and cross-referencing of Life Science data.  ...  Jimenez and Greg Jenee for ongoing discussions on identifier harmonisation. Funding  ... 
doi:10.1093/bioinformatics/btaa864 pmid:33031499 pmcid:PMC8289372 fatcat:5swpz4co4bh7plvcwnclpuk3ly

V-Lab-Protein: Virtual Collaborative Lab for protein sequence analysis

Jong Youl Choi, Youngik Yang, Sun Kim, Dennis Gannon
2007 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops  
We believe that this system design principle will be a new and effective paradigm for small biology research labs to handle the ever-increasing biological data.  ...  To response such requirements, we designed and implemented a virtual lab, named Virtual Collaborative Lab (V-Lab-Protein), using an efficient and flexible computing resource management and workflow engine  ...  To convert a bioinformatics application into an application service, we use a tool, called Generic Service Toolkit (Gfac) [5] . Gfac provides two services, a factory service and a registry service.  ... 
doi:10.1109/bibmw.2007.4425417 fatcat:zoybsmdq5rcc7agssuz65hukwa
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