Limits...
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.

Show MeSH
The Hierarchy of Relationship Types in GenomicDataRelationships.xsd. The GenomicDataRelationships schema (gdr, see additional file 4: GenomicDataRelationships.xsd) specifies an inheritance of xsd:complexTypes rooted on 'RelationshipType'. Textual definitions of these Relationships are provided by inline xsd:annotaions. A global Element is defined for each Type, with the document structure of the root Element 'Relationship' reflecting the inheritance pattern of the Types, which is shown here. Thus a 'SequenceSimilarity' is a type of 'Similarity' is a type of 'Relationship'.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2743669&req=5

Figure 1: The Hierarchy of Relationship Types in GenomicDataRelationships.xsd. The GenomicDataRelationships schema (gdr, see additional file 4: GenomicDataRelationships.xsd) specifies an inheritance of xsd:complexTypes rooted on 'RelationshipType'. Textual definitions of these Relationships are provided by inline xsd:annotaions. A global Element is defined for each Type, with the document structure of the root Element 'Relationship' reflecting the inheritance pattern of the Types, which is shown here. Thus a 'SequenceSimilarity' is a type of 'Similarity' is a type of 'Relationship'.

Mentions: By way of demonstration, we have defined a relationship type schema, GenomicDataRelationship.xsd, (gdr: provided as additional file 4: GenomicDataRelationships.xsd, and available with documentation at [19]). This schema defines complex types that represent real data relationship types in genomic datasets (based on the ArkDB database and others). The datatypes are derived by extension of parent types to represent the inheritance/subsumption hierarchy of relationship types. In order to visualize the relationship type inheritance in gdr, a global Element is declared for each type, and the schema places these Elements in a hierarchy mirroring the inheritance pattern of the types (see Figure 1). These types can be included in a GMD:DataSet document by import as types for <RelationshipType> and <SequenceRelationship> Elements (e.g. <RelationshipType xsi:type="gdr:OrthologyType">) or by adding content Elements (e.g. <RelationshipType><gdr:Orthology/></RelationshipType>).


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)

The Hierarchy of Relationship Types in GenomicDataRelationships.xsd. The GenomicDataRelationships schema (gdr, see additional file 4: GenomicDataRelationships.xsd) specifies an inheritance of xsd:complexTypes rooted on 'RelationshipType'. Textual definitions of these Relationships are provided by inline xsd:annotaions. A global Element is defined for each Type, with the document structure of the root Element 'Relationship' reflecting the inheritance pattern of the Types, which is shown here. Thus a 'SequenceSimilarity' is a type of 'Similarity' is a type of 'Relationship'.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: The Hierarchy of Relationship Types in GenomicDataRelationships.xsd. The GenomicDataRelationships schema (gdr, see additional file 4: GenomicDataRelationships.xsd) specifies an inheritance of xsd:complexTypes rooted on 'RelationshipType'. Textual definitions of these Relationships are provided by inline xsd:annotaions. A global Element is defined for each Type, with the document structure of the root Element 'Relationship' reflecting the inheritance pattern of the Types, which is shown here. Thus a 'SequenceSimilarity' is a type of 'Similarity' is a type of 'Relationship'.
Mentions: By way of demonstration, we have defined a relationship type schema, GenomicDataRelationship.xsd, (gdr: provided as additional file 4: GenomicDataRelationships.xsd, and available with documentation at [19]). This schema defines complex types that represent real data relationship types in genomic datasets (based on the ArkDB database and others). The datatypes are derived by extension of parent types to represent the inheritance/subsumption hierarchy of relationship types. In order to visualize the relationship type inheritance in gdr, a global Element is declared for each type, and the schema places these Elements in a hierarchy mirroring the inheritance pattern of the types (see Figure 1). These types can be included in a GMD:DataSet document by import as types for <RelationshipType> and <SequenceRelationship> Elements (e.g. <RelationshipType xsi:type="gdr:OrthologyType">) or by adding content Elements (e.g. <RelationshipType><gdr:Orthology/></RelationshipType>).

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