{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T07:02:03Z","timestamp":1761894123717},"reference-count":10,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,5,4]],"date-time":"2005-05-04T00:00:00Z","timestamp":1115164800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Med Inform Decis Mak"],"published-print":{"date-parts":[[2005,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats: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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats: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).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats: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.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1472-6947-5-12","type":"journal-article","created":{"date-parts":[[2005,5,5]],"date-time":"2005-05-05T06:13:27Z","timestamp":1115273607000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["The tissue microarray data exchange specification: A document type definition to validate and enhance XML data"],"prefix":"10.1186","volume":"5","author":[{"given":"David G","family":"Nohle","sequence":"first","affiliation":[]},{"given":"Leona W","family":"Ayers","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,5,4]]},"reference":[{"key":"63_CR1","unstructured":"AIDS and Cancer Specimen Resource web site. [http:\/\/acsr.ucsf.edu]"},{"key":"63_CR2","doi-asserted-by":"publisher","first-page":"844","DOI":"10.1038\/nm0798-844","volume":"4","author":"J Kononen","year":"1998","unstructured":"Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S, Torhorst J, Mihatsch MJ, Sauter G, Kallioniemi OP: Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med. 1998, 4: 844-847. 10.1038\/nm0798-844.","journal-title":"Nat Med"},{"key":"63_CR3","doi-asserted-by":"crossref","unstructured":"Berman JJ, Edgerton ME, Friedman BA: The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data. BMC Med Inform Decis Mak. 3: 5-10.1186\/1472-6947-3-5. 2003 May 23","DOI":"10.1186\/1472-6947-3-5"},{"key":"63_CR4","volume-title":"XML In A Nutshell","author":"ER Harold","year":"2002","unstructured":"Harold ER, Means WS: XML In A Nutshell. 2002, O'Reilly & Associates, Inc, 2","edition":"2"},{"key":"63_CR5","unstructured":"Bray T, Paoli J, Sperberg-McQueen CM, Maler E, Yergeau F: Extensible Markup Language (XML) 1.0 (Third Edition) W3C Recommendation 04 February 2004. W3C Recommendation. 2004 February 4, [http:\/\/www.w3.org\/TR\/2004\/REC-xml-20040204]"},{"key":"63_CR6","unstructured":"Brown University Scholarly Technology Group's XML Validation Form at. [http:\/\/www.stg.brown.edu\/service\/xmlvalid\/]"},{"key":"63_CR7","unstructured":"Richard Tobin's XML well-formedness checker and validator at. [http:\/\/www.cogsci.ed.ac.uk\/%7Erichard\/xml-check.html]"},{"key":"63_CR8","volume-title":"Proceedings of the Advancing Pathology Informatics Imaging and the Internet 8th annual conference: 8\u201310","author":"DG Nohle","year":"2003","unstructured":"Nohle DG, Hackman BA, Ayers LW: Web-based virtual tissue microarray slides with clinical data for researchers in HTML, Excel\u00ae and API standard XML data exchange specification formats produced with Microsoft Office\u00ae applications http:\/\/www.acsr.mid-region.org\/ [abstract]. Proceedings of the Advancing Pathology Informatics Imaging and the Internet 8th annual conference: 8\u201310. 2003, inpress, [http:\/\/apiii.upmc.edu\/abstracts\/posterarchive\/2003\/nohle.html]October ; Pittsburgh, Pennsylvania"},{"key":"63_CR9","unstructured":"Nohle DG, Hackman BA, Ayers LW: Tissue microarray data TMA standard and public tool for linked legend and clinical details at acsr.mid-region.org [abstract]. Proceedings of the 8th International Conference on Malignancies in AIDS and Other Immunodeficiencies (ICMAOI): Basic, Epidemiologic and Clinical Research:. 98-29\u201330 April 2004,, [http:\/\/www.nci.nih.gov\/dctd\/aids\/abstracts.pdf]"},{"key":"63_CR10","volume-title":"Proceedings of the Advancing Practice, Instruction and Innovation through Informatics 9th annual conference: 6\u20138","author":"DG Nohle","year":"2004","unstructured":"Nohle DG, Hackman BA, Ayers LW: A document type definition for the API standard tissue microarray XML data exchange specification http:\/\/www.acsr.mid-region.org\/ [abstract]. Proceedings of the Advancing Practice, Instruction and Innovation through Informatics 9th annual conference: 6\u20138. 2004, inpress, [http:\/\/apiii.upmc.edu\/abstracts\/DISPLAY.CFM?ID=317]October ; Pittsburgh, Pennsylvania"}],"container-title":["BMC Medical Informatics and Decision Making"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1472-6947-5-12.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1472-6947-5-12\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1472-6947-5-12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1472-6947-5-12.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T01:46:38Z","timestamp":1630460798000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcmedinformdecismak.biomedcentral.com\/articles\/10.1186\/1472-6947-5-12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,5,4]]},"references-count":10,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2005,12]]}},"alternative-id":["63"],"URL":"https:\/\/doi.org\/10.1186\/1472-6947-5-12","relation":{},"ISSN":["1472-6947"],"issn-type":[{"value":"1472-6947","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,5,4]]},"assertion":[{"value":"22 February 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 May 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 May 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"12"}}