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At least 19 recordsLinked to original sources
PubMed1992

[Data protection and data access (I): federal data protection law and the social welfare code with reference to carrying out occupational medicine epidemiologic studies in Germany].

The regulations applicable to research in occupational epidemiology are the federal data protection (confidentiality) law (BDSG), the social welfare code (SGB), medical professional secrecy regulations and the federal statistics law (BStatG). The SGB, medical professional secrecy, and BStatG codes take precedence over BDSG rulings. This paper discusses BDSG and SGB. Medical professional secrecy and BStatG will be the topic of another publication (Datenschutz and Datenzugang II). The BDSG permits processing and utilization of personal data only if 1. this is permitted by BDSG or a law with higher priority, or 2. if the individual concerned has given her or his informed consent. According to the BDSG private research institutes can have access to personal data collected within non-public institutions only via section 28 (2) without consent of the individual. The "research paragraph" section 40 governs the processing and utilisation of personal data by research institutions. As a rule, the SGB permits access to epidemiological data sources only with the informed consent of the individuals concerned. The exception is section 75 SGBX. This paragraph permits disclosure of personal data without the individual's consent by the relevant public institution only if public interest considerably outweighs the private concerns. To our knowledge, however, this clause has had no practical significance. The concept of "informed consent" is discussed in detail, including the requirements for a legal form for informed consent. The legal codes of the BDSG, professional secrecy, and BStatG permit the transfer of personal data if the individuals concerned remain anonymous. This paper deals in detail with the concept of "anonymity".(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Security↗
PubMed2003

The Stanford Microarray Database: data access and quality assessment tools.

The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code and providing full public access to data published by SMD users, along with many tools to explore and analyze those data. SMD currently provides public access to data from 3500 microarrays, including data from 85 publications, and this total is increasing rapidly. In this article, we describe some of SMD's newer tools for accessing public data, assessing data quality and for data analysis.

Animals↗
PubMed2025

Toward ethical provenance tracking: The GA4GH model data access agreement (DAA).

PURPOSE: Standardizing contractual clauses that govern data access enables research institutions to responsibly steward genomic and related health data while enabling its efficient downstream reuse. METHODS: We describe a document analysis study using both qualitative and comparative law analytical approaches to identify the most common categories of clauses from 29 different data access agreements used by human biomedical research consortia globally. We furthermore characterized the legal positions and standard practices for each common element of the agreement and synthesized across them to develop model clauses. A total of 3 discussion sessions were organized virtually to refine the clauses among members of the Ethical Provenance Subgroup of the Global Alliance for Genomics and Health. RESULTS: We developed 15 unique data access clauses corresponding to the most common legal elements identified in the sampled agreements. CONCLUSION: Model clauses can be used to drive administrative efficiencies and institutional compliance for managing access to human genomic data for research. Additional machine-readable consents and software solutions are needed to support traceable "ethical provenance" of human genomic data and communicate data use conditions throughout the data's life-cycle.

Humans↗
PubMedDate not supplied

Patient-borne memory device facilitates "point of care" data access.

Although electronic medical records and a central database have made accurate and consistent patient medical information more readily available than with the traditional patient chart, there are many locations in healthcare facilities where terminals for accessing patient data are not available. As patient care becomes decentralized and more patients require anesthesia outside of the operating suites, routing a network-based system to all these locations can be expensive and time consuming. We designed a system whereby essential patient data of interest to anesthesiologists is stored on an electronic memory device the size of a watch battery attached to the patient's wristband. Accessing and editing the data is done via a hand-held computer. This system provides secure patient data storage and management at the "point of care." At the conclusion of the patient's anesthesia-related care, the data is downloaded to a relational database for use in outcome analysis, billing, and quality assurance. After collecting preoperative evaluations, intraoperative data, and postoperative data on 560 patients anesthetized for surgery or other procedures, we find this system to be a reliable, low-cost, medical information management system, with possible application to other medical specialties.

Ambulatory Surgical Procedures↗
PubMed2006

ADAAPT: Amgen's data access, analysis, and prediction tools.

The Amgen's Data Access Analysis Prediction Tools (ADAAPT) system is a desktop decision support tool developed to provide flexible access and analysis of chemical and biological data. The system is platform independent, adaptable, easily deployed, and scalable. It consists of four main modules: access, analysis, prediction, and tools. The access module contains numerous user interfaces designed to retrieve data easily. The analysis module provides standard computational tools to perform property calculation, QSAR/QSPR, and statistical analyses. The prediction module contains in-house models to calculate a drug-likeness score and absorption index. Finally, the tools module provides a wide array of features that are of general interest to our scientists.

Computer Systems↗
PubMed1998

IMGT, the international ImMunoGeneTics database: a new design for immunogenetics data access.

IMGT, the international ImMunoGeneTics database is an integrated database specializing in Immunoglobulins (Ig), T-cell receptors (TcR) and MHC molecules of all vertebrate species, created by Marie-Paule Lefranc, University of Montpellier, CNRS, Montpellier, France (Nucleic Acids Research, Database issue, Vol 26, January 1998). IMGT includes three databases: LIGM-DB (for Ig and TcR), MHC/HLA-DB and IMGT/PRIMER-DB (an Ig, TcR and MHC-related primer database), the last two in development. IMGT comprises expertly annotated sequences and alignment tables. LIGM-DB contains more than 24.000 Immunoglobulin and T cell Receptor sequences from 81 different species. MHC/HLA-DB contains class I and class II Human Leucocyte Antigen alignment tables. An IMGT tool, DNAPLOT, developed for Ig, TcR and MHC sequence analysis, is also available. IMGT goals are to establish a common data access to all immunogenetics data, including nucleotide and protein sequences, oligonucleotide primers, gene maps and other genetic data of Ig, TcR and MHC molecules, from all species, and to provide a graphical user friendly data access. IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutical approaches (antibody engineering), genome diversity and genome evolution studies. In this paper, we describe our approach for the data modelisation, the automation of the annotation procedure and control of data quality in LIGM-DB database. IMGT is freely available on the CNUSC WWW server at Montpellier: http://imgt.cnusc.fr: 8104 (contact: Denys.Chaume@cnusc.fr) and on the EBI servers: http://www.ebi.ac.uk/imgt (contact: malik@ebi.ac.uk) and ftp.ebi.ac.uk/pub/databases/imgt. LIGM-DB users are encouraged to report errors or suggestions to giudi@ligm.crbm.cnrs-mop.fr. IMGT initiator and coordinator: Marie-Paule Lefranc, lefranc@ligm.crbm.cnrs-mop.fr. (fax: +33(0)467040231).

Amino Acid Sequence↗
PubMed2005

Graphical representation of ribosomal RNA probe accessibility data using ARB software package.

BACKGROUND: Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments. RESULTS: The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence associated information (SAI) can be visualized by user defined background colors within the ARB primary and secondary structure editors as well as in the PROBE Match tool. CONCLUSION: Using this tool, in silico probe design and evaluation can be performed with respect to in situ probe accessibility data. The evaluation of proposed probe targets with respect to higher-order rRNA structure is of importance for successful design and performance of in situ hybridization experiments. The entire ARB software package along with the probe accessibility data is available from the ARB home page http://www.arb-home.de

Algorithms↗
PubMed2006

Common carotid arterial interadventitial distance (diameter) as an indicator of the damaging effects of age and atherosclerosis, a cross-sectional study of the Atherosclerosis Risk in Community Cohort Limited Access Data (ARICLAD), 1987-89.

BACKGROUND: The effect of age on common carotid artery diameter is unclear for varying atherosclerosis risk levels. METHODS: Cross-sectional data from the Atherosclerosis Risk in Communities Limited Access Data set were used to estimate the association of age with B-mode ultrasound common carotid artery diameter for three atherosclerosis risk levels. Based on information from clinical examinations, B-mode ultrasounds, questionnaires, blood and other tests, participants were categorized into three groups: pre-existing disease (prevalent stroke and/or coronary heart disease), high risk group (no pre-existing disease, but prevalent diabetes, hypertension, plaques/shadowing, body mass index > or = 30, current smoking, or hyperlipidemia), and a low risk group (no pre-existing disease, no plaques/shadowing, and no major elevated risk factors). Multivariable linear regression analyses modeled the common carotid artery diameter relationship with age. RESULTS: Age was positively and significantly associated with common carotid artery diameter after risk factor adjustment in the overall sample, but age had a larger effect among persons with evidence of atherosclerosis (interaction p < 0.05). Each year of older age was associated with 0.03 mm larger diameter/year among persons with pre-existing disease, with 0.027 mm larger diameter/year in the high risk group, but only 0.017 mm/year among the low risk group. Results were qualitatively similar using plaques/shadowing status to indicate atherosclerosis severity. CONCLUSION: The significant impact of age on common carotid artery diameter among low risk, middle-aged, black and white men and women suggests arterial remodelling may occur in the absence of identified risk factors. The significantly larger impact of age among persons with, compared to persons without identified atherosclerosis or its risk factors, suggests that arterial remodelling may be an indicator of exposure duration.

Adult↗
PubMed1999

The EMBL Nucleotide Sequence Database. Contributing and accessing data.

The European Molecular Biology Laboratory Nucleotide Sequence Database receives sequence and sequence annotation data from genome projects, sequencing centers, individual scientists, and patent offices. Data may be most efficiently submitted to the database using the Internet based submission tool WEBIN or via previously established genome project accounts. Biologist curators will review the data and provide accession numbers within two working days. Non-confidential data are exchanged daily in an international collaboration between EMBL. DDBJ (the DNA Databank of Japan) and GenBank (USA) and may be accessed and retrieved via the Internet with the Sequence Retrieval System (SRS). Sequence database searching algorithms (e.g., Blitz, Fasta, Blast) are available for comparison of query to database sequences.

Amino Acid Sequence↗
PubMed1993

[Data protection and data access (II): Physician's responsibility for confidentiality, federal statistics law and data collection by authorization with reference to implementing occupational medicine epidemiologic studies in Germany].

The additional legal rulings governing access to personal data for epidemiological research are the medical professional secrecy regulators and the federal statistics law. These permit access to personal data only if the individual has given his or her informed constant. Beyond this, both laws contain clauses governing the transfer of anonymous data for research and science. Thus anonymized data may be transferred on request to authorized persons or institutions, such as a physician or the regional statistics office. Finally, a custodian model is presented which provides further possibilities for research in occupational medicine and epidemiology within this very restrictive legal framework.

Cause of Death↗
PubMed1998

The Genome Sequence DataBase (GSDB): improving data quality and data access.

In 1997 the primary focus of the Genome Sequence DataBase (GSDB; www. ncgr.org/gsdb ) located at the National Center for Genome Resources was to improve data quality and accessibility. Efforts to increase the quality of data within the database included two major projects; one to identify and remove all vector contamination from sequences in the database and one to create premier sequence sets (including both alignments and discontiguous sequences). Data accessibility was improved during the course of the last year in several ways. First, a graphical database sequence viewer was made available to researchers. Second, an update process was implemented for the web-based query tool, Maestro. Third, a web-based tool, Excerpt, was developed to retrieve selected regions of any sequence in the database. And lastly, a GSDB flatfile that contains annotation unique to GSDB (e.g., sequence analysis and alignment data) was developed. Additionally, the GSDB web site provides a tool for the detection of matrix attachment regions (MARs), which can be used to identify regions of high coding potential. The ultimate goal of this work is to make GSDB a more useful resource for genomic comparison studies and gene level studies by improving data quality and by providing data access capabilities that are consistent with the needs of both types of studies.

Base Sequence↗
PubMed2006

A remote data access architecture for home-monitoring health-care applications.

With the aging of the population and the increasing patient preference for receiving care in their own homes, remote home care is one of the fastest growing areas of health care in Taiwan and many other countries. Many remote home-monitoring applications have been developed and implemented to enable both formal and informal caregivers to have remote access to patient data so that they can respond instantly to any abnormalities of in-home patients. The aim of this technology is to give both patients and relatives better control of the health care, reduce the burden on informal caregivers and reduce visits to hospitals and thus result in a better quality of life for both the patient and his/her family. To facilitate their widespread adoption, remote home-monitoring systems take advantage of the low-cost features and popularity of the Internet and PCs, but are inherently exposed to several security risks, such as virus and denial-of-service (DoS) attacks. These security threats exist as long as the in-home PC is directly accessible by remote-monitoring users over the Internet. The purpose of the study reported in this paper was to improve the security of such systems, with the proposed architecture aimed at increasing the system availability and confidentiality of patient information. A broker server is introduced between the remote-monitoring devices and the in-home PCs. This topology removes direct access to the in-home PC, and a firewall can be configured to deny all inbound connections while the remote home-monitoring application is operating. This architecture helps to transfer the security risks from the in-home PC to the managed broker server, on which more advanced security measures can be implemented. The pros and cons of this novel architecture design are also discussed and summarized.

Ambulatory Care↗
PubMed2026

CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

MOTIVATION: Chromatin 3D folding creates numerous DNA interactions, participating in gene expression regulation. Single-cell chromatin-accessibility assays now profile hundreds of thousands of cells, challenging existing methods for mapping cis-regulatory interactions. RESULTS: We present CIRCE, a fast and scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data. CIRCE re-implements the Cicero workflow to analyse single-cell atlases, cutting runtime and memory use by several orders of magnitude. We also provide new options to compute metacells, grouping similar cells to reduce data sparsity. We benchmarked CIRCE against Cicero on two datasets of different sizes and demonstrated the improvement from CIRCE's metacells' strategy with promoter capture Hi-C data. We also evaluated how DNA interaction predictions are impacted by different pre-processing. We observed a negative impact of Cicero's count normalization, and the best performance was obtained with the single-cell count matrix directly. Finally, we demonstrated the scalability of CIRCE by processing a dataset of more than 700&#x2009;000 cells and 1 million DNA regions in less than an hour. CIRCE should greatly facilitate the prediction of DNA region interactions for scverse and Python users, while providing new and up-to-date pre-processing insights. AVAILABILITY AND IMPLEMENTATION: CIRCE is released as an open-source software under the AGPL-3.0 licence. The package source code is available on GitHub at https://github.com/cantinilab/CIRCE, and its documentation is accessible at https://circe.readthedocs.io. The code to reproduce the presented results is available as a Snakemake pipeline at https://github.com/cantinilab/circe_reproducibility.s.

Software↗
PubMed2004

Limited access data sets from studies funded by the National Heart, Lung, and Blood Institute.

The NHLBI has recently developed standards for protection of subject confidentiality which enable distribution of large data sets collected in completed epidemiological studies and clinical trials. This allows other investigators to pursue research using the data these studies have generated. An ethical commitment to protect the privacy of the research subjects requires careful review and some compromise in data details prior to distribution. To meet the challenge posed by the ethical and legal requirements to protect participants' privacy and making data sets useful for researchers, the NHLBI has devised a policy which seeks to balance these two opposing forces. This paper describes this policy as well as the limited access data sets currently available from NHLBI.

Clinical Trials as Topic↗
PubMed1987

A packetised remote visual access data system for space station interactive payload operations.

Potential users of the pressurised Columbus elements, (the Attached Pressurised Module and the Man-Tended Free Flyer), were consulted in order to establish the requirements necessary to achieve effective and efficient remote interactive payload operations. These are briefly described and clearly indicate that the key to such operations is a versatile remote visual access (video) system which is well-tuned to the requirements of the users in both the on-board and ground segments. A packetised remote visual access data system is proposed which accommodates these requirements and offers a very flexible operational environment. It incorporates a scheme for optimising users' remote visual access to their experiments. Methods of implementing the necessary multiplexing and compression aspects of the system are discussed. A scheme for centralized on-board monitoring, which is complicated by the wide range of video sources required by the users, is outlined and aspects of the ground segment, in particular the problem is link delays, are considered.

Computer Communication Networks↗
PubMed1997

Patient-Centered Access to Secure Systems Online (PCASSO): a secure approach to clinical data access via the World Wide Web.

The Internet's World-Wide Web (WWW) provides an appealing medium for the communication of health related information due to its ease of use and growing popularity. But current technologies for communicating data between WWW clients and servers are systematically vulnerable to certain types of security threats. Prominent among these threats are "Trojan horse" programs running on client workstations, which perform some useful and known function for a user, while breaching security via background functions that are not apparent to the user. The Patient-Centered Access to Secure Systems Online (PCASSO) project of SAIC and UCSD is a research, development and evaluation project to exploit state-of-the-art security and WWW technology for health care. PCASSO is designed to provide secure access to clinical data for healthcare providers and their patients using the Internet. PCASSO will be evaluated for both safety and effectiveness, and may provide a model for secure communications via public data networks.

Computer Communication Networks↗