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

Adapting integrity enforcement techniques for data reconciliation

Integration of data sources opens up possibilities for new and valuable applications of data that cannot be supported by the individual sources alone. Unfortunately, many data integration projects are hindered by the inherent heterogeneities in the sources to be integrated. In particular, differences in the way that real world data is encoded within sources can cause a range of difficulties, not least of which is that the conflicting semantics may not be recognised until the integration project is well under way. Once identified, semantic conflicts of this kind are typically dealt with by configuring a data transformation engine, that can convert incoming data into the form required by the integrated system. However, determination of a complete and consistent set of data transformations for any given integration task is far from trivial. In this paper, we explore the potential application of techniques for integrity enforcement in supporting this process. We describe the design of a data reconciliation tool (LITCHI) based on these techniques that aims to assist taxonomists in the integration of biodiversity data sets. Our experiences have highlighted several limitations of integrity enforcement when applied to this real world problem, and we describe how we have overcome these in the design of our system

Extending SWRL to express fully-quantified constraints

Abstract. Drawing on experience gained over a series of distributed knowledge base and database projects, we argue for the utility of an expressive quantified constraint language for the Semantic Web logic layer. Our Constraint Interchange Format (CIF) is based on classical range-restricted FOL. CIF allows the expression of invariant conditions in Semantic Web data models, but the choice of how to implement the constraints is left to local reasoners. We develop the quantified constraint representation as an extension of the current proposal for a Semantic Web Rule Language (SWRL). An RDF syntax for our extended CIF/SWRL is given in this paper. While our approach differs from SWRL in that existential quantifiers are handled explicitly rather than using OWL-DL constructs, we believe our proposal is still fully compatible with the use of the various OWL species as well as RDFS. We demonstrate the use of the CIF/SWRL representation in the context of a practical Semantic Web reasoning application, based on the CS AK-Tive Space demonstrator (the 2003 Semantic Web Challenge winner). We indicate where in our application it makes sense to use the existing SWRL directly, and where our CIF/SWRL allows more complex constraints to be expressed in a natural manner.

A novel haemophilia B defect due to partial duplication of the factor IX gene

Summary. A patient with mild FIX deficiency was found to have partial duplication of the 3' region of the gene, giving, in addition to the a normal gene, another piece of DNA containing exons 5', 6', 7' and 8' and the intervening sequences. Cloning and sequencing of the junction region revealed that crossover occurred at nt 31927 in the 3° untranslated region of one chromosome/chromatid and nt 10640 in intron 4 of the other. No homology or topoisomerase specific sequences were observed in the crossover region. PCR and sequencing of illegitimate FIX transcripts from the patient's lymphocytes showed at least three different species of mRNAs. Translation of two of these 'novel'mRNAs should result in truncated proteins. Possibilities for the splicing of the mature mRNA are offered to explain the translation of a normal-size FIX protein, which was the only product demonstrated on Western blot analysis