The tissue micro-array data exchange specification: a web based experience browsing imported data
| Autor: | Barbara A Hackman, David G. Nohle, Leona W. Ayers |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2005 |
| Předmět: |
Databases
Factual computer.internet_protocol Style sheet Computer science Information Storage and Retrieval Telepathology Health Informatics Efficiency XSLT Document type definition urologic and male genital diseases lcsh:Computer applications to medicine. Medical informatics Decision Support Techniques World Wide Web User-Computer Interface 03 medical and health sciences 0302 clinical medicine AIDS-Related Complex Web page Humans Web application natural sciences Virtual slide 030304 developmental biology computer.programming_language Internet 0303 health sciences business.industry Health Policy United States female genital diseases and pregnancy complications 3. Good health Computer Science Applications Tumor Virus Infections National Institutes of Health (U.S.) Tissue Array Analysis Data exchange 030220 oncology & carcinogenesis lcsh:R858-859.7 Programming Languages business computer Software XML |
| Zdroj: | BMC Medical Informatics and Decision Making, Vol 5, Iss 1, p 25 (2005) BMC Medical Informatics and Decision Making |
| ISSN: | 1472-6947 |
| Popis: | Background The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. Results Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11 blocks with 3812 cores from three other institutions were processed with the BrowseTMA tool. Fifty common data elements (CDE) from the TMA DES were used and 42 more created for site-specific data. Researchers can download TMA clinical data in the TMA DES format. Conclusion Virtual TMAs with clinical data can be viewed on the Internet by interested researchers using the BrowseTMA tool. We have organized our approach to producing, sorting, navigating and publishing TMA information to facilitate such review. We have converted Excel TMA data into TMA DES XML, and imported it and TMA DES XML from another institution into BrowseTMA to produce web pages that allow us to browse through the merged data. We proposed enhancements to the TMA DES as a result of this experience. We implemented improvements to the API TMA DES as a result of using exported data from several institutions. A document type definition was written for the API TMA DES (that optionally includes proposed enhancements). Independent validators can be used to check exports against the DTD (with or without the proposed enhancements). Linking tissue core images to readily navigable clinical data greatly improves the value of the TMA. |
| Databáze: | OpenAIRE |
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