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In 1991, we demonstrated a prototype version of the Clinical Workstation at SCAMC. At the present time 48 workstations have been implemented in the ambulatory care areas of the Hospital. We describe the present functionality of the workstation and the work done to date on the clinical data repository.
Clinical reports, notes, and other narratives are highly used components in the patient record. Unfortunately, the methods by which these reports are generated are as diverse as the fiscal autonomy of academic clinical departments in a university-based health science center. In this paper, we report on electronically capturing clinical reports, notes, and other text fragments from several hospital sources and many outpatient clinics. The purpose of the capture is to feed the ACIS (Advanced Clinical Information System) central patient data repository that is in use at the University of Utah Health Sciences Center (UUHSC). A survey conducted in early 1994 indicated that about 917,150 reports were generated per year at UUHSC representing about 1.2 million pieces of paper, occupying about 2.3 gigabytes of storage. The most crucial problem encountered in capturing the reports was linking them to the proper patient. Systems that had functioning and well-maintained admit-discharge-transfer (ADT) information performed well, but systems that relied on the human dictator to identify patients, produced patient linkage errors. In our open loop telephone dictation systems this error rate averaged between 6 and 10%. Subsequent to the wide-spread availability of clinical reports on ACIS, this error rate dropped to 3-5%, presumably due to increased demand for on-line availability of this information. From clinical secretaries who use their word processor to create the clinical reports, the linkage error rate was < 1% due to the use of our Advanced Text Upload (ATU) utility. The clinical text component in ACIS contributed significantly to the success of a JCAHO site visit in December 1995.
Policy-makers and researchers lament the absence of telehealth registries to enhance knowledge regarding outcomes and efficacy of telehealth interventions. A number of different organizations operate registries, but there do not appear to be any true telehealth registries. One reason is that federal requirements through such policies as the Health Insurance Portability and Accountability Act (HIPAA) have led to heightened fear of inadvertently releasing confidential or unauthorized information. Also, it would be more efficient if patient data were captured electronically at the local level, ideally through electronic medical records (EMRs), and then transferred electronically to registries. However, the diffusion of EMRs at the local level is in its infancy. As a result, it is unlikely that we will see a comprehensive telehealth data repository within the next decade.
TCP/IP and World-Wide-Web (WWW) technology have become the universal standards for networking and delivery of information. Personal digital assistants (PDAs), cellular telephones, and alphanumeric pagers are rapidly converging on a single pocket device that will leverage wireless TCP/IP networks and WWW protocols and can be used to deliver clinical information and alerts anytime, anywhere. We describe a wireless interface to clinical information for physicians based on Palm Corp.'s Palm VII pocket computer, a wireless digital network, encrypted data transmission, secure web servers, and a clinical data repository (CDR).
A central repository for diagnostic information about individual patients was created as a service to diagnostic laboratories participating in the Compentence Network for Acute and Chronic Leukemias in order to support health care delivery to patients suffering from leukemia. During the diagnostic phase several specialised laboratories perform different assays on samples from the same patient. The use of these assays in the diagnostic process and during the treatment phase may be improved in terms of both rapid delivery and cost if any one laboratory is aware of preliminary or final results from the assay carried out in other laboratories. In order to support a more efficient communication of these results, a central diagnostic data repository (CDDR) was created and web-based user interface was developed. Currently, the CDDR maintains documents in the form of portable document format (PDF) files. Several other formats are accepted and converted automatically upon entry. Patient identification is accomplished by pseudonym rather than proper name and the data is held on the CDDR for a limited time interval to accommodate the stringent privacy regulations in Germany. The principle operation of a CDDR may also be applied to the diagnostic or therapeutic process of other diseases.
Single-cell RNA sequencing has transformed cell biology by enabling precise transcriptomic measurements of individual cells. The Sequence Read Archive (SRA) is the largest public repository of sequencing reads, yet much of it remains underutilized due to unstandardized metadata. Here, we introduce scBaseCount, a database that leverages an AI agent to automate discovery and metadata extraction and standardize data processing. Built by mining all 10x Genomics datasets, scBaseCount is the largest public repository of single-cell gene expression data, comprising over 502 million cells across 27 organisms and 75 tissues. It offers an unbiased view of the data landscape within the SRA and enables the training of more performant computational models through access to broader phenotypic diversity. Uniform processing enables measurement of both intronic and exonic reads and non-coding gene expression and improves alignment across experiments. Moreover, scBaseCount provides a blueprint for how AI can be leveraged to autonomously curate biological data repositories.
The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.
CADRE is a public resource for housing and analysing genomic data extracted from species of Aspergillus. It arose to enable maintenance of the complete annotated genomic sequence of Aspergillus fumigatus and to provide tools for searching, analysing and visualizing features of fungal genomes. By implementing CADRE using Ensembl, a framework is in place for storing and comparing several genomes: the resource will thus expand by including other Aspergillus genomes (such as Aspergillus nidulans) as they become available. CADRE is accessible at http://www.cadre. man.ac.uk.
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As a result of increased attention to medical errors, many institutions are contemplating increased use of information technology and clinical decision support. We conducted a retrospective analysis to estimate the frequency and cost of adverse drug events (ADEs) for inpatients at the University of Virginia. Applying published criteria for the detection of potential adverse events, we used a clinical data warehouse to identify patients and cases with potential ADEs. Again using published criteria, we then estimated the actual number of adverse drug events and preventable adverse drug events, as well as their attributable costs and excess length of stay. Our results showed a higher estimate (10.4-11.5 events per 100 admissions) for ADEs than seen in the ADE Prevention Study, highlighting the importance of considering the generalizability of published ADE studies to other settings. Our analysis demonstrates that retrospective analysis can be an efficient and powerful technique to evaluate rules and criteria used to detect ADEs and to assess their impact.
UNLABELLED: Ochsner Health Plan, New Orleans. PROBLEM: The health plan's information systems were inflexible and ineffective in meeting the needs of healthcare administrators, clinicians and others within the organization. SOLUTION: Ochsner officials reorganized the information systems by restructuring the computing architecture and building an enterprisewide relational database. RESULTS: Separate departments within the health plan now can share the same base of clinical and financial data online. KEYS TO SUCCESS: "The new server gave us the benefits of a centralized system combined with powerful back-end processing capabilities that enabled online analytical processing."
BACKGROUND & AIMS: Endoscopy is commonly performed to evaluate symptoms of dyspepsia. The aim of this study was to characterize patients who receive endoscopy for dyspepsia and measure predictors of primary endoscopic outcomes, utilizing a large national endoscopic database. METHODS: The Clinical Outcomes Research Initiative (CORI) receives endoscopy reports from a network of 74 sites in the United States. Sixty-one percent of reports come from private practice settings. Patients with reflux dyspepsia and nonreflux dyspepsia were identified from January 2000 to June 2002. Patients with dysphagia and known Barrett's esophagus were excluded. Primary endoscopic outcomes included esophageal inflammation and stricture, gastric ulcer, duodenal ulcer, suspected Barrett's esophagus (> or =2 cm), and suspected esophageal and gastric malignancy. The presence or absence of alarm symptoms (vomiting, weight loss, and evidence of GI blood loss) was determined. Adjusted relative risk (RR) for predicting serious outcomes was calculated in a multivariate model. RESULTS: We received 117,497 endoscopic reports, representing 99,558 unique patients. Dyspepsia, with and without reflux symptoms, accounted for 43% of upper endoscopies. Among dyspeptic patients, 36.5% were younger than 50 years of age without alarm symptoms. Esophageal or gastric malignancy in patients with dyspepsia was associated with increasing age, male sex, Asian race, Native American race, and symptoms of weight loss and vomiting. Suspected Barrett's esophagus (> or =2 cm) was associated with reflux symptoms, male sex, age, and white race. Ulcers were associated with evidence of bleeding, vomiting, male sex, black race, and Hispanic ethnicity. CONCLUSIONS: These practice-based data reveal important practice behaviors and outcomes.
Over recent years databases have become an extremely important resource for biomedical research. Immunology research is increasingly dependent on access to extensive biological databases to extract existing information, plan experiments, and analyse experimental results. This review describes 15 immunological databases that have appeared over the last 30 years. In addition, important issues regarding database design and the potential for misuse of information contained within these databases are discussed. Access pointers are provided for the major immunological databases and also for a number of other immunological resources accessible over the World Wide Web (WWW).
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