Bioinformatics Service Reconciliation by Heterogeneous Schema Transformation

Zamboulis, Lucas; Martin, Nigel; Poulovassilis, Alexandra

doi:10.1007/978-3-540-73255-6_10

Cited by 11 publications

(5 citation statements)

References 17 publications

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“…These include a virtual integrated resource combining data from PRIDE ( 8 ), PEDRO ( 13 ) and PepSeeker ( 11 ), using the AutoMed heterogeneous data integration toolkit ( 27 ). Development of web services underpins much of this, either for integration into the existing framework or via proteome-specific workflows using myGrid ( 28 , 29 ). We aim to add these services to the ISPIDER portal, as well as provide a reanalysis pipeline for protein/peptide identification, to improve computation services for proteome biologists.…”

Section: Discussionmentioning

confidence: 99%

ISPIDER Central: an integrated database web-server for proteomics

Siepen¹,

Belhajjame²,

Selley³

et al. 2008

Nucleic Acids Research

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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.

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Section: Discussionmentioning

confidence: 99%

ISPIDER Central: an integrated database web-server for proteomics

Siepen¹,

Belhajjame²,

Selley³

et al. 2008

Nucleic Acids Research

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“…Once relations have been identified, the corresponding elements can be unified under a coherent approach in the integrated scheme (overview). During this integration, as separate step, programs and queries are created for data translation schemas sources integrated in the new representation (Zamboulis, 2009).…”

Section: Integration Schemamentioning

confidence: 99%

Fmams

Yazidi

Zellou

Idri

2013

International Journal of Applied Evolutionary Computation

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To access a unified way to different information sources while hiding the user autonomy, heterogeneity, distribution and evolution of these sources, the authors thought to integrate its different sources of information, one of the existing integration approaches is mediation or virtual approach. The integration in mediation approach is done with a schema, called schema mediation, and a set of mapping (links) associating schemas of sources to integrate with the global schema. The problem arises in creating the set of correspondences between the elements of the schema global and all the elements of local schemas, in this paper the authors present their approach FMAMS: Fuzzy Mapping Approach for Mediation Systems, a new approach based on fundamental principles of the theory of fuzzy sets. The authors’ approach is to define and associate to each link between two elements a weight that reflects the degree of its existence, it is present in an analysis using two components: syntactic and semantic.

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“…Both As View-BAV-) combine both aspects, there is a loosely defined global schema which is mapped to the set of reconciled local schemas (e.g. [ 65 ]). Figure 2 illustrates these three ways to generate an integrated global view.…”

Section: Biological Data Integrationmentioning

confidence: 99%

XML-based approaches for the integration of heterogeneous bio-molecular data

et al. 2009

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BackgroundThe today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing.ResultsIn this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML.ConclusionXML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

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Bioinformatics Service Reconciliation by Heterogeneous Schema Transformation

Cited by 11 publications

References 17 publications

ISPIDER Central: an integrated database web-server for proteomics

ISPIDER Central: an integrated database web-server for proteomics

Fmams

XML-based approaches for the integration of heterogeneous bio-molecular data

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