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Practice databases and their uses in clinical research.

A few large clinical information databases have been established within larger medical information systems. Although they are smaller than claims databases, these clinical databases offer several advantages: accurate and timely data, rich clinical detail, and continuous parameters (for example, vital signs and laboratory results). However, the nature of the data vary considerably, which affects the kinds of secondary analyses that can be performed. These databases have been used to investigate clinical epidemiology, risk assessment, post-marketing surveillance of drugs, practice variation, resource use, quality assurance, and decision analysis. In addition, practice databases can be used to identify subjects for prospective studies. Further methodologic developments are necessary to deal with the prevalent problems of missing data and various forms of bias if such databases are to grow and contribute valuable clinical information.

Clinical Medicine↗

Database challenges and solutions in neuroscientific applications.

In the scientific community, the quality and progress of various endeavors depend in part on the ability of researchers to share and exchange large quantities of heterogeneous data with one another efficiently. This requires controlled sharing and exchange of information among autonomous, distributed, and heterogeneous databases. In this paper, we focus on a neuroscience application, Neuroanatomical Rat Brain Viewer (NeuART Viewer) to demonstrate alternative database concepts that allow neuroscientists to manage and exchange data. Requirements for the NeuART application, in combination with an underlying network-aware database, are described at a conceptual level. Emphasis is placed on functionality from the user's perspective and on requirements that the database must fulfill. The most important functionality required by neuroscientists is the ability to construct brain models using information from different repositories. To accomplish such a task, users need to browse remote and local sources and summaries of data and capture relevant information to be used in building and extending the brain models. Other functionalities are also required, including posing queries related to brain models, augmenting and customizing brain models, and sharing brain models in a collaborative environment. An extensible object-oriented data model is presented to capture the many data types expected in this application. After presenting conceptual level design issues, we describe several known database solutions that support these requirements and discuss requirements that demand further research. Data integration for heterogeneous databases is discussed in terms of reducing or eliminating semantic heterogeneity when translations are made from one system to another. Performance enhancement mechanisms such as materialized views and spatial indexing for three-dimensional objects are explained and evaluated in the context of browsing, incorporating, and sharing. Policies for providing the system with fault tolerance and avoiding possible intellectual property abuses are presented. Finally, two existing systems are evaluated and compared using the identified requirements.

Animals↗

Pesticide exposure monitoring databases in applied risk analysis.

Faced with the need to evaluate under what conditions chemicals can be used with "reasonable certainty of no harm" to workers and consumers, industry and government agencies have embraced quantitative risk analysis as a science-based approach for product development, regulatory evaluations, and associated risk management decision making. Beginning in the 1990s, a variety of industry-sponsored task forces have been formed to develop exposure-related data to support safety evaluations for pesticide chemicals used in agricultural, industrial, institutional, residential, and other settings. Human exposure assessment and the underlying data (e.g., personal exposure and biological monitoring measurements, media-specific residue measurements, product use, and time-activity information) represent a critical component of the risk assessment process and a rapidly advancing science. While task forces have been created to develop databases for supporting the continued safe use of products, the development of these databases has served to advance general understanding of the basic principles underlying exposure assessment methodology and thereby provide the basis for improved science-based risk management by both industry and government. Given that developing chemical-specific data for every product use pattern and associated worker or consumer exposure scenario (e.g., professional mixer, loader and applicator activities associated with the use of a low-pressure sprayer, consumer residential lawn application via a ready-to-use hose-end sprayer product) is prohibitively expensive and time consuming, alternative approaches have been developed based upon meta-analyses and generalizations derived from databases of exposure monitoring studies for multiple chemicals, sorted by significant exposure covariates such as formulation type, method of application, amount of active ingredient applied, site of application, protective equipment and clothing, and task or activity. These generalizations can be used for predictive exposure analyses and have clearly demonstrated the value of "generic databases." Although data in these databases and associated generalizations are subject to interpretation, e.g., during the regulatory decision-making processes, and may be used in conjunction with additional considerations or assessment methods that result in conservative biases, the role of generic databases for risk management decision making, and advancing the science of applied exposure analysis continues to be realized.

Adult↗

Long-term ST database: a reference for the development and evaluation of automated ischaemia detectors and for the study of the dynamics of myocardial ischaemia.

The long-term ST database is the result of a multinational research effort. The goal was to develop a challenging and realistic research resource for development and evaluation of automated systems to detect transient ST segment changes in electrocardiograms and for supporting basic research into the mechanisms and dynamics of transient myocardial ischaemia. Twenty-four hour ambulatory ECG records were selected from routine clinical practice settings in the USA and Europe, between 1994 and 2000, on the basis of occurrence of ischaemic and non-ischaemic ST segment changes. Human expert annotators used newly developed annotation protocols and a specially developed interactive graphic editor tool (SEMIA) that supported paperless editing of annotations and facilitated international co-operation via the Internet. The database contains 86 two- and three-channel 24 h annotated ambulatory records from 80 patients and is stored on DVD-ROMs. The database annotation files contain ST segment annotations of transient ischaemic (1155) and heart-rate related ST episodes and annotations of non-ischaemic ST segment events related to postural changes and conduction abnormalities. The database is intended to complement the European Society of Cardiology ST-T database and the MIT-BIH and AHA arrhythmia databases. It provides a comprehensive representation of 'real-world' data, with numerous examples of transient ischaemic and non-ischaemic ST segment changes, arrhythmias, conduction abnormalities, axis shifts, noise and artifacts.

Adult↗

Bluetooth wireless database for scoliosis clinics.

A database system with Bluetooth wireless connectivity has been developed so that scoliosis clinics can be run more efficiently and data can be mined for research studies without significant increases in equipment cost. The wireless database system consists of a Bluetooth-enabled laptop or PC and a Bluetooth-enabled handheld personal data assistant (PDA). Each patient has a profile in the database, which has all of his or her clinical history. Immediately prior to the examination, the orthopaedic surgeon selects a patient's profile from the database and uploads that data to the PDA over a Bluetooth wireless connection. The surgeon can view the entire clinical history of the patient while in the examination room and, at the same time, enter in any new measurements and comments from the current examination. After seeing the patient, the surgeon synchronises the newly entered information with the database wirelessly and prints a record for the chart. This combination of the database and the PDA both improves efficiency and accuracy and can save significant time, as there is less duplication of work, and no dictation is required. The equipment required to implement this solution is a Bluetooth-enabled PDA and a Bluetooth wireless transceiver for the PC or laptop.

Computers, Handheld↗

Comparison of national administrative and commercial databases to monitor expenditure and costs of statins across Europe.

OBJECTIVES: To compare data on statin utilisation and costs across Europe from routine administrative databases with those from a commercial source. METHODS: Observational study in European Union member states and Norway. Comparison of data collected from national administrative databases used to reimburse pharmacists and data from a standard commercial source (Intercontinental Marketing Services Health): detailed data by drug for the year 2000. RESULTS: There were differences among the data from administrative databases and those from the commercial source; these differences were of a consistent pattern in each country. In general, the commercial data recorded greater utilisation (reflecting both public and private use, range from 0 to +55%, median +15%), lower cost per defined daily doses (as commercial data sources used ex-factory price rather than expenditure to the state used in administrative databases, range from -70% to -6%, median -39%) and similar utilisation per 1000 head of population per day (range from -15 to +47%, median -1%). CONCLUSIONS: Administrative databases can give useful utilisation data, which are broadly comparable with those from commercial sources. Cost data differ more, and the figures for each may be useful in different settings. Standards for data collection from the administrative databases are required.

Databases, Factual↗

Current status of the European Association for Cardio-Thoracic Surgery and the Society of Thoracic Surgeons Congenital Heart Surgery Database.

BACKGROUND: After utilizing separate congenital databases in the early 1990s, the Society of Thoracic Surgeons (STS) and the European Association for Cardio-Thoracic Surgery (EACTS) collaborated on several joint database initiatives. METHODS: In 1998, the joint EACTS-STS International Congenital Heart Surgery Nomenclature and Database Project Committee was created and a common nomenclature and common core minimum database dataset were adopted and published by the STS and the EACTS. In 1999, the joint EACTS-STS Aristotle Committee was created and the Aristotle Score was adopted and published as a method to provide complexity adjustment for congenital heart surgery. Collaborative efforts involving the EACTS and STS are underway to develop mechanisms to verify data completeness and accuracy. RESULTS: Since 1998, this nomenclature, database, and methodology of complexity adjustment have been used by both the STS and EACTS to analyze outcomes of over 40,000 patients. A huge amount of data have been generated which allow comparison of practice patterns and outcomes analysis between Europe and North America. The aggregate data from the first 5 years of data collection not only make for interesting comparison but also allow examination of regional difference in practice patterns. For example, in the EACTS, out of 4,273 neonates, 885 (20.7%) underwent arterial switch procedures and 297 (6.95%) underwent Norwood stage 1 procedures. In the STS, out of 3,988 neonates, 472 (11.8%) underwent arterial switch procedures and 575 (14.4%) underwent Norwood stage 1 procedures. CONCLUSIONS: This analysis of the EACTS-STS multi-institutional outcomes database confirms that in both Europe and North America, case complexity and mortality is highest among neonates, then infants, and then children. Regional differences in practice patterns are demonstrated, with the overall goal being the continued upgrade in the quality of surgery for congenital heart disease worldwide.

Databases, Factual↗

Customizable neuroinformatics database system: XooNIps and its application to the pupil platform.

The developing field of neuroinformatics includes technologies for the collection and sharing of neuro-related digital resources. These resources will be of increasing value for understanding the brain. Developing a database system to integrate these disparate resources is necessary to make full use of these resources. This study proposes a base database system termed XooNIps that utilizes the content management system called XOOPS. XooNIps is designed for developing databases in different research fields through customization of the option menu. In a XooNIps-based database, digital resources are stored according to their respective categories, e.g., research articles, experimental data, mathematical models, stimulations, each associated with their related metadata. Several types of user authorization are supported for secure operations. In addition to the directory and keyword searches within a certain database, XooNIps searches simultaneously across other XooNIps-based databases on the Internet. Reviewing systems for user registration and for data submission are incorporated to impose quality control. Furthermore, XOOPS modules containing news, forums schedules, blogs and other information can be combined to enhance XooNIps functionality. These features provide better scalability, extensibility, and customizability to the general neuroinformatics community. The application of this system to data, models, and other information related to human pupils is described here.

Computational Biology↗

European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations (ECARUCA); an online database for rare chromosome abnormalities.

During recent years a considerable improvement in diagnostic techniques has enabled cytogeneticists to find more and smaller chromosomal aberrations. However, accurate clinical knowledge about rare chromosome disorders is frequently lacking, mostly due to a significant decline in publishable cases. On the other hand, there is an increasing demand from parents and physicians for reliable information. In order to improve the quality and the quantity of data available, we designed a new database named the European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations (ECARUCA) at http://www.ecaruca.net. This Internet-database contains cytogenetic and clinical data of patients with rare chromosome abnormalities, including microscopically visible aberrations, as well as microdeletions and -duplications. Cases with certain breakpoints collected in the Zurich Cytogenetic Database were transferred to ECARUCA. The advantages of ECARUCA compared to existing sources are that ECARUCA is interactive, dynamic and has long-term possibilities to store cytogenetic, molecular and clinical data. Professionals can login to submit new cases and perform searches in the database through the Internet. Currently the database contains 1500 unique chromosomal aberrations from almost 4000 patients. A frequent submission of new data ensures the up-to-date quality of the collection. Individual parent accounts allow parents to inform the ECARUCA team about the follow-up of their child. The ECARUCA database provides health care workers with accurate information on clinical aspects of rare chromosome disorders. Additionally, detailed correlations between chromosome aberrations and their phenotypes are of invaluable help in localising genes for mental retardation and congenital anomalies.

Chromosome Aberrations↗

Entamoeba histolytica: construction and applications of subgenomic databases.

Knowledge about the influence of environmental stress such as the action of chemotherapeutic agents on gene expression in Entamoeba histolytica is limited. We plan to use oligonucleotide microarray hybridization to approach these questions. As the basis for our array, sequence data from the genome project carried out by the Institute for Genomic Research (TIGR) and the Sanger Institute were used to annotate parts of the parasite genome. Three subgenomic databases containing enzymes, cytoskeleton genes, and stress genes were compiled with the help of the ExPASy proteomics website and the BLAST servers at the two genome project sites. The known sequences from reference species, mostly human and Escherichia coli, were searched against TIGR and Sanger E. histolytica sequence contigs and the homologs were copied into a Microsoft Access database. In a similar way, two additional databases of cytoskeletal genes and stress genes were generated. Metabolic pathways could be assembled from our enzyme database, but sometimes they were incomplete as is the case for the sterol biosynthesis pathway. The raw databases contained a significant number of duplicate entries which were merged to obtain curated non-redundant databases. This procedure revealed that some E. histolytica genes may have several putative functions. Representative examples such as the case of the delta-aminolevulinate synthase/serine palmitoyltransferase are discussed.

5-Aminolevulinate Synthetase↗

The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives.

This paper presents an overview of the organisation and the results of the collaborative exercises (CE) of the European DNA Profiling (EDNAP) Group's mitochondrial DNA population database project (EMPOP). The aim of the collaborative exercises was to determine whether uniformity of mtDNA sequencing results could be achieved among different laboratories. These were asked to sequence either the complete mtDNA control region or the two hypervariable regions HVI (16024-16365) and HVII (73-340) from DNA extracts, buccal swabs or bloodstains, proceeding in accordance with the protocol and strategies used in each individual laboratory. The results of the collaborative exercises were employed to identify possible sources of errors that could arise during the analysis and interpretation of mtDNA profiles. These findings were taken as a basis to tentatively make suitable arrangements for the construction of a high quality mtDNA database. One hundred fifty mtDNA profiles were submitted to the evaluating laboratory, and disaccording profiles were classified into four groups corresponding to the source of error: clerical errors, sample mix-ups, contaminations and discrepancies with respect to the mtDNA nomenclature. Overall, 14 disaccording haplotypes (16 individual errors) were observed. The errors included 10 clerical errors, 3 interpretation problems, 2 cases of sample mix-up and 1 case of point heteroplasmic mixture, where the 2 sequencing reactions brought inconsistent base calls. This corresponds to an error rate of 10.7% in a virtual mtDNA database consisting of the collaborative exercise results. However, this estimate is still conservative compared to conclusions drawn by authors of meanwhile numerous publications critically reviewing published mtDNA population databases. Our results and earlier published concerns strongly emphasize the need for appropriate safety regulations when mtDNA profiles are compiled for database purposes in order to accomplish the high standard required for mtDNA databases that are used in the forensic context.

Clinical Laboratory Techniques↗

PSSARD (2.0): a database server for making flexible queries relating amino acid sequences to main-chain secondary structure conformations for proteins of known three-dimensional structure and certain useful applications.

We have updated the Protein Sequence-Structure Analysis Relational Database (PSSARD) first published in the Int. J. Biol. Macromol. 36 (2005) 259-262 corresponding to 1573 representative protein chains selected from the Protein Data Bank (PDB). In this, the updated and revised PSSARD (Version 2.0), we have included all proteins in the Protein Data Bank available at the time of developing this database including the NMR PDB entries. The current database corresponds to 22,752 XRAY PDB entries and 3977 NMR PDB entries and is separated accordingly in order to facilitate the appropriate database search. The representative protein chains can also be separately accessed within the current database. We have made a provision to combine more than one field to query the database and the results of any search can be used to carry out further nested searches using a combination of queries. We have provided hyperlinks to the individual PDB entries obtained as the result of any search in PSSARD in order to obtain additional details relevant to the protein structure. Certain applications useful to identify domains and structural motifs are discussed.

Amino Acid Sequence↗

Developing a large electronic primary care database (Doctors' Independent Network) for research.

BACKGROUND AND OBJECTIVES: Primary care databases form a unique source of population-based clinical information on the prevalence and management of diagnosed disorders. Historically such databases have lacked individual level socio-economic markers. We describe the development of the Doctors' Independent Network (DIN) database for epidemiological and health services research. DIN includes a socio-economic marker (ACORN) based on postcode linkage at individual patient level. The validity of DIN is assessed against the General Practice Research Database (GPRD). METHODS: External validity is assessed by comparing the demographic structure and prevalence rates for treated ischemic heart disease (IHD) and treated hay fever with those from the GPRD. We assess the utility of a socio-economic measure (ACORN) based on postcode-linkage at individual patient level by examining the trend in prevalence rates of IHD and hay fever by ACORN index. RESULTS: 142 practices providing high quality data were selected, with 1827361 fully registered patients contributing data between 1992 and 2001, representing an identical age-sex structure to that for England & Wales and GPRD. Regionally adjusted prevalence of treated IHD (7.29 and 5.37%, respectively for men and women aged 35+ in 1998) in DIN was highly comparable to GPRD (7.27 and 5.42%). In DIN, the odds ratio of IHD was 1.37 (95% CI 1.30-1.44) in subjects living in "striving" compared to "thriving" areas. The prevalence of treated hay fever prevalence was similar across databases, with inverse associations seen with ACORN in DIN (higher rates in "thriving" areas). CONCLUSIONS: DIN provides comparable period prevalence rates to GPRD for two common conditions, with social trends as expected. Primary care databases such as these have the potential to replace the decennial national morbidity surveys carried out in UK general practices, with DIN having the important advantage of including a socio-economic index.

Adolescent↗

Ophthalmology and vision science research: part 5: surfing or sieving--using literature databases wisely.

Literature databases are an ever-expanding resource available to the field of medical sciences. Understanding how to use such databases efficiently is critical for those involved in research. However, for the uninitiated, getting started is a major hurdle to overcome and for the occasional user, the finer points of database searching remain an unacquired skill. In the fifth and final article in this series aimed at those embarking on ophthalmology and vision science research, we look at how the beginning researcher can start to use literature databases and, by using a stepwise approach, how they can optimize their use. This instructional paper gives a hypothetical example of a researcher writing a review article and how he or she acquires the necessary scientific literature for the article. A prototype search of the Medline database is used to illustrate how even a novice might swiftly acquire the skills required for a medium-level search. It provides examples and key tips that can increase the proficiency of the occasional user. Pitfalls of database searching are discussed, as are the limitations of which the user should be aware.

Biomedical Research↗

Development of a nosocomial outbreak investigation database.

A pilot web-based database was created to facilitate epidemiological investigation of nosocomial outbreaks. The database provides highly structured abstracts in a case study format to serve as a guide for investigations. Problems encountered in abstracting over 330 published reports included missing information and classification of study methods. The database offers a new way to review outbreaks, for example, in terms of their impact measured by various combinations of database fields, such as the number of cases, attack rate, pathogens, service/ward and mode of transmission. Feedback from users of the database suggests its usefulness. Creation of a large web-based database seems to be both desirable and feasible.

Abstracting and Indexing↗

A novel database of disulfide patterns and its application to the discovery of distantly related homologs.

Disulfide bonds are conserved strongly among proteins of related structure and function. Despite the explosive growth of protein sequence databases and the vast numbers of sequence search tools, no tool exists to draw relations between the disulfide patterns of homologous proteins. We present a comprehensive database of disulfide bonding patterns and a search method to find proteins with similar disulfide patterns. The disulfide database was constructed using disulfide annotations extracted from SwissProt, and was expanded significantly from 16,736 to 94,499 disulfide-containing domains by an inference method that combines SwissProt annotations with Pfam multiple alignments. To search the database, we define a disulfide description, called the disulfide signature, which encodes both spacings between cysteine residues and cysteine connectivity. A web tool was developed that allows users to search for related disulfide patterns and for subpatterns resulting from the removal of one or more disulfides from the pattern. We explore the possibility of using disulfide pattern conservation to identify protein homologs that are undetectable by PSI-BLAST. Examples include the homology between a sea anemone antihypertensive/antiviral protein and a sea anemone neurotoxin, and the homology between tick anticoagulant peptide and bovine trypsin inhibitor. In both examples, there is a clear structural similarity and a functional relationship. We used the database to find structural homologs for the Cripto CFC domain. The identification of a von Willebrand Factor C (VWFC)-like domain agrees with its functional role and explains mutation data. We believe that the rapid increase in structure determinations arising from structural genomics efforts and advances in mass spectrometry techniques will greatly increase the number of disulfide annotations. This information will become a valuable resource for structural and functional annotations of proteins. The availability of a searchable disulfide pattern database will thus provide a powerful new addition to existing homolog discovery methods.

Amino Acid Sequence↗

Percolation of annotation errors through hierarchically structured protein sequence databases.

Databases of protein sequences have grown rapidly in recent years as a result of genome sequencing projects. Annotating protein sequences with descriptions of their biological function ideally requires careful experimentation, but this work lags far behind. Instead, biological function is often imputed by copying annotations from similar protein sequences. This gives rise to annotation errors, and more seriously, to chains of misannotation. [Percolation of annotation errors in a database of protein sequences (2002)] developed a probabilistic framework for exploring the consequences of this percolation of errors through protein databases, and applied their theory to a simple database model. Here we apply the theory to hierarchically structured protein sequence databases, and draw conclusions about database quality at different levels of the hierarchy.

Amino Acid Sequence↗

Molecular immunology databases and data repositories.

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).

Allergy and Immunology↗