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PubMed2005

Integrating feedback from a clinical data warehouse into practice organisation.

A patient oriented hospital information system (ARIANE) was inaugurated at the Sherbrooke University hospital (CHUS) in 1990 and a clinical data warehouse (CDW) completed 2004. The CDW is updated from ARIANE every 24h and includes ICD discharge diagnosis data, visit DRG and SNOMED encoding. The data is encrypted on storage. Data is accessed according to institutional approval. To facilitate data access two levels of tool have been made accessible using a web-browser. The first level consists of a 'dashboard' that has a defined design and enables a set of pre-determined dynamic queries about a patient population. This level can be operated with minimal training. The second level uses a convivial database query tool, which requires some prior training. Two prototype dashboards have been designed and evaluated for acceptability. The first for the emergency department enables analysis of patient occupancy. The second for the biochemistry department enables quality assurance evaluation. In most cases worldwide the clinical data warehouse is only beginning to be exploited, often impeded by lack of connection between different enterprise databases. Our CDW is expected rapidly to create a culture change so that clinical practice can be continuously evaluated using compiled data readily available from the electronic health record/hospital information system.

Consumer Behavior↗
PubMed2001

Accessing and using hospital activity data.

Hospital activity data can be accessed from a variety of sources ranging from hospitals to the Department of Health. These data provide valuable and widely used information, but care is needed in their use and interpretation. Hospital activity rates reflect not only the underlying prevalence and severity of disease, individual factors and referral practices, but also variations related to provider-specific factors: the 'provider effect'. This includes completeness in the data, supply of hospital beds, admission policies, hospital access and distance from hospital. The provider effect can be controlled to a certain extent in statistical analyses. Although data quality has improved considerably in the last decade, this should still be investigated where trusts are being compared and in small area studies because missing data may lead to artefactual differences in rates. 'Dump' postcodes, where missing or unknown postcodes are assigned to a local postcode such as that of the hospital, may affect small area analyses and linkage if a proxy patient identifier is constructed that includes postcode.

Data Collection↗
PubMed2002

EpiQMS: an Internet application for access to public health data for citizens, providers, and public health investigators.

Access to epidemiologic data is critical to public health practice. Unfortunately, most published data are out of date and live databases are inaccessible because of issues of confidentiality, varying user needs, cost, security concerns, and other reasons. EpiQMS is a Web-based application that allows exploratory, statistical, and geographic analysis of public health data. Tables, graphs, and maps with adjustments for small areas are available at three levels: (1) the general public, (2) public health and medical practitioners, and (3) epidemiologists and health officers. The difference in each level is with respect to the presentation of small cell sizes and small geographies as set by the data set custodians.

Databases, Factual↗
PubMed1999

The impact of outcomes data reporting on access to health care of high-risk patients to interventional cardiologists in the United States.

BACKGROUND: Pressure is increasingly being placed on medical sub-specialists to lower procedural costs while improving overall outcomes. Outcomes data reporting has been utilized in an attempt to improve procedural results; however, some negative aspects of this type of reporting have emerged. METHODS: We surveyed 5,229 interventional cardiologists practicing in the United States regarding the effect of outcomes data reporting on their approach to high-risk patients who required interventional procedures. The results were analyzed one month after mailing the survey. RESULTS: One thousand, four hundred and forty-four cardiologists responded to the survey. Ninety-three percent of the respondents indicated that outcomes data reporting would have some effect on their approach to high-risk patients. Only 7% said outcomes reporting would have no effect on their willingness to perform interventions on high-risk patients. The majority of respondents performed between 51 and 100 interventions per year; those who performed more than 500 interventions per year reported that they would be less affected if outcomes data were reported from their results. CONCLUSIONS: Our survey indicates that outcomes data reporting would have a significant effect on the willingness of cardiologists to perform procedures on high-risk patients; this effect may limit access to needed care for this high-risk population.

Angioplasty, Balloon, Coronary↗
PubMed1993

Rapid access to pharmacokinetics data and correlation between antimicrobial susceptibility results and drug tissue distribution using a personal computer.

MYMIC is a computer-aided system capable of integrating antibiotic susceptibility data with the concentrations the drugs reach in various body tissues and fluids by calculating site concentration/minimal inhibitory concentration quotients. The program can be run on any low-cost personal computer operating under MS-DOS, provided it is equipped with a hard-disk drive and with a minimum of 512 kilobytes of random access memory. The use of the program does not require any knowledge of computer languages. The antibiotic susceptibility data can be entered either as minimal inhibitory concentrations or as inhibitory zone diameters; in the latter case, minimal inhibitory concentrations are automatically calculated via regression formulas. The concentrations obtained by 90 antibiotics in 51 different human tissues and fluids are recorded in a data base of over 1,000 records, obtained from roughly 700 original papers. A MYMIC sample session was simulated by mimicking infections of three different body districts (namely bone, prostate, and sputum) caused by Pseudomonas aeruginosa, Escherichia coli or Providencia stuartii.

Anti-Bacterial Agents↗
PubMed2002

A rule driven bi-directional translation system for remapping queries and result sets between a mediated schema and heterogeneous data sources.

As the number of online biomedical data sources increases, so too do the number of ways to access such data. The research described herein focuses on creating a data access system that provides bi-directional translation and mapping of data between heterogeneous databases and a mediated schema. Semantic mapping rules stored in a knowledge base are used by our generalized software to convert XML query results obtained from each data source to a common schema representing a single ontology. We apply this approach to the domain of online genetic databases, demonstrating the system's scalability and integratability.

Databases as Topic↗
PubMed2004

EnsMart: a generic system for fast and flexible access to biological data.

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets.

Animals↗
PubMed2005

Munich information center for protein sequences plant genome resources: a framework for integrative and comparative analyses 1(W).

With several plant genomes sequenced, the power of comparative genome analysis can now be applied. However, genome-scale cross-species analyses are limited by the effort for data integration. To develop an integrated cross-species plant genome resource, we maintain comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa). Integration of data and resources is emphasized, both in house as well as with external partners and databases. Manual curation and state-of-the-art bioinformatic analysis are combined to achieve quality data. Easy access to the data is provided through Web interfaces and visualization tools, bulk downloads, and Web services for application-level access. This allows a consistent view of the model plant genomes for comparative and evolutionary studies, the transfer of knowledge between species, and the integration with functional genomics data.

Computational Biology↗
PubMed1991

Ownership of research data.

The author reviews the conventional "works for hire" principle that an institution, not its employees, owns the rights to its employees' written products or other forms of expression, including primary research data. This principle is not open to debate as a legal matter. The tough problems giving rise to debates regarding data ownership and access are ethical problems rather than legal ones; these will remain unsettled for some time because at present there is no consensus concerning what constitutes ethical conduct among scholars and scientists and how seriously and in what manner to penalize breaches of that conduct. Access to data is a thorny issue; case histories illustrate the legal and ethical difficulties involved in questions of who has access to information compiled in the course of academic inquiry, and for what purpose. Much depends on the ethics and established procedures of the employing institution, but current case law suggests that a faculty member or institutional researcher does not have any legal right to review the data developed by a colleague. The author recommends that institutions clearly state their policies regarding ownership of data, and presents guidelines for such a policy.

Copyright↗
PubMed2026

The Network of National COVID-19 Data Portals: public health equity through collaboration.

The network of the national COVID-19 Data Portals was developed and linked to the COVID-19 Data Portal (https://www.covid19dataportal.org/)inresponsetothe need for rapid data sharing and analysis during the 2020-2022 SARS-CoV-2 pandemic. Built on open-source code developed by the Swedish COVID-19 Data Portal (now the Swedish Pathogens Portal, www.pathogens.se) the network included 12 national portals addressing demand for local open data sharing and access, across data types and resources. It provides a robust case study of national initiatives for FAIR (Findable, Accessible, Interoperable and Reusable) resources and a foundation for future pandemic preparedness across pathogens globally. In this paper we outline the structure of the origins of the network of National COVID-19 Datal Portals, the technical aspects and code originating from the Swedish Portal and provide an overview of the services and tools offered by each Portal. The paper showcases the process and operation of four Portals: Sweden, Poland, Spain, Norway and The Netherlands. In this study, we observe that pandemic response greatly benefits from an established infrastructure that can be quickly mobilised, developed and extended. Collaborations and preparation built on solid foundations over several years, supported by investment in the form of national and international research grants, is key for sustainability, continuation and readiness to deploy such efforts.

COVID-19↗
PubMed1999

Improved secondary structure predictions for a nicotinic receptor subunit: incorporation of solvent accessibility and experimental data into a two-dimensional representation.

Abstract A refined prediction of the nicotinic acetylcholine receptor (nAChR) subunits' secondary structure was computed with third-generation algorithms. The four selected programs, PHD, Predator, DSC, and NNSSP, based on different prediction approaches, were applied to each sequence of an alignment of nAChR and 5-HT3 receptor subunits, as well as a larger alignment with related subunit sequences from glycine and GABA receptors. A consensus prediction was computed for the nAChR subunits through a "winner takes all" method. By integrating the probabilities obtained with PHD, DSC, and NNSSP, this prediction was filtered in order to eliminate the singletons and to more precisely establish the structure limits (only 4% of the residues were modified). The final consensus secondary structure includes nine alpha-helices (24.2% of the residues, with an average length of 13.9 residues) and 17 beta-strands (22.5% of the residues, with an average length of 6.6 residues). The large extracellular domain is predicted to be mainly composed of beta-strands, with only two helices at the amino-terminal end. The transmembrane segments are predicted to be in a mixed alpha/beta topology (with a predominance of alpha-helices), with no known equivalent in the current protein database. The cytoplasmic domain is predicted to consist of two well-conserved amphipathic helices joined together by an unfolded stretch of variable length and sequence. In general, the segments predicted to occur in a periodic structure correspond to the more conserved regions, as defined by an analysis of sequence conservation per position performed on 152 superfamily members. The solvent accessibility of each residue was predicted from the multiple alignments with PHDacc. Each segment with more than three exposed residues was assumed to be external to the core protein. Overall, these data constitute an envelope of structural constraints. In a subsequent step, experimental data relative to the extracellular portion of the complete receptor were incorporated into the model. This led to a proposed two-dimensional representation of the secondary structure in which the peptide chain of the extracellular domain winds alternatively between the two interfaces of the subunit. Although this representation is not a tertiary structure and does not lead to predictions of specific beta-beta interaction, it should provide a basic framework for further mutagenesis investigations and for fold recognition (threading) searches.

Algorithms↗