{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,5]],"date-time":"2024-02-05T05:27:20Z","timestamp":1707110840673},"reference-count":10,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations (at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can be generated in a single TMA experiment a systematic approach is required for the storage and analysis of such data.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Description<\/jats:title>\n                <jats:p>To analyse TMA output a relational database (known as TmaDB) has been developed to collate all aspects of information relating to TMAs. These data include the TMA construction protocol, experimental protocol and results from the various immunocytological and histochemical staining experiments including the scanned images for each of the TMA cores. Furthermore the database contains pathological information associated with each of the specimens on the TMA slide, the location of the various TMAs and the individual specimen blocks (from which cores were taken) in the laboratory and their current status i.e. if they can be sectioned into further slides or if they are exhausted. TmaDB has been designed to incorporate and extend many of the published common data elements and the XML format for TMA experiments and is therefore compatible with the TMA data exchange specifications developed by the Association for Pathology Informatics community. Finally the design of the database is made flexible such that TMA experiments from several types of cancer can be stored in a single database, which incorporates the national minimum data set required for pathology reports supported by the Royal College of Pathologists (UK).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>TmaDB will provide a comprehensive repository for TMA data such that a large number of results from the numerous immunostaining experiments can be efficiently compared for each of the TMA cores. This will allow a systematic, large-scale comparison of tumour samples to facilitate the identification of gene products of clinical importance such as therapeutic or prognostic markers. In addition this work will contribute to the establishment of a standard for reporting TMA data analogous to MIAME in the description of microarray data.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-218","type":"journal-article","created":{"date-parts":[[2005,9,1]],"date-time":"2005-09-01T18:13:39Z","timestamp":1125598419000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["TmaDB: a repository for tissue microarray data"],"prefix":"10.1186","volume":"6","author":[{"given":"Archana","family":"Sharma-Oates","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philip","family":"Quirke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David R","family":"Westhead","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,9,1]]},"reference":[{"key":"543_CR1","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1093\/hmg\/10.7.657","volume":"10","author":"OP Kallioniemi","year":"2001","unstructured":"Kallioniemi OP, Wagner U, Kononen J, Sauter G: Tissue microarray technology for high-throughput molecular profiling of cancer. Hum Mol Genet 2001, 10: 657\u2013662. 10.1093\/hmg\/10.7.657","journal-title":"Hum Mol Genet"},{"key":"543_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\u2013847. 10.1038\/nm0798-844","journal-title":"Nat Med"},{"key":"543_CR3","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1023\/B:JOMG.0000010034.43145.86","volume":"3","author":"S Henshall","year":"2003","unstructured":"Henshall S: Tissue microarrays. J Mammary Gland Biol Neoplasia 2003, 3: 347\u2013358. 10.1023\/B:JOMG.0000010034.43145.86","journal-title":"J Mammary Gland Biol Neoplasia"},{"key":"543_CR4","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/1472-6947-3-5","volume":"3","author":"JJ Berman","year":"2003","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 2003, 3: 5. 10.1186\/1472-6947-3-5","journal-title":"BMC Med Inform Decis Mak"},{"key":"543_CR5","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1016\/S0002-9440(10)61759-2","volume":"159","author":"S Manley","year":"2001","unstructured":"Manley S, Mucci NR, De Marzo AM, Rubin MA: Relational database structure to manage high-density tissue microarray data and images for pathology studies focusing on clinical outcome: the prostate specialized program of research excellence model. Am J Pathol 2001, 159: 837\u2013843.","journal-title":"Am J Pathol"},{"key":"543_CR6","doi-asserted-by":"publisher","first-page":"1557","DOI":"10.1016\/S0002-9440(10)64434-3","volume":"161","author":"CL Liu","year":"2002","unstructured":"Liu CL, Prapong W, Natkunam Y, Alizadeh A, Montgomery K, Gilks CB, van de Rijn M: Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays. Am J Pathol 2002, 161: 1557\u20131565.","journal-title":"Am J Pathol"},{"key":"543_CR7","first-page":"155","volume":"1","author":"KR Coombes","year":"2002","unstructured":"Coombes KR, Zhang L, Bueso-Ramos , Brisbay S, Logothetis C, Roth J, Keating MJ, McDonnell TJ: TAD: a web interface and database for tissue microarrays. Appl Bioinformatics 2002, 1: 155\u2013158.","journal-title":"Appl Bioinformatics"},{"key":"543_CR8","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1471-2105-5-19","volume":"5","author":"JJ Berman","year":"2004","unstructured":"Berman JJ, Datta M, Kajdacsy-Balla A, Melamed J, Orenstein J, Dobbin K, Patel A, Dhir R, Becich MJ: The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. BMC Bioinformatics 2004, 5: 19. 10.1186\/1471-2105-5-19","journal-title":"BMC Bioinformatics"},{"key":"543_CR9","doi-asserted-by":"publisher","first-page":"RESEARCH0046","DOI":"10.1186\/gb-2002-3-9-research0046","volume":"3","author":"PT Spellman","year":"2002","unstructured":"Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A: Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 2002, 3: RESEARCH0046. 10.1186\/gb-2002-3-9-research0046","journal-title":"Genome Biol"},{"key":"543_CR10","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/ng1201-365","volume":"29","author":"A Brazma","year":"2001","unstructured":"Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29: 365\u201371. 10.1038\/ng1201-365","journal-title":"Nat Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-218.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T17:52:09Z","timestamp":1706809929000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-218"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,9,1]]},"references-count":10,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["543"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-218","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,9,1]]},"assertion":[{"value":"19 April 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 September 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 September 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"218"}}