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A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis
Gabriela D A Guardia1, Luís Ferreira Pires2, Ricardo Z N Vêncio1
1Department of Computer Science and Mathematics-Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP)-University of São Paulo (USP), Ribeirão Preto, Brazil.
Plos One
|July 25, 2015
Summary
This study introduces a new methodology for creating semantic web services for gene expression analysis. This approach integrates various tools, enabling reproducible research in functional genomics.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Gene expression studies involve complex multi-step analyses using diverse tools.
- Existing methods for adapting software to semantic web services have limitations, especially in functional genomics.
Purpose of the Study:
- To define an integrated methodology for implementing and semantically annotating RESTful semantic web services for gene expression analysis tools.
- To address the lack of suitable approaches in the functional genomics domain.
Main Methods:
- Developed a methodology for creating RESTful semantic web services from gene expression analysis tools.
- Implemented services for microarray and RNA-Seq data analysis.
- Created integrated analysis scenarios using developed services.
Main Results:
- A publicly available Gene Expression Analysis Services (GEAS) Repository was established.
- Methodology demonstrated through reproducible analysis of microarray and RNA-Seq studies.
- Services facilitate systematic development and reuse for integrated gene expression analysis.
Conclusions:
- The proposed methodology offers guidelines for developing semantic web services for gene expression analysis.
- Encourages the creation and reuse of these services for semantically integrated functional genomics solutions.
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