The tissue microarray data exchange specification: A document type definition to validate and enhance XML data
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2005-05-01
|
| Series: | BMC Medical Informatics and Decision Making |
| Online Access: | http://www.biomedcentral.com/1472-6947/5/12 |
| _version_ | 1811244591487123456 |
|---|---|
| author | Ayers Leona W Nohle David G |
| author_facet | Ayers Leona W Nohle David G |
| author_sort | Ayers Leona W |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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. 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.</p> <p>Results</p> <p>A 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).</p> <p>Conclusion</p> <p>ACSR 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.</p> |
| first_indexed | 2024-04-12T14:27:52Z |
| format | Article |
| id | doaj.art-c3c688c517474d59b24e3c45d7ee6dea |
| institution | Directory Open Access Journal |
| issn | 1472-6947 |
| language | English |
| last_indexed | 2024-04-12T14:27:52Z |
| publishDate | 2005-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Informatics and Decision Making |
| spelling | doaj.art-c3c688c517474d59b24e3c45d7ee6dea2022-12-22T03:29:24ZengBMCBMC Medical Informatics and Decision Making1472-69472005-05-01511210.1186/1472-6947-5-12The tissue microarray data exchange specification: A document type definition to validate and enhance XML dataAyers Leona WNohle David G<p>Abstract</p> <p>Background</p> <p>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. 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.</p> <p>Results</p> <p>A 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).</p> <p>Conclusion</p> <p>ACSR 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.</p>http://www.biomedcentral.com/1472-6947/5/12 |
| spellingShingle | Ayers Leona W Nohle David G The tissue microarray data exchange specification: A document type definition to validate and enhance XML data BMC Medical Informatics and Decision Making |
| title | The tissue microarray data exchange specification: A document type definition to validate and enhance XML data |
| title_full | The tissue microarray data exchange specification: A document type definition to validate and enhance XML data |
| title_fullStr | The tissue microarray data exchange specification: A document type definition to validate and enhance XML data |
| title_full_unstemmed | The tissue microarray data exchange specification: A document type definition to validate and enhance XML data |
| title_short | The tissue microarray data exchange specification: A document type definition to validate and enhance XML data |
| title_sort | tissue microarray data exchange specification a document type definition to validate and enhance xml data |
| url | http://www.biomedcentral.com/1472-6947/5/12 |
| work_keys_str_mv | AT ayersleonaw thetissuemicroarraydataexchangespecificationadocumenttypedefinitiontovalidateandenhancexmldata AT nohledavidg thetissuemicroarraydataexchangespecificationadocumenttypedefinitiontovalidateandenhancexmldata AT ayersleonaw tissuemicroarraydataexchangespecificationadocumenttypedefinitiontovalidateandenhancexmldata AT nohledavidg tissuemicroarraydataexchangespecificationadocumenttypedefinitiontovalidateandenhancexmldata |