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Executing SADI services in Galaxy.

Mikel Egaña Aranguren1, Alejandro Rodríguez González2, Mark D Wilkinson2

  • 1Biological Informatics, Centre for Plant Biotechnology and Genomics (CBGP), Technical University of Madrid (UPM), Campus of Montegancedo, 28223 Pozuelo de Alarcón, Spain ; Genomic Resources, Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena auzoa z/g, 48940 Leioa - Bilbo, Spain.

Journal of Biomedical Semantics
|October 14, 2014
PubMed
Summary
This summary is machine-generated.

SADI-Galaxy integrates Semantic Web Services (SADI) into the Galaxy workflow system, enabling bioinformatics researchers to leverage semantic web technologies within their existing workflows. This tool generator enhances Galaxy

Keywords:
GalaxyOWLRDFSADISPARQLWeb services

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Area of Science:

  • Bioinformatics
  • Semantic Web Technologies
  • Computational Biology

Background:

  • Galaxy is a widely adopted workflow management system in bioinformatics.
  • Limited availability of Semantic Web-oriented tools and Semantic Web Services (SADI) within Galaxy.
  • SADI services consume and produce Resource Description Framework (RDF) data.

Purpose of the Study:

  • To present SADI-Galaxy, a novel tool generator.
  • To deploy SADI Services as standard Galaxy tools.
  • To bridge the gap between Galaxy and SADI frameworks.

Main Methods:

  • Developed SADI-Galaxy as a tool generator for Galaxy.
  • Enabled SADI-compliant services to function as Galaxy tools.
  • Semi-automated data packing and unpacking for RDF compatibility.

Main Results:

  • Any SADI-compliant service can be deployed as a Galaxy tool via SADI-Galaxy.
  • SADI services seamlessly integrate with Galaxy features like data storage, history, workflow creation, and publication.
  • Facilitated the execution and combination of SADI services within Galaxy workflows.
  • Enabled easy integration of SADI Semantic Web Services into the Galaxy ecosystem.

Conclusions:

  • SADI-Galaxy effectively connects the user-friendly Galaxy workflow system with the sophisticated SADI Semantic Web Service framework.
  • Enhances the capabilities of both Galaxy and SADI by enabling interoperability.
  • Benefits a broad user community by providing access to advanced semantic web functionalities within a familiar workflow environment.