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PubMed1995

Challenges in integrating biological data sources.

Scientific data of importance to biologists reside in a number of different data sources, such as GenBank, GSDB, SWISS-PROT, EMBL, and OMIM, among many others. Some of these data sources are conventional databases implemented using database management systems (DBMSs) and others are structured files maintained in a number of different formats (e.g., ASN.1 and ACE). In addition, software packages such as sequence analysis packages (e.g., BLAST and FASTA) produce data and can therefore be viewed as data sources. To counter the increasing dispersion and heterogeneity of data, different approaches to integrating these data sources are appearing throughout the bioinformatics community. This paper surveys the technical challenges to integration, classifies the approaches, and critiques the available tools and methodologies.

Chromosomes, Artificial, Yeast↗

PubMed2006

Mapping data elements to terminological resources for integrating biomedical data sources.

BACKGROUND: Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration. METHODS: We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings. RESULTS: 82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed. CONCLUSION: Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources.

Abstracting and Indexing↗

PubMed1993

On the influence of data source in aggregated data studies: a comparative study of suicide information based on death certificates and judicial files.

STUDY OBJECTIVE: The aim was to assess the differences in suicide data obtained from different database sources. DESIGN: Death certificate based data on suicidal deaths were compared with the information obtained from the non-natural death investigation files at the Public Prosecutor's Office. SETTING: The study was confined to the time period of 1981-1984 and to the residents of the district of Leuven (Belgium) who died in the district. MAIN RESULTS: Differences were found in the number of suicidal deaths reported as well as in the demographic variables, the distribution of suicide methods, and the place of death. Sixty percent of the records in both databases could be matched for all variables studied (age, gender, civil state, place of death, and suicide method), and another 10% if only place of death was allowed to differ. For 4.5% of the cases in the judicial files and for 8% of the records in the official statistics database no corresponding record from the other data source could be found. Based on simple probability statistics [P(missing record)+P(different information[present)] the possible minimum global information bias could be estimated to range from 7 to 42%. CONCLUSIONS: Different epidemiological pictures of suicide mortality may result from studying different data sources.

Belgium↗

PubMedDate not supplied

The epidemiology of Parkinson's disease in the Republic of Ireland: observations from routine data sources.

Routine data sources can provide clues to the temporal and geographical patterns of Parkinson's disease. Mortality trends show divergent age specific rates, with decreasing mortality for younger age-groups and increasing mortality for older age-groups. Cohort analysis showed a pattern consistent with the hypothesis that Parkinson's disease may have increased after the encephalitis lethargica pandemic. Hospital admission data suggest a rural excess of cases. The interpretation of this finding is complicated by the role of a variety of potential biases. Research is needed to examine urban-rural differences and environmental risk factors.

Age Factors↗

PubMedDate not supplied

Corroboration of drug abusers' self-reports through the use of multiple data sources.

Multiple data sources were used to evaluate the validity of 31 drug abusers' self-reports of recent drug use as well as related behaviors occurring 1 year before and 1 year immediately after admission to a drug-free therapeutic community. Interviews were conducted by individuals not associated with the program. At the initial interview subjects provided a breath test for alcohol and a urine sample to test for other recent drug use. Subjects also signed releases of information so that official records could be checked both before and after admission to treatment to document any hospitalizations, arrests, drug treatment facility stays, and driver's license suspensions or revocations. These multiple data checks showed that drug abusers' self-reports of recent alcohol and drug use and of arrests and hospitalizations over a 2-year period are sufficiently valid for use in treatment outcome research. When differences occurred, it was usually due to subjects reporting more events than appeared on the records.

Adolescent↗

PubMedDate not supplied

[Fatal occupational accidents: estimates based on more data sources].

The data reported by INAIL (Istituto Nazionale Assicurazione Infortuni sul Lavoro) on fatal occupational injuries have always been considered complete and reliable. The authors of this article verified the completeness of this information source crossing it with data bases existing in different registration systems (Regional Mortality Registry of Tuscany--RMR; registers and data of the Operative Units of Prevention, Hygiene and Safety in the Workplace--UOPISLL) for the period between 1992 and 1996. In the five years concerned, a total of 458 cases were reported. These cases could be considered fatal injuries at work without taking into account traffic accidents, which were not included in the present study. The results show that the most complete information source was RMR, reporting 80% of the total data, while INAIL reports only 62.2% of the total cases. On the contrary, the UOPISLL source is the least reliable. Using the capture/recapture method, the estimate of events in the period concerned (1992-1996) amounts to nearly 500 (499.8 LC 475.9-523.7), while the three sources systematically explored for the whole period (INAIL, RMR, UOSPILL) report 458 cases. An additional information source, the daily press, which could be systematically tested only two months for each of the five years, reports 10 additional cases, which were ignored by the 3 other sources, indirectly confirming in this way how reliable the performed estimate was. The main cases among the 157 fatal accidents reported by RMR, but not by INAIL, occurred among farmers (70), most of them already retired, but there were several fatal accidents reported in the construction sector (30). Other categories were included only in the RMR data because, in the period concerned, they were not covered by INAIL insurance (18 cases in the Army and Police, 7 on the railways). The survey that was carried out confirms the essential importance of INAIL data for the surveillance system applied to this phenomenon. This also confirms the need--which has been already stressed in the scientific literature--to combine INAIL's registration system at least with the mortality registries. In this way the knowledge and comprehension of the phenomenon could be integrated and completed especially for marginal work areas, where obligatory insurance may be evaded; and for groups of workers not covered by insurance. The relevance of an integrated system of registration of occupational fatal accidents is discussed.

Accidents, Occupational↗

PubMed1987

New approaches to the estimation of migration flows from census and administrative data sources.

Census data represent an important source of information about migration flows. However, existing estimation procedures based on intercensal projection are often inconvenient to apply and are sensitive to even quite small changes in enumeration completeness. 2 new estimation procedures applicable to data from 2 censuses are developed and illustrated using US data. The 1st method is essentially a modification of traditional intercensal projection techniques, but as a result of working with age groups rather than cohorts, it is simpler to apply and allows mortality of the migrants to be incorporated over the intercensal period. The 2nd method also uses information from 2 censuses, but also uses independent information on the age pattern of migration from administrative sources or from other census questions. The method uses the fact that the age pattern of recent migration is likely to be different from the age distribution of the overall population to distinguish between intercensal change due to migration and apparent intercensal change due to changes in enumeration completeness. If the method's assumptions are met, it is possible to estimate the relative coverage of the 2 censuses as well as the scale of the independent age pattern of migration relative to the coverage of 1 or other of the censuses. The illustrative applications of the methods to US data suggest that both can work reasonably well.

Age Factors↗

PubMed2000

Epidemiological data sources in Estonia: a survey of registries and databases.

BACKGROUND: Central and Eastern European countries offer opportunities for studying the health effects of historical and present exposures, as well as the transition to a market economy. A prerequisite for research is the availability of good-quality information. This study was undertaken to describe sources of individual data that are available for epidemiological research in Estonia. Particular attention was paid to the methods of operation of health registries. METHODS: Information was collected during site visits, interviews with registry personnel and from published reports. For health registries, information was specifically requested on data collection, scope of recorded data, quality control, electronic linkage capability and use of data in research. RESULTS: The authors describe 35 data sources containing individual information on vital status, mortality, morbidity, natality and women's health, health and health care, and occupation. The most important health registries are the cancer registry, with data from 1968, and the medical birth registry, with data from 1992. Computerised cause-of-death information is available from 1983. Electronic linkage can be done with most of the data sources, the main matching variable being the eleven-digit personal identification number. Factors potentially affecting data-quality in health registries are undefined legal basis, scarcity of funding and staff, poor acknowledgement of problems, and rare scientific use of registry DISCUSSION: Various data sources are available for epidemiological research in Estonia. Thus far, collected data have largely been an under-used scientific resource. In health registries, more attention should be paid to quality control and continuous involvement of researchers.

Birth Certificates↗

PubMedDate not supplied

Evaluating the quality of sexual health care provided to adolescents in medicaid managed care: a comparison of two data sources.

This study compares 2 data sources to evaluate the quality of sexual health care provided to adolescents in Medicaid managed care: (a) Medicaid encounter data and (b) medical record data. Data from 1998 for 1112 adolescent enrollees came from 3 Seattle-area managed care organizations (MCOs): a group model health maintenance organization, an independent practice association, and a clinic network. Quality of care was tracked by estimating within-MCO chlamydia testing rates for sexually active female enrollees. Rates varied dramatically depending on which data source was used. Logistic regression models indicated substantially less difference between MCOs when analysis was based on data from the 2 sources combined than when based on either data source alone. Study results did not support the use of Medicaid encounter data as a sole data source for evaluating quality of adolescent sexual health care, despite the cost savings this would represent. However, encounter data, used as an adjunct to medical record review, may increase the reliability of quality evaluations.

Adolescent↗

PubMed2003

Occupational health of Southeast Asian immigrants in a US city: a comparison of data sources.

OBJECTIVES: This study sought to characterize occupational injury and illness cases identified through 3 different sources of data on a population of immigrant workers. METHODS: Participants were Cambodian and Lao workers living in Lowell, Mass. A household survey allowed comparisons between characteristics of work-related cases documented in workers' compensation wage replacement records and hospital records and characteristics of self-reported cases. RESULTS: The household survey captured types of cases missing from existing data, particularly illnesses self-reported to be associated with chemical exposures. Injuries and illnesses affecting the study population appeared to be significantly underrepresented in workers' compensation wage replacement data. CONCLUSIONS: Community-based methods can supplement available occupational health data sources.

Accidents, Occupational↗

PubMed1987

Records as a data source: the case for health visitor records.

Health records as a source of research data are examined. A case study approach is adopted to evaluate the reliability of health visitor records as a data source. It is argued that such records may be a rich source of epidemiological data although their deficiencies should be acknowledged.

Child↗

PubMed2004

Policy and environmental indicators for heart disease and stroke prevention: data sources in two states.

INTRODUCTION: Investigators in South Carolina and Alabama assessed the availability of data for measuring 31 policy and environmental indicators for heart disease and stroke prevention. The indicators were intended to determine policy and environmental support for adopting heart disease and stroke prevention guidelines and selected risk factors in 4 settings: community, school, work site, and health care. METHODS: Research teams used literature searches and key informant interviews to explore the availability of data sources for each indicator. Investigators documented the following 5 qualities for each data source identified: 1) the degree to which the data fit the indicator; 2) the frequency and regularity with which data were collected; 3) the consistency of data collected across time; 4) the costs (time, money, personnel) associated with data collection or access; and 5) the accessibility of data. RESULTS: Among the 31 indicators, 11 (35%) have readily available data sources and 4 (13%) have sources that could provide partial measurement. Data sources are available for most indicators in the school setting and for tobacco control policies in all settings. CONCLUSION: Data sources for measuring policy and environmental indicators for heart disease and stroke prevention are limited in availability. Effort and resources are required to develop and implement mechanisms for collecting state and local data on policy and environmental indicators in different settings. The level of work needed to expand data sources is comparable to the extensive work already completed in the school setting and for tobacco control.

Alabama↗

PubMed2006

Limitation of a single clinical data source for measuring physicians' performance on quality indicators.

OBJECTIVES: To determine the extent to which relying on only one source of data leads to incomplete assessment of pneumococcal polysaccharide vaccine (PPV) or mammography. DESIGN: Cross-sectional survey. SETTING: An urban Midwestern academic medical center in 1998/99. PARTICIPANTS: Medicare beneficiaries aged 65 and older with at least one health encounter. MEASUREMENTS: Completion of PPV and mammography was assessed using local and Medicare records. The study compared sources of records and assessed association between services and demographics and comorbidity. RESULTS: Adding Medicare data to local data increased the computed 1-year PPV from 8.8% (264/3,002) to 15.0% and increased the 1998/99 mammography rate from 40% (343/847) to 67%. Local data sources missed 40% of PPV and 39% of mammography; Centers for Medicare and Medicaid Services sources missed 50% of PPV and 2% of mammography. The vaccinated were younger than the nonvaccinated (74 vs 76, P<.001). African Americans and those with more comorbidity were less likely to receive PPV over 8 years. Of 555 patients with a Medicare record of mammography, whites and those without Medicaid were significantly less likely to have a local record of mammography (P<.001). CONCLUSION: Neither administrative nor local clinical records provide a complete or accurate assessment of these quality indicators. Accurate assessment of quality indicators requires pooling data from multiple sources across a broad region.

Aged↗

PubMed2002

Data sources: use in the epidemiologic study of medical devices.

Medical device epidemiology is the study of the prevalence and incidence of use, effectiveness, and adverse events associated with medical devices in a population. The identification of large data sources with medical device data provides a large population for epidemiologic studies. Two challenges in medical device epidemiology are the ability to find data on the specific device and the exposure of a patient to that device. This paper identifies data sources both from the govenment and from the private sector that can be used for epidemiologic studies of medical devices and, to a limited degree, studies of medical devices in women. Each source provides data for different types of devices and in differing specificity. The paper also discusses briefly the strengths and weaknesses of each data source. More data sources are needed to enhance the study of medical device epidemiology. Additional efforts and focus are needed to enhance the ability to study medical devices in women.

Centers for Disease Control and Prevention, U.S.↗

PubMed2001

New Jersey's electronic birth certificate program: variations in data sources.

OBJECTIVES: This study sought to determine primary sources of data for electronic birth certificates. METHODS: A survey was administered from 1997 through 1998 to maternity facilities in New Jersey requesting information about what primary information sources were used for 53 electronic birth certificate variables. Potential information sources included the facilities' maternal and infant medical records, the prenatal record, and a parent-completed birth certificate worksheet. RESULTS: Among the 66 maternity facilities responding, there was significant variation in the choice of primary data sources for the electronic birth certificate variables examined. CONCLUSIONS: The variability of primary sources for electronic birth certificate data acquisition represents a potential cause of systematic error in reported vital statistics information.

Birth Certificates↗

PubMed1999

Prescribing patterns in general practice. A comparison of two data sources.

OBJECTIVE: To compare data captured by an electronic general practice prescribing package with prescribing data from the Health Insurance Commission (HIC). METHODS: Twenty GPs from the Hunter Urban Division of General Practice (HUDGP) used the electronic prescribing package. Data for June-July 1996 were analysed. Prescribing data for all GPs (n = 369) in the HUDGP were extracted from HIC files to provide the comparison. RESULTS: Each data source had limitations, and provided different, but complementary information. HIC data allowed calculation of prescribing rates (prescriptions per 100 Medicare services), but had incomplete capture of information on some classes of drugs, and no information on the patients receiving the drugs or the indications for the use of the drugs. The HUDGP database could only provide information on choice of agent when the decision to prescribe something had been made. However, it provided the context information (patient characteristics, indication for use, other medications) that could permit some assessment of the appropriateness of therapy. CONCLUSIONS: HIC data may be useful for an overall assessment of divisional activities. However, for a full assessment of the quality of prescribing at the level of individual GPs, additional patient related information is required. This requires much wider use of electronic prescribing packages that can capture the clinical details needed to review the appropriateness of treatment decisions.

Australia↗

PubMed2004

GDPC: connecting researchers with multiple integrated data sources.

UNLABELLED: The goal of this project is to simplify access to genomic diversity and phenotype data, thereby encouraging reuse of this data. The Genomic Diversity and Phenotype Connection (GDPC) accomplishes this by retrieving data from one or more data sources and by allowing researchers to analyze integrated data in a standard format. GDPC is written in JAVA and provides (1) data sources available as web services that transfer XML formatted data via the SOAP protocol; (2) a JAVA API for programmatic access to data sources; and (3) a front-end application that allows users to manage data sources, retrieve data based on filters, sort/group data based on property values and save/open the data as XML files. AVAILABILITY: The source code, compiled code, documentation and GDPC Browser are freely available at: www.maizegenetics.net/gdpc/index.html the current release of GDPC is version 1.0, with updated releases planned for the future. Comments are welcome.

Database Management Systems↗

PubMed2005

An innovative approach to enhancing the surveillance capacity of state-based diabetes prevention and control programs: the Diabetes Indicators and Data Sources Internet Tool (DIDIT).

The Diabetes Indicators and Data Sources Internet Tool (DIDIT) is an interactive Web-based resource with information on 38 diabetes indicators (e.g., diabetes-associated complications, care, lifestyle) and 12 associated data sources frequently used by state diabetes prevention and control programs. This tool is designed to strengthen the ability of states to conduct diabetes surveillance and to promote consistency in defining and tracking indicators across states. In this way, the DIDIT supports one of the 10 essential public health services: the timely and accurate assessment of public health. In addition to serving as a central repository of information on diabetes surveillance, the DIDIT also allows users to share experiences of using these indicators and data sources in their diabetes surveillance activities, data analysis, and tracking of diabetes-related objectives stated by Healthy People 2010. The DIDIT is an innovative approach to enhancing public health surveillance at the state and national levels.

Delphi Technique↗