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A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

Guardia GD, Pires LF, Vêncio RZ, Malmegrim KC, de Farias CR - PLoS ONE (2015)

Bottom Line: In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain.Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services.Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Mathematics-Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP)-University of São Paulo (USP), Ribeirão Preto, Brazil.

ABSTRACT
Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

No MeSH data available.


Related in: MedlinePlus

Architecture of a generic web service (wrapper).Service operations A and B provide access to different functions of an existing software application, while the service operation C was independently implemented of the tool being wrapped. Functionality 4 of the software application is not accessed by the service.
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pone.0134011.g001: Architecture of a generic web service (wrapper).Service operations A and B provide access to different functions of an existing software application, while the service operation C was independently implemented of the tool being wrapped. Functionality 4 of the software application is not accessed by the service.

Mentions: When wrapping a software tool into a web service, a subset of the functions provided by this tool can be accessed by one or more service operations. The service designer may disregard some functions of the tool when designing the wrapper, due to reasons possibly related to the way in which the wrapper is expected to be used. Moreover, additional operations, which do not directly access the tool itself, can also be defined by the service developer in order to enable proper remote access to the tool. For example, a service developer may have to define an operation to manage the execution of an analysis been performed by the tool or to return the result of a completed analysis. Fig 1 shows the architecture of a generic web service implemented as a wrapper of an existing software application.


A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

Guardia GD, Pires LF, Vêncio RZ, Malmegrim KC, de Farias CR - PLoS ONE (2015)

Architecture of a generic web service (wrapper).Service operations A and B provide access to different functions of an existing software application, while the service operation C was independently implemented of the tool being wrapped. Functionality 4 of the software application is not accessed by the service.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4514690&req=5

pone.0134011.g001: Architecture of a generic web service (wrapper).Service operations A and B provide access to different functions of an existing software application, while the service operation C was independently implemented of the tool being wrapped. Functionality 4 of the software application is not accessed by the service.
Mentions: When wrapping a software tool into a web service, a subset of the functions provided by this tool can be accessed by one or more service operations. The service designer may disregard some functions of the tool when designing the wrapper, due to reasons possibly related to the way in which the wrapper is expected to be used. Moreover, additional operations, which do not directly access the tool itself, can also be defined by the service developer in order to enable proper remote access to the tool. For example, a service developer may have to define an operation to manage the execution of an analysis been performed by the tool or to return the result of a completed analysis. Fig 1 shows the architecture of a generic web service implemented as a wrapper of an existing software application.

Bottom Line: In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain.Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services.Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Mathematics-Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP)-University of São Paulo (USP), Ribeirão Preto, Brazil.

ABSTRACT
Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

No MeSH data available.


Related in: MedlinePlus