title: The development and deployment of Common Data Elements for tissue banks for translational research in cancer - an emerging standard based approach for the Mesothelioma Virtual Tissue Bank.
abstract: BACKGROUND
  Recent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) - compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC).
  
  
  METHODS
  The purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML).
  
  
  RESULTS
  Common Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, clinical history, pathology data including block level annotation, and follow-up data including treatment, recurrence and vital status. The end result of such an effort would eventually provide an increased sample set to the researchers, and makes the system interoperable between institutions.
  
  
  CONCLUSIONS
  The CAP, ADASP and the NAACCR elements represent widely established data elements that are utilized in many cancer centers. Herein, we have shown these representations can be combined and formalized to create a core set of annotations for banked mesothelioma specimens. Because these data elements are collected as part of the normal workflow of a medical center, data sets developed on the basis of these elements can be easily implemented and maintained.
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. mohantys2@upmc.edu
authors.forename: Sambit K
authors.initials: SK
authors.lastname: Mohanty
authors.forename: Amita T
authors.initials: AT
authors.lastname: Mistry
authors.forename: Waqas
authors.initials: W
authors.lastname: Amin
authors.forename: Anil V
authors.initials: AV
authors.lastname: Parwani
authors.forename: Andrew K
authors.initials: AK
authors.lastname: Pople
authors.forename: Linda
authors.initials: L
authors.lastname: Schmandt
authors.forename: Sharon B
authors.initials: SB
authors.lastname: Winters
authors.forename: Erin
authors.initials: E
authors.lastname: Milliken
authors.forename: Paula
authors.initials: P
authors.lastname: Kim
authors.forename: Nancy B
authors.initials: NB
authors.lastname: Whelan
authors.forename: Ghada
authors.initials: G
authors.lastname: Farhat
authors.forename: Jonathan
authors.initials: J
authors.lastname: Melamed
authors.forename: Emanuela
authors.initials: E
authors.lastname: Taioli
authors.forename: Rajiv
authors.initials: R
authors.lastname: Dhir
authors.forename: Harvey I
authors.initials: HI
authors.lastname: Pass
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Becich
mesh_terms: D019295:Computational Biology; D019992:Databases as Topic; D006801:Humans; D008491:Medical Informatics Applications; D008654:Mesothelioma; D010997:Pleural Neoplasms; D012984:Software; D018511:Systems Integration; D014015:Tissue Banks