National Mesothelioma Virtual Bank: A standard based biospecimen and clinical data resource to enhance translational research

Background: Advances in translational research have led to the need for well characterized biospecimens for research. The National Mesothelioma Virtual Bank is an initiative which collects annotated datasets relevant to human mesothelioma to develop an enterprising biospecimen resource to fulfill researchers' need. Methods: The National Mesothelioma Virtual Bank architecture is based on three major components: (a) common data elements (based on College of American Pathologists protocol and National North American Association of Central Cancer Registries standards), (b) clinical and epidemiologic data annotation, and (c) data query tools. These tools work interoperably to standardize the entire process of annotation. The National Mesothelioma Virtual Bank tool is based upon the caTISSUE Clinical Annotation Engine, developed by the University of Pittsburgh in cooperation with the Cancer Biomedical Informatics Grid™ (caBIG™, see http://cabig.nci.nih.gov). This application provides a web-based system for annotating, importing and searching mesothelioma cases. The underlying information model is constructed utilizing Unified Modeling Language class diagrams, hierarchical relationships and Enterprise Architect software. Result: The database provides researchers real-time access to richly annotated specimens and integral information related to mesothelioma. The data disclosed is tightly regulated depending upon users' authorization and depending on the participating institute that is amenable to the local Institutional Review Board and regulation committee reviews. Conclusion: The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. Furthermore, it protects patient privacy by disclosing only de-identified datasets to assure that biospecimens can be made accessible to researchers. © 2008 Amin et al; licensee BioMed Central Ltd

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

<p>Abstract</p> <p>Background</p> <p>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).</p> <p>Methods</p> <p>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).</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p

A Prototype Tutoring System for Subject Cataloging

This report describes a prototype tutoring system, currently under development, whose purpose is to provide practice for students of subject cataloging. The system is designed to provide practice problems for students and to provide analyses of their mistakes, particularly when the mistakes are thoughtful "near-misses" that differ from an appropriate response in relatively well-defined ways. The system provides these analyses by comparing what the student has provided these analyses answer with what the system "knows" about the rules of classification and the relevant attributes of the particular book in question. The prototype domains are those of literature and biography, and the tutoring system is based on the Library of Congress system of subject cataloging

Automatic Extraction of Facts from Press Releases to Generate News Stories

While complete understanding of arbitrary input text remains in the future, it is currently possible to construct natural language processing systems that provide a partial understanding of text with limited accuracy. Moreover, such systems can provide cost-effective solutions to commercially-significant business problems. This paper describes one such system: JASPER. JASPER is a fact extraction system recently developed and deployed by Carnegie Group for Reuters Ltd. JASPER uses a template-driven approach, partial understanding techniques, and heuristic procedures to extract certain key pieces of information from a limited range of text., We believe that many significant business problems can be solved by fact extraction applications which involve locating and extracting specific, predefined types of information from a limited range of texL The information extracted by such systems can be used in a variety of ways, such as filling in values in a database, generating summaries of the input text, serving as a part of the knowledge in an expert system, or feeding into another program which bases decisions on it. We expect to develop many such applications in the future using similar techniques

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-4

<p><b>Copyright information:</b></p><p>Taken from "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"</p><p>http://www.biomedcentral.com/1471-2407/8/91</p><p>BMC Cancer 2008;8():91-91.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2329649.</p><p></p

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-3

Ssociation of Directors of Anatomic and Surgical Pathology.<p><b>Copyright information:</b></p><p>Taken from "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"</p><p>http://www.biomedcentral.com/1471-2407/8/91</p><p>BMC Cancer 2008;8():91-91.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2329649.</p><p></p

The overall architecture and tiers of caTISSUE Clinical Annotation Engine

<p><b>Copyright information:</b></p><p>Taken from "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"</p><p>http://www.biomedcentral.com/1471-2407/8/91</p><p>BMC Cancer 2008;8():91-91.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2329649.</p><p></p

Overview of caTISSUE Clinical Annotation Engine depicting data import, integration and query interface in a web-based environment

caTIES is a tool to extract important information on archival surgical pathology report and caTISSUE core is an enterprise biospecimen repository.<p><b>Copyright information:</b></p><p>Taken from "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"</p><p>http://www.biomedcentral.com/1471-2407/8/91</p><p>BMC Cancer 2008;8():91-91.</p><p>Published online 8 Apr 2008</p><p>PMCID:PMC2329649.</p><p></p