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Document Information

Specification for Clinical XSD and XML
Version 2.6
March 25, 2013

XML Schema Description (XSD)

Clinical, Biospecimen and Auxiliary data received from the BCRs in XML format. This content is described by and can be validated against the corresponding XSD documents. The XSDs define, among other things, the XML data elements that are allowed and required, their types and allowed values.

The complete XML schema is maintained in a Subversion repository at the DCC. The root of the repository can be found here:

From this URL, users can browse the XSD documents.

Design

Namespaces


As part of a modular and reusable architecture, each disease specific XSD imports the following XSDs: 

Clinical

The clinical XSDs have the following list of imports:

XSD

Namespace Alias

Namespace

TCGA_BCR.Utility.xsd

utility

http://tcga.nci/bcr/xml/utility/2.6

TCGA_BCR.Administration.xsd

admin

http://tcga.nci/bcr/xml/administration/2.6

TCGA_BCR.Shared_Clinical_Elements.xsd

shared

http://tcga.nci/bcr/xml/clinical/shared/2.6

TCGA_BCR.Stage_Clinical_Elements.xsd

shared_stage

http://tcga.nci/bcr/xml/clinical/shared/stage/2.6
TCGA_BCR.Radiation.xsd

rad

http://tcga.nci/bcr/xml/clinical/radiation/2.6
TCGA_BCR.Pharmaceutical.xsdrx
http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.6
TCGA_BCR.CQCF.xsdcqcf
http://tcga.nci/bcr/xml/clinical/cqcf/2.6

Note that the version information of these imported XSD files are included in the namespace. 

Biospecimen

The Biospecimen XSD has the following list of imports:

XSD

Namespace Alias

Namespace

TCGA_BCR.Utility.xsd

utility

http://tcga.nci/bcr/xml/utility/2.6

TCGA_BCR.Administration.xsd

admin

http://tcga.nci/bcr/xml/administration/2.6
TCGA_BCR.Shared_Clinical_Elements.xsdshared
http://tcga.nci/bcr/xml/clinical/shared/2.6
TCGA_BCR.CQCF.xsdcqcf
http://tcga.nci/bcr/xml/clinical/cqcf/2.6
TCGA_BCR.Shared_Bio_Elements.xsdbio_shared
http://tcga.nci/bcr/xml/biospecimen/shared/2.6


Each element that is referenced in the XSD needs to be qualified by the namespace in which it is defined. For example, the XSD for BRCA references the element <day_of_birth>. This element is defined in TCGA_BCR.Shared_Clinical_Elements.xsd. So, the reference in the XSD for BRCA looks like: 
<xs:element ref="shared:day_of_birth" />

We see in this reference that the element name is 'day_of_birth' and the location (i.e., namespace) in which this element is defined is identified via the 'shared' alias. 
In the XML instance document the 'day_of_birth' element will look like: 
<shared:day_of_birth cde="2896952" xsd_ver="1.12" tier="1" owner="TSS" procurement_status="Completed">1</shared:day_of_birth>

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