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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

UML class diagram representing the semantic annotation of the WSDL operation generateKeggPathwayImage.A named rectangle represents a UML class. A white class represents a WSDL element, while a gray class represents a concept from the GEXPASO ontology. A directed solid line (UML association) stereotyped as < < sawsdl:modelReference > > represents the use of the modelReference extension attribute to annotate a WSDL element with a GEXPASO concept. A directed dashed line (UML dependency) stereotyped as < < references > > indicates that a WSDL element references another one. Finally, a solid line with an hollow diamond (UML aggregation) is used to indicate a WSDL element contained as part of another one.
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pone.0134011.g006: UML class diagram representing the semantic annotation of the WSDL operation generateKeggPathwayImage.A named rectangle represents a UML class. A white class represents a WSDL element, while a gray class represents a concept from the GEXPASO ontology. A directed solid line (UML association) stereotyped as < < sawsdl:modelReference > > represents the use of the modelReference extension attribute to annotate a WSDL element with a GEXPASO concept. A directed dashed line (UML dependency) stereotyped as < < references > > indicates that a WSDL element references another one. Finally, a solid line with an hollow diamond (UML aggregation) is used to indicate a WSDL element contained as part of another one.

Mentions: Fig 6 shows a UML class diagram representing the syntactical structure and semantic annotation of WSDL operation generateKeggPathwayImage. This WSDL operation was associated to the GEXPASO concept gene expression data rendering into KEGG pathway graph and the input elements of this operation, identifier, speciesIdentifier, pathwayIdentifier and geneIdType, were associated to the GEXPASO concepts analysis identifier, biological species identifier, KEGG pathway graph identifier and gene identifier type, respectively.


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)

UML class diagram representing the semantic annotation of the WSDL operation generateKeggPathwayImage.A named rectangle represents a UML class. A white class represents a WSDL element, while a gray class represents a concept from the GEXPASO ontology. A directed solid line (UML association) stereotyped as < < sawsdl:modelReference > > represents the use of the modelReference extension attribute to annotate a WSDL element with a GEXPASO concept. A directed dashed line (UML dependency) stereotyped as < < references > > indicates that a WSDL element references another one. Finally, a solid line with an hollow diamond (UML aggregation) is used to indicate a WSDL element contained as part of another one.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134011.g006: UML class diagram representing the semantic annotation of the WSDL operation generateKeggPathwayImage.A named rectangle represents a UML class. A white class represents a WSDL element, while a gray class represents a concept from the GEXPASO ontology. A directed solid line (UML association) stereotyped as < < sawsdl:modelReference > > represents the use of the modelReference extension attribute to annotate a WSDL element with a GEXPASO concept. A directed dashed line (UML dependency) stereotyped as < < references > > indicates that a WSDL element references another one. Finally, a solid line with an hollow diamond (UML aggregation) is used to indicate a WSDL element contained as part of another one.
Mentions: Fig 6 shows a UML class diagram representing the syntactical structure and semantic annotation of WSDL operation generateKeggPathwayImage. This WSDL operation was associated to the GEXPASO concept gene expression data rendering into KEGG pathway graph and the input elements of this operation, identifier, speciesIdentifier, pathwayIdentifier and geneIdType, were associated to the GEXPASO concepts analysis identifier, biological species identifier, KEGG pathway graph identifier and gene identifier type, respectively.

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