Abstract
BackgroundThe Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such data facilitates viewing, sharing and merging TMA data from different laboratories. The AIDS and Cancer Specimen Resource (ACSR) is a HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers HIV-related malignancies and uninfected control tissues in microarrays (TMA) accompanied by de-identified clinical data to approved researchers. Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness.ResultsA document type definition (DTD) that governs the allowed common data elements (CDE) in TMA DES export XML files was written, tested and evolved and is in routine use by the ACSR. This DTD defines TMA DES CDEs which are implemented in an external file that can be supplemented by internal DTD extensions for locally defined TMA data elements (LDE).ConclusionACSR implementation of the TMA DES demonstrated the utility of the specification and allowed application of a DTD to validate the language of the API specified XML elements and to identify possible enhancements within our TMA data management application. Improvements to the specification have additionally been suggested by our experience in importing other institution's exported TMA data. Enhancements to TMA DES to remove ambiguous situations and clarify the data should be considered. Better specified identifiers and hierarchical relationships will make automatic use of the data possible. Our tool can be used to reorder data and add identifiers; upgrading data for changes in the specification can be automatically accomplished. Using a DTD (optionally reflecting our proposed enhancements) can provide stronger validation of exported TMA data.
Highlights
The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format
ACSR implementation of the TMA DES demonstrated the utility of the specification and allowed application of a document type definition (DTD) to validate the language of the API specified XML elements and to identify possible enhancements within our TMA data management application
Designing the DTD The XML document type definition (DTD) for the TMA DES must represent the rules given in the specification and the 80 common data elements (CDE) defined in the associated Tissue MicroArray Common Data Elements document
Summary
Verifying XML data We used our DTD with the Internet Explorer MSXML2 4.0 parser (set to verify) and at two public web sites to verify a few TMA DES block files. 1. Internet Explorer MSXML2 4.0 parser – No errors or warnings were reported in either mode. Enforces that at least one block, one slide, and one core element are required. These elements may be empty and serve no purpose. 2. Brown University Scholarly Technology Group's XML Validation Form [6] – Reported "Document validates OK" in either mode. 3. Richard Tobin's XML well-formedness checker and validator [7] – Reported that the document appears to be well-formed and listed no validity or namespace errors in either mode
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