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 CAMH Neuroinformatics Platform: A Hospital-Focused Brain-CODE Implementation

Investigations of mental illness have been enriched by the advent and maturation of neuroimaging technologies and the rapid pace and increased affordability of molecular sequencing techniques, however, the increased volume, variety and velocity of research data, presents a considerable technical and analytic challenge to curate, federate and interpret. Aggregation of high-dimensional datasets across brain disorders can increase sample sizes and may help identify underlying causes of brain dysfunction, however, additional barriers exist for effective data harmonization and integration for their combined use in research. To help realize the potential of multi-modal data integration for the study of mental illness, the Centre for Addiction and Mental Health (CAMH) constructed a centralized data capture, visualization and analytics environment—the CAMH Neuroinformatics Platform—based on the Ontario Brain Institute (OBI) Brain-CODE architecture, towards the curation of a standardized, consolidated psychiatric hospital-wide research dataset, directly coupled to high performance computing resources

Roadmap to a Comprehensive Clinical Data Warehouse for Precision Medicine Applications in Oncology

Leading institutions throughout the country have established Precision Medicine programs to support personalized treatment of patients. A cornerstone for these programs is the establishment of enterprise-wide Clinical Data Warehouses. Working shoulder-to-shoulder, a team of physicians, systems biologists, engineers, and scientists at Rutgers Cancer Institute of New Jersey have designed, developed, and implemented the Warehouse with information originating from data sources, including Electronic Medical Records, Clinical Trial Management Systems, Tumor Registries, Biospecimen Repositories, Radiology and Pathology archives, and Next Generation Sequencing services. Innovative solutions were implemented to detect and extract unstructured clinical information that was embedded in paper/text documents, including synoptic pathology reports. Supporting important precision medicine use cases, the growing Warehouse enables physicians to systematically mine and review the molecular, genomic, image-based, and correlated clinical information of patient tumors individually or as part of large cohorts to identify changes and patterns that may influence treatment decisions and potential outcomes

Longitudinal Patient Records: A Re-Examination of the Possibility

It has long been recognized that the Longitudinal Patient Record (LPR) has been defined as “A life-long incremental process where each clinical encounter is merely an updating of the file” (Gabrieli, 1997) Understanding the health condition of patient longitudinally is very important to the care of the patient. However, it is not clear to what extent a longitudinal patient record is in fact possible, since a true longitudinal patient record would need to include all information for a patient, from cradle to grave, across all healthcare providers and systems, across all corporate or geographic or national boundaries. Compiling or maintaining such a record is a problem of staggering practical difficulties. Yet, there is no doubt of the potential benefit to the patient of the availability of such a record to the patient’s caregivers and providers. In this thesis, we re-examine the possibility of a longitudinal patient record, both in its pure logical sense, and in a practical sense. One point of view that we stress is to model the longitudinal patient record not so much as a static thing, but rather as a functional entity. That is, the longitudinal patient record is understood as a set of processes that provide the physician or other clinician decision maker (or for that matter the patient himself) with whatever longitudinal view of the patient information is available and practical to serve the current context of decision making. That is, the model we suggest is one of making the most out of whatever patient information is available to the decision maker

Effects of EMR on Community Health Center Communication

Electronic medical record (EMR) systems impact healthcare communication in a significant number of ways. The physical presence of the EMR in the examination room can negatively impacts patient-provider communication. This research examined the impact of EMR on patient-provider communication within the microcosm of the community health center. The data for this research was collected via a quantitative survey using a random sample of 513 (10%) of the 5,101 patients of the Northwest Community Health Center (August 2021 to August 2022). These participants were at least 18 years of age and had seen their medical provider in the previous 12 months. Many themes arose from the research participants who were uncomfortable with the EMR or the use of technology in the exam room. Understanding the benefits or even the general functionality of the EMR allows the patient to feel more comfortable with its use and to become more tolerant of the presence and use of technology during the physician encounter. Furthermore, as the possession and use of current technologies diminishes amongst the study’s participants, so does their preference for their provider to use an EMR. To comprehend the impact EMR knowledge has on the patients’ perception of its utilization, a crosstabulation between staff and non-staff patients underlined the fundamental difference. When asked what type of chart they would prefer their medical provider to use, a quarter of non-staff patients preferred electronic medical records, whereas two-thirds of the staff, who are also patients of the community health center, preferred the same. These findings indicate a need to educate patients about the benefits of the EMR and the advantage of accessing the EMR in the exam room. Furthermore, enhancing the providers’ communication skills will help them comprehend the prevalent communication barriers created by accessing the EMR in the exam room. The quality of the interaction between the patient and provider is critical to the patient’s health outcomes. Improved communication leads to better emotional and physiological health, compliance with treatment recommendations, pain management, and symptom resolution

An informatics model for tissue banks – Lessons learned from the Cooperative Prostate Cancer Tissue Resource

BACKGROUND: Advances in molecular biology and growing requirements from biomarker validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control. METHODS: Data managers review the medical records to collect and continuously update information for the 145 clinical, pathological and inventorial CDEs that the Resource maintains for each case. An Access-based data entry tool provides de-identification and a standard communication mechanism between each group and a central CPCTR database. Standardized automated quality control audits have been implemented. Centrally, an Oracle database has web interfaces allowing multiple user-types, including the general public, to mine de-identified information from all of the sites with three levels of specificity and granularity as well as to request tissues through a formal letter of intent. RESULTS: Since July 2003, CPCTR has offered over 6,000 cases (38,000 blocks) of highly characterized prostate cancer biospecimens, including several tissue microarrays (TMA). The Resource developed a website with interfaces for the general public as well as researchers and internal members. These user groups have utilized the web-tools for public query of summary data on the cases that were available, to prepare requests, and to receive tissues. As of December 2005, the Resource received over 130 tissue requests, of which 45 have been reviewed, approved and filled. Additionally, the Resource implemented the TMA Data Exchange Specification in its TMA program and created a computer program for calculating PSA recurrence. CONCLUSION: Building a biorepository infrastructure that meets today's research needs involves time and input of many individuals from diverse disciplines. The CPCTR can provide large volumes of carefully annotated prostate tissue for research initiatives such as Specialized Programs of Research Excellence (SPOREs) and for biomarker validation studies and its experience can help development of collaborative, large scale, virtual tissue banks in other organ systems

BMC Cancer

BackgroundAdvances 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.MethodsThe 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\ue2\u201e\ua2 (caBIG\ue2\u201e\ua2, see ). 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.ResultThe 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.ConclusionThe 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.1U19OH009077-01/OH/NIOSH CDC HHS/United StatesIRB #0608194/PHS HHS/United StatesUL1 TR000005/TR/NCATS NIH HHS/United State

Data Sovereignty in Data Donation Cycles - Requirements and Enabling Technologies for the Data-driven Development of Health Applications

Personalized healthcare is expected to increase the efficiency and the effectiveness of health services using different kinds of algorithms on existing data. This approach is currently confronted with the lack of digital data and the desire for self-determined personal data handling. However, the issue of health data donation is on the political agenda of some governments. Within this work, a knowledge base will be created by reviewing existing approaches and technologies regarding this topic with the focus on chronic diseases. A list of requirements will be derived from which we conceptualize a data donation cycle to demonstrate the challenges and opportunities of health data sovereignty and its future possibilities concerning data-driven health application development. By linking the requirements to technological approaches, the baseline for future open ecosystems will be presented