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PubMed1994

Building a Database of Data Sets for Health Services Research.

The Database of Data Sets (DB/DS) for Health Services Research will be an online searchable directory of data sets which are available, often with restrictions and confidentiality safeguards, for use by health care researchers. The DB/DS project is aimed at a wide audience, and intends to include a very broad range of health care data sets, ranging from state hospital discharge data bases, to national registries and health survey data sets, to institutional clinical databases. The intended users are the same community of researchers, policy-makers, administrators and practitioners who are served by the National Library of Medicine's current bibliographic databases. This paper describes a pilot phase of the DB/DS project in which the issues involved in creating such a database were explored with an initial set of 20 representative data sets.

Databases, Factual↗

PubMed1993

Desperately seeking data: knowledge base-database links.

Linking a knowledge-based system (KBS) to a clinical database is a difficult task, but critical if such systems are to achieve widespread use. The Columbia-Presbyterian Medical Center's clinical event monitor provides alerts, interpretations, research screening, and quality assurance functions for the center. Its knowledge base consists of Arden Syntax Medical Logic Modules (MLMs). The knowledge base was analyzed in order to quantify the use and impact of KBS-database links. The MLM data slot, which contains the definition of these links, had almost as many statements (5.8 vs. 8.8, ns with p = 0.15) and more tokens (122 vs. 76, p = 0.037) than the logic slot, which contains the actual medical knowledge. The data slot underwent about twice as many modifications over time as the logic slot (3.0 vs. 1.6 modifications/version, p = 0.010). Database queries and updates accounted for 97.2% of the MLM's total elapsed execution time. Thus, KBS-database links consume substantial resources in an MLM knowledge base, in terms of coding, maintenance, and performance.

Academic Medical Centers↗

PubMed1993

Creation of state-level Medicare database for healthcare evaluation applications.

The Health Care Quality Improvement Initiative (HCQII) of the Health Care Financing Administration (HCFA) calls for Professional Review Organizations (PROs) to undertake pattern analysis of large administrative datasets for the purposes of quality of care assessment. The limitations of such administrative databases (primarily the MEDPAR file and derivatives thereof) include impoverished information regarding clinical attributes of Medicare enrollees and the process and outcome of their healthcare. This paper describes preliminary efforts to address this problem by the creation of a database, the PRO Concatenated Database (PCD), from the pooled implicit judgment review data of four Peer Review Organizations (PROs). The data elements comprising the PCD were carefully selected to provide important information regarding quality and appropriateness of care. Preliminary inter-state comparative studies employing the PCD are discussed. A method is also described by which the analytical power of state-level databases may be enhanced by linkage to state-level Modeled MEDPAR data which are issued by HCFA and contain patient-level risk-adjusted mortality data. This approach to the acquisition of data whose clinical content is enriched may prove to be particularly useful to the PRO community during the pattern analysis phase of the HCQII. Such analyses will evolve into more detailed studies involving primary data collection followed by dissemination of the results to local healthcare providers. In this manner, the PCD may facilitate rapid feedback regarding the effectiveness of healthcare delivery to the local community.

Aged↗

PubMed1993

The contemporary AIDS database and brain bank--lessons from the past.

This paper addresses the issues in establishing a contemporary AIDS Brain Bank with a Database. It draws comparisons from the past when a similar approach was made towards the understanding of mental illness and its treatment. The aim of the Brain Bank is to provide a comprehensive range of neuropathologically characterised tissues from the nervous system to researchers and scientists as a resource for research. The aim of the Database is to provide the up-to-date clinical and pathological information relating to the material supplied by the Brain Bank. The paper describes the mechanics of establishing the Database, the importance of efficiency as well as discussing the sensitive issues that need to be addressed when designing and AIDS Database and Brain Bank.

Acquired Immunodeficiency Syndrome↗

PubMed1993

[Development of an anesthesia ledger using relational database].

An anesthesia ledger was developed using relational database KIRI Ver3. This anesthesia database includes 33 items for input, for example patient's name, patient's I.D. number, data of operation, diagnosis, operative procedure, name of surgeon, name of anesthesiologists and so on. One can select data from displayed menu cards only by rolling down or rolling up the cursor at 19 items and can input numbers by keyboard at twelve items. Even a computer beginner can easily operate it after a minimal training. Only patient's name must be input by text style. We can construct this anesthesia database only by use of functions of KIRI Ver3 without programming. One can use this anesthesia ledger at any operative facilities by changing a part of database and a file of doctor's name.

Anesthesia↗

PubMed1993

A comprehensive evaluation of family history and breast cancer risk. The Utah Population Database.

OBJECTIVE: The purpose of this study is to assess the impact of family history on the risk of developing breast cancer. DESIGN: A case-control study design was used. SETTING: To provide a comprehensive assessment of family history risk, we used the Utah Population Database, a linked database compiled of genealogy data of the descendants of Mormon pioneer families, cancer data from the Utah Cancer Registry, and mortality data from the Utah Department of Vital Statistics. PATIENTS: All women diagnosed with breast cancer who were in the genealogy database and the Utah Cancer Registry were included. Controls were women selected from the genealogy, who like cases had no record of previous cancer. They were matched to the cases by age and place of birth. OUTCOME: Several definitions of family history were used. The total familial risk variable, developed to work effectively in the Utah Genealogy Database, accounts for all family members, their degree of relatedness to the case, and the amount of time they were observed for possible cancer diagnosis. RESULTS: A threefold increase in risk, estimated by the odds ratio (OR), of breast cancer among those with the highest family history score (6% of cases) was observed when compared with those with the lowest family history score. The OR for women with a first-degree relative with breast cancer was 2.45 (95% confidence interval [CI], 1.84 to 3.06). If the nearest relative was a second-degree relative, the OR was 1.82 (95% CI, 1.39 to 2.24); if the nearest relative was a third-degree relative, the OR was 1.35 (95% CI, 1.07 to 1.64). A slightly greater risk was observed if the first-degree relative was a woman's mother (OR, 2.44; 95% CI, 1.77 to 3.42) rather than a sister (OR, 2.01; 95% CI, 1.66 to 2.43). Among subjects diagnosed before the age of 50 years, the disease experience of relatives prior to age 50 was most important, while for older subjects the experience of relatives of all ages was of roughly equal importance. Women who developed contralateral breast cancer within 3 years of initial diagnosis were nearly 10 times as likely as women without breast cancer to have a first-degree relative with breast cancer. Based on the risk estimates in this study, we have estimated that approximately 17% to 19% of breast cancer in the population could be attributed to family history. Women who had a first-degree relative with colon cancer had a 30% increased risk of breast cancer. CONCLUSIONS: In this study population, women with a family history of breast cancer, even if the nearest relative with breast cancer is a third-degree relative, are at increased risk of the disease.

Adult↗

PubMed1996

Discovering empirically conserved amino acid substitution groups in databases of protein families.

This paper introduces a method for identifying empirically conserved amino acid substitution groups. In contrast with existing approaches that view amino acid substitution as a pairwise phenomenon, the method presented here identifies conserved groups of amino acids using a data structure called a conditional distribution matrix. The conditional distribution matrix extends the concept of a pairwise substitution matrix by changing the context of substitution from a single amino acid to a group of amino acids. The matrix tabulates information from a database of protein families that contains numerous aligned positions. Each row in the matrix contains the distribution of amino acids in those aligned positions that contain a given conditioning group of amino acids. The method converts a database of protein families into a conditional distribution matrix and then examines each possible substitution group for evidence of conservation. The algorithm is applied to the BLOCKS and HSSP databases. Twenty amino acid substitution groups are found to be conserved empirically in both databases. These groups provide insight into biochemical properties that are conserved in protein evolution.

Algorithms↗

PubMed1996

The project ARIANE: conceptual queries to information databases.

As information databases we consider all the collections of data records indexed by key-words, stored and delivered by computer systems. In previous research works we demonstrated the interest to design a conceptual model, in the conceptual graphs formalism, and to implement a computational model for information retrieval in large information databases. These models are based on the UMLS knowledge sources. This paper reminds briefly these models and describes tests done in querying a patients database and a bibliographical database.

Databases, Bibliographic↗

PubMedDate not supplied

The development of The Society of Thoracic Surgeons voluntary national database system: genesis, issues, growth, and status.

BACKGROUND: The purpose of this communication is to demonstrate the feasibility of a voluntary national cardiac surgical database. METHODS: The genesis of the Society of Thoracic Surgeons (STS) National Cardiac and General Thoracic Surgery Databases in the interval of 1986 to 1990 is described. The issues facing the Committee in the initial decision making processes are discussed choosing a society-based, in-house activity versus using an outside vendor, private practice needs versus academic ones; open versus closed membership and vendors, risk stratification; data quality; audit; and access to data. RESULTS: In the 6 years of operation the STS cardiac surgical database has grown from 41,000 to 706,000 patients. The number of practice groups, hospitals, and surgeons has increased from 26 to 624, 32 to 750, and 120 to 1850, respectively. All but one state is represented, as are more than 400 teaching hospitals, including 28 Veterans Administration hospitals and 60 university centers. CONCLUSIONS: The STS database system has become firmly established and is a model for other societies and associations. The data placed yearly in the public domain have become a national standard.

Cardiology Service, Hospital↗

PubMed1997

Modelling antibody side chain conformations using heuristic database search.

We have developed a knowledge-based system which models the side chain conformations of residues in the variable domains of antibody Fv fragments. The system is written in Prolog and uses an object-oriented database of aligned antibody structures in conjunction with a side chain rotamer library. The antibody database provides 3-dimensional clusters of side chain conformations which can be copied en masse into the model structure. The object-oriented database architecture facilitates a navigational style of database access, necessary to assemble side chains clusters. Around 60% of the model is built using side chain clusters and this eliminates much of the combinatorial complexity associated with many other side chain placement algorithms. Construction and placement of side chain clusters is guided by a heuristic cost function based on a simple model of side chain packing interactions. Even with a simple model, we find that a large proportion of side chain conformations are modelled accurately. We expect our approach could be used with other homologous protein families, in addition to antibodies, both to improve the quality of model structures and to give a "smart start" to the side chain placement problem.

Algorithms↗

PubMed1997

A UMLS-based method for integrating information databases into an Intranet.

The Internet and the World Wide Web provide today end-users with capabilities to access universally to information in various and heterogeneous databases. The biomedical domain benefits from this new technology, specially for information retrieval by searching and browsing various sites. Nevertheless, end-users may be disoriented by specific ways to access information on different servers. In the framework of an Intranet design and development, we present a method for integrating information databases based on knowledge sources of the UMLS. The method provides designers of a Web site with facilities to implement an easy and homogeneous access to information. The pages are built dynamically and displayed according to a style sheet and their content stored in a database during the design phase. The database also describes the links between pages. Moreover, this organization provides administrators with powerful capabilities to manage Web sites.

Databases as Topic↗

PubMed1998

[Organization and quality control of a clinical database on intensive care medicine in central and suburban Paris].

BACKGROUND: Epidemiology and medical care appraisal of intensive care medicine relies on the homogeneity of information systems. This work is about a collaborative database related to intensive care units in Paris and its suburb. METHODS: A college of intensivists defined a standard dataset about stays, outcomes, severity of illness, diagnoses and work load, which are collected and analysed by a data management center. A quality control of the database was performed on a random sample of 199 stays. RESULTS: In 1996, 25 intensive care units participated in the database which encompassed more than 35,000 stays. The control of data quality showed a good reliability of data about stays, severity and workload but reproducibility of diagnosis coding has to be improved by means of more accurate coding guidelines. CONCLUSION: This database of case-mix and outcome information allows comparison and medical care appraisal of intensive care units.

Critical Care↗

PubMed1998

Medical reference databases used by Army primary care physicians in field environments.

A cross-sectional survey of U.S. Army primary care physicians was done to answer two questions: (1) which medical reference materials are Army primary care physicians currently using when deployed to a field environment? and (2) what would they like to have for medical reference in a field environment? Of 740 surveys delivered to their intended recipients, 445 (60%) were returned. Currently, 96% of primary care physicians use books, 37% use journals, and 11% use computer software in their medical reference database. Of those now using books, 72% were satisfied with them, compared with 61% of those using journals and 45% of those using software. The most common book used was the Merck Manual. The most important characteristics desired in a field medical database were broad coverage, ease of use, and light weight. The majority of respondents believe that a good medial reference database is important but that current medical databases limit the quality of the medicine they practice in the field.

Attitude of Health Personnel↗

PubMed1998

Design and development of a multimedia database for emergency telemedicine.

Recent studies conclude that early and specialised pre-hospital patient management contributes to emergency cases survival. Recent developments in telecommunication and medical informatics by means of telemedicine can be extremely useful to accomplish such tasks in a cost-effective manner. Along that direction, we have designed a portable device for emergency telemedicine. This device is able to telematically "bring" the expert doctor at the emergency site, have him perform an accurate diagnosis, and subsequently direct the Emergency Medical Technicians on how to treat the patient until he arrives to the hospital. The need for storing and archiving all data being interchanged during the telemedicine sessions is very crucial for clinical, legal and administrative purposes. For this, we have developed a multimedia database able to store and manage the data collected by the AMBULANCE system. The database was equipped with a user-friendly graphical interface to enable use from computer naive users. Furthermore, the database has the possibility to display, in an standard way, ECG's, X-ray, CT and MRI images. The application is password protected with a three-level hierarchy access for users with different privileges. The scope of this application is to enhance the capabilities of the doctor on duty for a more precise and prompt diagnosis. The application has the ability to store audio files related to each emergency case and still images of the scene. Finally, this database can become a useful multimedia tool which will work together with the AMBULANCE portable device, the HIS and the PACS of the hospital. The system has been validated in selected non-critical cases and proved to be functional and successful in enhancing the ability of the doctor's on duty for prompt and accurate diagnosis and specialised pre-hospital treatment.

Ambulances↗

PubMedDate not supplied

A brain image database for structure/function analysis.

BACKGROUND AND PURPOSE: Lesion-deficit-based structure-function analysis has traditionally been empirical and nonquantitative. Our purpose was to establish a new brain image database (BRAID) that allows the statistical correlation of brain functional measures with anatomic lesions revealed by clinical brain images. METHODS: Data on 303 participants in the MR Feasibility Study of the Cardiovascular Health Study were tested for lesion/deficit correlations. Functional data were derived from a limited neurologic examination performed at the time of the MR examination. Image data included 3D lesion descriptions derived from the MR examinations by hand segmentation. MR images were normalized in-plane using local, linear Talairach normalization. A database was implemented to support spatial data structures and associated geometric and statistical operations. The database stored the segmented lesions, patient functional scores, and several anatomic atlases. Lesion-deficit association was sought by contingency testing (chi2-test) for every possible combination of each neurologic variable and each labeled atlas structure. Significant associations that confirmed accepted lesion-deficit relationships were sought. RESULTS: Two-hundred thirty-five infarctlike lesions in 117 subjects were viewed collectively after mapping into Talairach cartesian coordinates. Anatomic structures most strongly correlated with neurologic deficits tended to be situated in anatomically appropriate areas. For example, infarctlike lesions associated with visual field defects were correlated with structures in contralateral occipital structures, including the optic radiations and occipital gyri. CONCLUSION: Known lesion-deficit correlations can be established by a database using a standard coordinate system for representing spatial data and incorporating functional and structural data together with appropriate query mechanisms. Improvements and further applications of this methodology may provide a powerful technique for uncovering new structure-function relationships.

Brain↗

PubMedDate not supplied

Development of a computerized database for evaluation of nurse practitioner student clinical experiences in primary health care. Report of three pilot studies.

A computerized database for the collection of patient encounter information by nurse practitioner students provides insight into the number and diversity of cases seen. Menu-driven data entry and controlled vocabulary in the form of diagnostic clusters provide a mechanism to categorize and analyze the data. Faculty are able to review student clinical experience by quantitative measures such as number of patient encounters, diagnostic cluster of the encounter, and patient demographic data. Qualitative measures such as student's level of responsibility and student prior experience with stated encounter also are included in the database. Data analysis of two interdisciplinary pilots provided comparisons across disciplines of nursing, medicine, and physical therapy. A subsequent nurse practitioner student pilot provided further refinement and a broadened database terminology more inclusive of a nursing perspective. Educational and clinical issues involved in development, maintenance, and future use of the database are discussed.

Clinical Competence↗

PubMed2005

Ranking the whole MEDLINE database according to a large training set using text indexing.

BACKGROUND: The MEDLINE database contains over 12 million references to scientific literature, with about 3/4 of recent articles including an abstract of the publication. Retrieval of entries using queries with keywords is useful for human users that need to obtain small selections. However, particular analyses of the literature or database developments may need the complete ranking of all the references in the MEDLINE database as to their relevance to a topic of interest. This report describes a method that does this ranking using the differences in word content between MEDLINE entries related to a topic and the whole of MEDLINE, in a computational time appropriate for an article search query engine. RESULTS: We tested the capabilities of our system to retrieve MEDLINE references which are relevant to the subject of stem cells. We took advantage of the existing annotation of references with terms from the MeSH hierarchical vocabulary (Medical Subject Headings, developed at the National Library of Medicine). A training set of 81,416 references was constructed by selecting entries annotated with the MeSH term stem cells or some child in its sub tree. Frequencies of all nouns, verbs, and adjectives in the training set were computed and the ratios of word frequencies in the training set to those in the entire MEDLINE were used to score references. Self-consistency of the algorithm, benchmarked with a test set containing the training set and an equal number of references randomly selected from MEDLINE was better using nouns (79%) than adjectives (73%) or verbs (70%). The evaluation of the system with 6,923 references not used for training, containing 204 articles relevant to stem cells according to a human expert, indicated a recall of 65% for a precision of 65%. CONCLUSION: This strategy appears to be useful for predicting the relevance of MEDLINE references to a given concept. The method is simple and can be used with any user-defined training set. Choice of the part of speech of the words used for classification has important effects on performance. Lists of words, scripts, and additional information are available from the web address http://www.ogic.ca/projects/ks2004/.

Abstracting and Indexing↗

PubMed2005

PRIME: automatically extracted PRotein Interactions and Molecular Information databasE.

With the exponentially increasing amount of information in the biomedical field, the significance of advanced information retrieval and information extraction, as well as the role of databases, has been increasing. PRIME is an integrated gene/protein informatics database based on natural language processing. It provides automatically extracted protein/family/gene/compound interaction information including both physical and genetic interactions, gene ontology based functions, and graphic pathway viewers. Gene/protein/family names and functional terms are recognized based on dictionaries developed in our laboratory. The interaction and functional information are extracted by syntactic dependencies and various phrase patterns. We have included about 920,000 (non-redundant) protein interactions and 360,000 annotated gene-function relationships for major eukaryotes. By combining the sequence and text information, the pathway comparison between two organisms and simple pathway deduction based on other organism interaction data, and pathway filtering using tissue expression data, are also available. This database is accessible at http://prime.ontology.ims.u-tokyo.ac.jp:8081.

Abstracting and Indexing↗