title: The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides.
abstract: BACKGROUND
  Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exchange Specification (TMA DES) is a set of eXtensible Markup Language (XML)-based protocols for storing and sharing digitized Tissue Microarray data. XML data are enclosed by named tags which serve as identifiers. These tag names can be Common Data Elements (CDEs), which have a predefined meaning or semantics. By using this specification in a laboratory setting with increasing demands for digital pathology integration, we found that the data structure lacked the ability to cope with digital slide imaging in respect to web-enabled digital pathology systems and advanced scoring techniques.
  
  
  METHODS
  By employing user centric design, and observing behavior in relation to TMA scoring and associated data, the TMA DES format was extended to accommodate the current limitations. This was done with specific focus on developing a generic tool for handling any given scoring system, and utilizing data for multiple observations and observers.
  
  
  RESULTS
  DTDs were created to validate the extensions of the TMA DES protocol, and a test set of data containing scores for 6,708 TMA core images was generated. The XML was then read into an image processing algorithm to utilize the digital pathology data extensions, and scoring results were easily stored alongside the existing multiple pathologist scores.
  
  
  CONCLUSIONS
  By extending the TMA DES format to include digital pathology data and customizable scoring systems for TMAs, the new system facilitates the collaboration between pathologists and organizations, and can be used in automatic or manual data analysis. This allows complying systems to effectively communicate complex and varied scoring data.
authors.affiliation: Department of Pathology and Tumour Biology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, U.K.
authors.forename: Alexander
authors.initials: A
authors.lastname: Wright
authors.forename: Oliver
authors.initials: O
authors.lastname: Lyttleton
authors.forename: Paul
authors.initials: P
authors.lastname: Lewis
authors.forename: Philip
authors.initials: P
authors.lastname: Quirke
authors.forename: Darren
authors.initials: D
authors.lastname: Treanor