Ontology based data integration in life sciences

• Autores: Dmitri Repchevskiy Belavin
• Directores de la Tesis: Josep Lluis Gelpi Buchaca (dir. tes.)
• Lectura: En la Universitat de Barcelona ( España ) en 2016
• Idioma: inglés
• Tribunal Calificador de la Tesis: Jaime Delgado Mercé (presid.), Oswaldo Trelles (secret.), Mark Wilkinson (voc.)
• Materias:
  • Matemáticas
    • Ciencia de los ordenadores
      • Bancos de datos
      • Informática
• Enlaces
  • Tesis en acceso abierto en:  TDX  Dipòsit Digital de la UB 
• Resumen

  • The aim of this thesis is to develop standard and practical approaches for the semantic integration of biological data and services. The thesis considers various scenarios where ontologies may benefit bioinformatics web services development, integration and provenance. In spite of the broad use of ontologies in biology, their usage is usually limited to a definition of taxonomic hierarchies. This thesis examines the utility of ontologies for data integration in context of semantic web services development. The biological datatypes ontologies are very valuable for the data integration, especially in a context of continuous standards changes. The thesis evaluates the outdated BioMoby ontology for the generation of modern WS-I and RESTful web services. Another important aspect is the use of ontologies for the web services description. The thesis evaluates the W3C standard WSDL ontology for bioinformatics web services description and provenance. Finally, the integration with modern workflow execution platforms such as Taverna and Galaxy is also considered. Despite the growing popularity of JSON format, web services vastly depend on XML type system. The OWL2XS tool facilitates semantic web services development providing the automatic XML Schema generation from an appropriate OWL 2 datatype ontology. Web services integration is hardly achievable without a broad standard adoption. The BioNemus application automatically generates standard-based web services from BioMoby ontologies. Semantic representation of web services description simplifies web services search and annotation. Semantic Web Services Registry (BioSWR) is based on W3C WSDL ontology and provides a multifaceted web services view in different formats: OWL 2, WSDL 1.1, WSDL 2.0 and WADL. To demonstrate benefits of ontology-based web services descriptions, BioSWR Taverna OSGI plug-in has been developed. The new, experimental, Taverna WSDL generic library has been used in Galaxy Gears tool which allows integrating web services into the Galaxy workflows. The thesis explores the scopes of ontologies application for the biological data and services integration, providing a broad set of original tools.