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the cancergrid metadata registry and toolset University of Cambridge: Irene Papatheodorou, Lorna Morris; James Brenton. University of Oxford: Charles Crichton; Andrew Tsui; Steve Harris; Jim Davies; Jeremy Gibbons. reasoning the software • workgroup-scale ISO11179 metadata registry • free BSD license • open standards implementation: eXist; XSLT; XQuery; SKOS; RDF; XForms; XML Schema; WSDL • platform independent: five minute install • transforms caDSR shopping cart content • simple data element registration • user classification through SKOS/Protégé smart documents We’ve connected our metadata registry, our lexBig servers, the EVS and caDSR to a query service manager giving a uniform query interface to these knowledge resources that may be accessed from both Java and .NET. You can use this service to: • compose new UML models out of CDEs and register new CDEs in Enterprise Architect without leaving the class diagram • ‘type a column range’ in MS Excel according to a CDE, naming the column, controlling cell display and creating a new metadata sheet with CDE definitions persisted alongside your data • use CDE and concept references to design case report forms in MS InfoPath • allow the user to access terminology resources when completing InfoPath based CRFs (with the VA) cgMDR lexBIG caDSR EVS SAWSDL annotations of schemas and WSDL documents support reasoning about content • SQIV/XQuery uplifts the schema data model into appropriate RDF • assertions from SKOS classification schemes or OWL ontologies classify elements in the data model according to the type of data and the type of user • SPARQL/DL Queries can answer simple questions reliably and scalably: • does the data contain personal information? • which elements contain personal data? • is the data suitable for the user requesting the data? • XML elements/RDF triples can be replaced/blurred according to the results of the queries query service manager (web service) transformation with the METABRIC project •pathology data collected from UK and Canada • metadata defined for each data type • metadata defined for the transformation target with common semantics • SPARQL rules defined for the transformation • combined dataset used for tissue analysis • similar transformation work done in XSLT • working through issues of registration of transformation functions CDE: histological type of breast tumour Guy’s Enumerated Value Domain: 1 In-situ ductal only 10 Tubular/Cribiform 11 Ductal Grade Unknown 12 Mixed… CDE: histological type of breast tumour Manitoba Enumerated Value Domain: 1 Ductal NOS 10 Ductal and Spec 11 Invasive tumour 12 DCIS… CDE: histological type of breast tumour Nottingham Enumerated Value Domain: 1 Inv. ductal/no spec type 10 Tubular 11 Mucinous 12 Invasive cribriform… CDE: histological type of breast tumour Addenbrookes Enumerated Value Domain: A None D DCIS ID Invasive ductal ID-IL … CDE: histological type of breast tumour Vancouver Enumerated Value Domain: 1 Carcinoma, NOS 10 Tubular adenocarcinoma 11 Merkel Cell Carcinoma 12 Papillary adenocarci… object class: breast tumour sample metadata mining property: assessment with the VA Xforms Post generation customisation Generated view element ‘mining’ metadata out of CRFs from a SharePoint CTMS. • custom program annotates schema elements with form text • XML Schema uplifted into MDR, creating names and identifiers • metadata elements curated/rationalised • ‘standard’ data elements re-create schemas with SAWSDL annotations • annotated schemas create registered forms <xforms:input ref="//cgMDR:change_description"> <xforms:label>Change Description</xforms:label> </xforms:input> Transformation <xsl:template match= "xforms:input[ends-with(./@ref,'cgMDR:change_description')]"> <xforms:textarea ref="//cgMDR:change_description"> <xforms:label>Change Description </xforms:label> </xforms:textarea> </xsl:template> Customised view element <xforms:textarea ref="//cgMDR:change_description"> <xforms:label>Change Description</xforms:label> </xforms:textarea> data element concept: histological type of breast tumour Jena rules for transformation CDE: histological type of breast tumour METABRIC metaanalysis Enumerated Value Domain: common semantics conceptual domain: breast tumour histology