title: The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data.
abstract: BACKGROUND
  Tissue microarrays (TMAs) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject-Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration.
  
  
  METHODS
  A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format.
  
  
  RESULTS
  We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES) to OWL.
  
  
  CONCLUSIONS
  By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.
authors.affiliation: Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo 14263, NY, USA.
authors.forename: Hyunseok P
authors.initials: HP
authors.lastname: Kang
authors.forename: Charles D
authors.initials: CD
authors.lastname: Borromeo
authors.forename: Jules J
authors.initials: JJ
authors.lastname: Berman
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Becich
references.citation: J Mol Histol. 2007 May;38(2):113-21
references.pmid: 17318343
references.citation: BMC Cancer. 2008 Apr 08;8:91
references.pmid: 18397527
references.citation: Nat Med. 1998 Jul;4(7):844-7
references.pmid: 9662379
references.citation: BMC Cancer. 2008 Aug 13;8:236
references.pmid: 18700971
references.citation: BMC Med Inform Decis Mak. 2003 May 23;3:5
references.pmid: 12769826
references.citation: Bioinformatics. 2006 Apr 1;22(7):866-73
references.pmid: 16428806
references.citation: Cancer Res. 2002 May 15;62(10):2890-6
references.pmid: 12019169
references.citation: BMC Bioinformatics. 2004 Feb 27;5:19
references.pmid: 15040818
references.citation: Arch Pathol Lab Med. 2006 Jul;130(7):1004-13
references.pmid: 16831026
references.citation: J Clin Oncol. 2004 Jul 15;22(14):2790-9
references.pmid: 15254046
references.citation: Mol Diagn. 2000 Dec;5(4):287-99
references.pmid: 11172493
references.citation: Cancer Res. 2002 Mar 1;62(5):1256-60
references.pmid: 11888886
references.citation: BMC Med Inform Decis Mak. 2005 Aug 08;5:25
references.pmid: 16086837
references.citation: J Biomed Inform. 2010 Jun;43(3):435-41
references.pmid: 19835983
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W170-3
references.pmid: 19483092
references.citation: BMC Med Inform Decis Mak. 2005 May 04;5:12
references.pmid: 15871741
references.citation: BMC Cancer. 2005 Aug 21;5:108
references.pmid: 16111498