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An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow.

Paterson T, Law A - BMC Bioinformatics (2009)

Bottom Line: The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data.The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards.Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK. trevor.paterson@roslin.ed.ac.uk

ABSTRACT

Background: Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an ad hoc manner.

Results: We have developed a simple generic XML schema (GenomicMappingData.xsd - GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows.

Conclusion: The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.

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Taverna Workflow 1. Graphical representation of a workflow using ArkDB web services captured from Taverna Workbench v1.7.0.0. A species name is handed in as a parameter to karyotypeService. The result returned from this web service is a DataSet document conforming to the GenomicMapping Data schema, which can be parsed by the Taverna XMLSplitter, to drill down through Elements in the document structure to retrieve the chromosome names for the input species name parameter. Together with the initial species name each chromosome name in turn is entered as a parameter for iteration over the fetchMapsForChromosome service, which returns a set of DataSet documents each containing the list of available maps for each specified chromosome. The Workflow document is available as additional file 5: demoWorkFlow1.xml, and one of the resulting data documents is available as additional file 2: demo1result1.xml.
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Figure 2: Taverna Workflow 1. Graphical representation of a workflow using ArkDB web services captured from Taverna Workbench v1.7.0.0. A species name is handed in as a parameter to karyotypeService. The result returned from this web service is a DataSet document conforming to the GenomicMapping Data schema, which can be parsed by the Taverna XMLSplitter, to drill down through Elements in the document structure to retrieve the chromosome names for the input species name parameter. Together with the initial species name each chromosome name in turn is entered as a parameter for iteration over the fetchMapsForChromosome service, which returns a set of DataSet documents each containing the list of available maps for each specified chromosome. The Workflow document is available as additional file 5: demoWorkFlow1.xml, and one of the resulting data documents is available as additional file 2: demo1result1.xml.

Mentions: In an example workflow we join two service methods 'fetchNamedSpeciesKaryotype' and 'fetchMapsForChromosome' by extracting all the Chromosome Names from the first response and chaining into an iteration over the second service, passing in the parsed Chromosome Name from the first result set together with original Species Name. The workflow is shown in Figure 2 and the Workflow document is available as additional file 5: demoWorkFlow1.xml. When initiated with the input parameter Species Name 'Pig' the resulting output is a set of 20 DataSet documents which are conformant with the GMD schema, each containing details of the maps found on one of the chromosomes. (One such result document is available as additional file 2: demo1result1.xml.) The level of detail for each map is determined by the 'fetchMapsForChromosome' service and includes Species, Chromosome, Map, and Analysis data. The details of genetic entities mapped on these maps could be obtained by parsing out each Map Accession, again using the Taverna XML Splitter, and passing this as the input mapAccession parameter for the 'fetchMappingsForMap' service. Additional Taverna Processors could be added as widgets to the workflow that could generically parse any result document, because they all conform to the same XSD schema. For example it would be trivial to add an XSLT processor or Java DOM processing bean to combine multiple result sets into a single DataSet document.


An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow.

Paterson T, Law A - BMC Bioinformatics (2009)

Taverna Workflow 1. Graphical representation of a workflow using ArkDB web services captured from Taverna Workbench v1.7.0.0. A species name is handed in as a parameter to karyotypeService. The result returned from this web service is a DataSet document conforming to the GenomicMapping Data schema, which can be parsed by the Taverna XMLSplitter, to drill down through Elements in the document structure to retrieve the chromosome names for the input species name parameter. Together with the initial species name each chromosome name in turn is entered as a parameter for iteration over the fetchMapsForChromosome service, which returns a set of DataSet documents each containing the list of available maps for each specified chromosome. The Workflow document is available as additional file 5: demoWorkFlow1.xml, and one of the resulting data documents is available as additional file 2: demo1result1.xml.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2743669&req=5

Figure 2: Taverna Workflow 1. Graphical representation of a workflow using ArkDB web services captured from Taverna Workbench v1.7.0.0. A species name is handed in as a parameter to karyotypeService. The result returned from this web service is a DataSet document conforming to the GenomicMapping Data schema, which can be parsed by the Taverna XMLSplitter, to drill down through Elements in the document structure to retrieve the chromosome names for the input species name parameter. Together with the initial species name each chromosome name in turn is entered as a parameter for iteration over the fetchMapsForChromosome service, which returns a set of DataSet documents each containing the list of available maps for each specified chromosome. The Workflow document is available as additional file 5: demoWorkFlow1.xml, and one of the resulting data documents is available as additional file 2: demo1result1.xml.
Mentions: In an example workflow we join two service methods 'fetchNamedSpeciesKaryotype' and 'fetchMapsForChromosome' by extracting all the Chromosome Names from the first response and chaining into an iteration over the second service, passing in the parsed Chromosome Name from the first result set together with original Species Name. The workflow is shown in Figure 2 and the Workflow document is available as additional file 5: demoWorkFlow1.xml. When initiated with the input parameter Species Name 'Pig' the resulting output is a set of 20 DataSet documents which are conformant with the GMD schema, each containing details of the maps found on one of the chromosomes. (One such result document is available as additional file 2: demo1result1.xml.) The level of detail for each map is determined by the 'fetchMapsForChromosome' service and includes Species, Chromosome, Map, and Analysis data. The details of genetic entities mapped on these maps could be obtained by parsing out each Map Accession, again using the Taverna XML Splitter, and passing this as the input mapAccession parameter for the 'fetchMappingsForMap' service. Additional Taverna Processors could be added as widgets to the workflow that could generically parse any result document, because they all conform to the same XSD schema. For example it would be trivial to add an XSLT processor or Java DOM processing bean to combine multiple result sets into a single DataSet document.

Bottom Line: The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data.The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards.Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK. trevor.paterson@roslin.ed.ac.uk

ABSTRACT

Background: Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an ad hoc manner.

Results: We have developed a simple generic XML schema (GenomicMappingData.xsd - GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows.

Conclusion: The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.

Show MeSH
Related in: MedlinePlus