Bioinformatics service reconciliation by heterogeneous schema transformation

This paper focuses on the problem of bioinformatics service reconciliation in a generic and scalable manner so as to enhance interoperability in a highly evolving field. Using XML as a common representation format, but also supporting existing flat-file representation formats, we propose an approach for the scalable semi-automatic reconciliation of services, possibly invoked from within a scientific workflows tool. Service reconciliation may use the AutoMed heterogeneous data integration system as an intermediary service, or may use AutoMed to produce services that mediate between services. We discuss the application of our approach for the reconciliation of services in an example bioinformatics workflow. The main contribution of this research is an architecture for the scalable reconciliation of bioinformatics services

ISPIDER Central: an integrated database web-server for proteomics

Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics

Information sharing for the Semantic Web - a schema transformation approach

This paper proposes a set of algorithms for the transformation and integration of heterogeneous XML data sources which make use of correspondences from them to ontologies expressed in the form of RDFS schemas. Our algorithms generate schema transformation/integration rules which are im-plemented in the AutoMed heterogeneous data integration system. These rules can then be used to perform virtual or materialised transformation and integration of the XML data sources. The paper first illustrates how correspondences to a single ontology can be exploited. The approach is then ex-tended to the more general setting where correspondences may refer to multiple ontologies, themselves interconnected via schema transformation pathways. The contribution of this research is a set of au-tomatic, XML-specific algorithms for the transformation and integration of XML data, making use of RDFS ontologies as a ‘semantic bridge’.

XML Data Integration by Graph Restructuring

This technical report describes the XML data integration framework being built within the AutoMed heterogeneous data integration system. It presents a description of the overall framework, as well as an overview of and comparison with related work and solutions by other researchers. The contributions of this research are the development of two algorithms for XML data integration, the first for schema integration and the second for view materialization, both based on graph restructuring

XML Data Integration by Graph Restructuring

This technical report describes the XML data integration framework being built within the AutoMed heterogeneous data integration system. It presents a description of the overall framework, as well as an overview of and comparison with related work and solutions by other researchers. The contributions of this research are the development of two algorithms for XML data integration, the first for schema integration and the second for view materialization, both based on graph restructuring.

Bioinformatics service reconciliation by heterogeneous schema transformation. Birkbeck TR

Abstract. This paper focuses on the problem of bioinformatics service reconciliation in a generic and scalable manner so as to enhance interoperability in a highly evolving field. Using XML as a common representation format, but also supporting existing flat-file representation formats, we propose an approach for the scalable semi-automatic reconciliation of services, possibly invoked from within a scientific workflows tool. Service reconciliation may use the AutoMed heterogeneous data integration system as an intermediary service, or may use AutoMed to produce services that mediate between services. We discuss the application of our approach for the reconciliation of services in an example bioinformatics workflow. The main contribution of this research is an architecture for the scalable reconciliation of bioinformatics services.