Biomedical subjects

P L Miller

Publications and source records attributed to P L Miller.

At least 19 recordsLinked to original sources

PubMed2004

Approaches and informatics tools to assist in the integration of similar clinical research questionnaires.

OBJECTIVE: The integration of similar clinical research questionnaires is a complex process that can benefit from informatics approaches and tools that provide a systematic structure for performing mapping and integration. This systematic approach is necessary to address complex issues in integration such as data heterogeneity, differing levels of granularity of questions and responses, and other issues involving semantic differences. Informatics tools and approaches have been successfully applied to various standard clinical vocabulary integration processes but not for questionnaire integration or mapping. METHODS: A systematic approach to questionnaire integration was developed in the context of a collaboration of researchers using Trial/DB, a database designed to support clinical research. This approach was applied to the integration of questionnaires involving breast cancer risk factors from each of three research sites. RESULTS: From 375 questions on the three original questionnaires, we identified 65 concepts that were measured by two or three of the sites. An algorithm was developed and used to formalize the process of mapping questions and answers across the questionnaires. The approach was applied to previously collected data and prospective data in disparate data-base systems to import and merge the data from these three sites into Trial/DB. CONCLUSION: Informatics tools that support a systematic approach to mapping questionnaires can be used throughout the research process from questionnaire integration and creation, legacy data integration to data library maintenance and curation.

Biomedical Research↗

PubMed2003

ALFRED: the ALelle FREquency Database. Update.

Elaboration of ALFRED (http://alfred.med.yale.edu) is being continued in two directions. One of which is developing tools for efficiently annotating the entries and checking the integrity of the data already in the database while the other is to increase the quantity and accessibility of data. Information contained in ALFRED such as, polymorphic sites, number of populations and frequency tables (one sample typed for one site) has significantly increased.

Alleles↗

PubMed2003

TrialDB: A web-based Clinical Study Data Management System.

Clinical Study Data Management Systems (CSDMSs) are a class of software that support centralized management of data generated during the conduct of clinical studies. Commercial CSDMSs include Oracle Clinical, ClinTrial and MetaTrial. Such systems, which are typically deployed at an institutional or organizational level, must accommodate diverse types of data from different clinical domains that is generated by different groups of clinical investigators. Large-scale CSDMSs typically employ a high-end database engine that is usually accessed over an intranet or the Internet using Web-based technologies. CSDMSs in institution-wide use for a variety of clinical domains are best served by entity-attribute-value (EAV) modeling for the clinical data: all the commercial CSDMSs that we are aware of use EAV design. However, de novo development of EAV databases for data management is a challenging task. A large body of generic metadata-driven code must be developed before a basic EAV application can be written. Clearly, the availability of pre-existing software with the requisite functionality would be very valuable. We will discuss the benefits of such software being in open-source form.

Clinical Trials as Topic↗

PubMed2001

ALFRED: an allele frequency database for diverse populations and DNA polymorphisms--an update.

ALFRED (the ALelle FREquency Database) is designed to store and disseminate frequencies of alleles at human polymorphic sites for multiple populations, primarily for the population genetics and molecular anthropology communities. Currently ALFRED has information on over 180 polymorphic sites for more than 70 populations. Since our initial release of the database we have focussed on increasing the quantity and quality of data, making reciprocal links between ALFRED and other related databases, and providing useful tools to make the data more comprehensible to the end user. ALFRED is accessible from the Kidd Lab home page (http://info.med.yale. edu/genetics/kkidd/) or from ALFRED directly (http://alfred.med.yale. edu/alfred/index.asp).

Alleles↗

PubMed2001

Exploring the utility of demographic data and vaccination history data in the deduplication of immunization registry patient records.

Duplicate patient records pose a major problem for many immunization registries, as well as for many electronic patient record systems. This paper reports two complementary studies exploring the deduplication of immunization registry records. One study explores the utility of different demographic data elements, singly and in combination, to assist in the deduplication process. The second study explores how clinical patient data (vaccination history data) might assist in this process. To assess the utility of demographic data elements, data were used from three registries after duplicates had been identified. A computer program, IMM/Scan, was written to count the number of true-positive (TP) matches and false-positive (FP) matches found when using different Boolean combinations of demographic data elements. In this study, a strategy of "ORing high value ANDed pairs of data elements" appeared to be most powerful. To assess the utility of vaccination history data, record pairs were drawn from 440,000 patient records. Two metrics on patient history were tested: (1) the number of identical doses shared by two records, and (2) the number of "extra" doses in the combined history of two records. In this study, sample findings include: (1) for pairs of nonduplicate records, 93% had no identical doses and 90.6% had "extra" doses, and (2) for pairs of duplicate records, 83.8% had one or more identical doses and 82% contained no "extra" doses. These studies demonstrate potentially useful approaches to using demographic data and patient history data to assist the automated deduplication of immunization patient records.

Demography↗

PubMed2001

Maintaining and incrementally revalidating a computer-based clinical guideline: a case study.

The paper explores the issues involved in maintaining the logic within a complex computer-based clinical guideline, using as a case study IMM/Serve, an operational guideline whose domain is childhood immunization. For a period of more than a year and a half, we have maintained a log of (1) the national changes to the immunization recommendations, (2) the local customizations of IMM/Serve's logic, and (3) certain logic problems that arose in the process of accommodating these changes and customizations. We describe the nature of these changes, customizations, and problems. We also discuss how different types of domain knowledge might assist in the automated process of validating successive versions of the logic. The paper's goal is to use the immunization domain to provide specific examples of the issues and problems that arise in maintaining a computer-based clinical guideline.

Child↗

PubMed2001

Issues in computer-based decision support in public health illustrated using projects involving childhood immunization.

The article discusses issues that arise in implementing computer-based decision support using childhood immunization as a source of examples. The examples include (1) IMM/Serve, a program that provides patient-specific recommendations, (2) informatics tools developed to help validate IMM/Serve's knowledge and functionality, and (3) tools developed to explore how computers can help ensure immunization data quality. Issues discussed include the complexity of creating computer-based decision support, the need for a continuing process of revision and testing as the health field evolves over time, and the potential value of computer-based tools to assist in this process.

Child↗

PubMed2000

Olfactory receptor database: a sensory chemoreceptor resource.

The Olfactory Receptor Database (ORDB) is a WWW-accessible database that has been expanded from an olfactory receptor resource to a chemoreceptor resource. It stores data on six classes of G-protein-coupled sensory chemoreceptors: (i) olfactory receptor-like proteins, (ii) vomeronasal receptors, (iii) insect olfactory receptors, (iv) worm chemo-receptors, (v) taste papilla receptors and (vi) fungal pheromone receptors. A complementary database of the ligands of these receptors (OdorDB) has been constructed and is publicly available in a pilot mode. The database schema of ORDB has been changed from traditional relational to EAV/CR (Entity-Attribute-Value with Classes and Relationships), which allows the interoperability of ORDB with other related databases as well as the creation of intra-database associations among objects. This inter-operability facilitates users to follow information from odor molecule binding to its putative receptor, to the properties of the neuron expressing the receptor, to a computational model of activity of olfactory bulb neurons. In addition, tools and resources have been added allowing users to access interactive phylogenetic trees and alignments of sensory chemoreceptors. ORDB is available via the WWW at http://ycmi.med. yale.edu/senselab/ordb/

Base Sequence↗

PubMed2000

ALFRED: an allele frequency database for diverse populations and DNA polymorphisms.

We have developed a publicly accessible database (ALFRED, the ALlele FREquency Database) that catalogues allele frequency data for a wide range of population samples and DNA polymorphisms. This database is web-accessible through our laboratory (Kidd Lab) Web site: http://info.med.yale.edu/genetics/kkidd. ALFRED currently contains data on 60 populations and 156 genetic systems including single nucleotide polymorphisms (SNPs), short tandem repeat polymorphisms (STRPs), variable number of tandem repeats (VNTRs) and insertion-deletion polymorphisms. While data are not available for all population-DNA polymorphism combinations, over 2000 allele frequency tables have been entered. Our database is designed (i) to address our specific research requirements as well as broader scientific objectives; (ii) to allow researchers and interested educators to easily navigate and retrieve data of interest to them; and (iii) to integrate links to other related public databases such as dbSNP, GenBank and PubMed.

Alleles↗

PubMed2000

IMM/Scrub: a domain-specific tool for the deduplication of vaccination history records in childhood immunization registries.

IMM/Scrub is a pilot tool developed to assist in the deduplication of vaccination history records in childhood immunization registries. This problem is complicated by a number of factors including that fact that: (1) some doses are numbered and some are not, (2) doses may have different dose numbers, (3) doses may specify different preparations within a vaccine series, (4) one dose may indicate a combination vaccine and the other dose may specify one component of that combination, (5) two doses may have slightly different dates, and (6) combinations of any of these problems may occur together. IMM/Scrub is designed to help detect 10 different types of vaccination dose duplicates and also allows the user to specify flexibly the conditions in which a duplicate dose might be automatically eliminated. In addition, IMM/Scrub is linked to the IMM/Serve immunization forecasting program, which can provide additional assistance in the data cleaning process. The paper describes (1) the design of the current pilot implementation of IMM/Scrub, (2) the lessons learned during its implementation, and (3) our preliminary experience applying it to data from three immunization databases, from a state, a metropolitan area, and an academic medical center.

Child↗

PubMed2000

Reengineering a database for clinical trials management: lessons for system architects.

This paper describes the process of enhancing Trial/DB, a database system for clinical studies management. The system's enhancements have been driven by the need to maximize the effectiveness of developer personnel in supporting numerous and diverse users, of study designers in setting up new studies, and of administrators in managing ongoing studies. Trial/DB was originally designed to work over a local area network within a single institution, and basic architectural changes were necessary to make it work over the Internet efficiently as well as securely. Further, as its use spread to diverse communities of users, changes were made to let the processes of study design and project management adapt to the working styles of the principal investigators and administrators for each study. The lessons learned in the process should prove instructive for system architects as well as managers of electronic patient record systems.

Clinical Trials as Topic↗

PubMed2000

ALFRED: a Web-accessible allele frequency database.

We present a Web-accessible database (ALFRED) that allows public access to gene frequency data for a diverse set of population samples and genetic systems. The data in ALFRED are modeled based on the experience and needs of a single laboratory, but with the expectation that the database will meet the needs of a much broader scientific community that needs population-specific gene frequency estimates. Our database currently contains data on more than 40 populations representing most major regions of the world and data on more than 150 genetic systems including SNPs, STRPs, and insertion-deletion polymorphisms. While data are not available for all population-genetic system combinations, over 2000 allele frequency tables already exist. In this paper, we enumerate the broad needs in the scientific domain, describe their significance, and describe how we have designed the database to meet those needs. We compare our database with dbSNP, the NCBI database that has a broader but overlapping purpose.

Alleles↗

PubMed2000

Using a computer database to monitor compliance with pharmacotherapeutic guidelines for schizophrenia.

OBJECTIVE: The study examined whether prescription data from a computerized database could be used to measure conformance with treatment recommendations of the Schizophrenia Patient Outcomes Research Team (PORT). METHODS: Records of an academically affiliated Veterans Affairs medical center were reviewed to identify patients who were hospitalized for schizophrenia and later seen for at least two outpatient visits in the six months after discharge (N=353). RESULTS: Conformance with only three of the 18 PORT pharmacotherapeutic recommendations could be measured with the available data. In regard to the recommendation to use antipsychotics other than clozapine as first-line treatments in acute episodes, 77 percent of the sample filled a prescription for an antipsychotic during the acute episode. Of these, only 6 percent received an antipsychotic regimen that included clozapine. In regard to the PORT recommendation on dosage during acute symptom episodes, 42 percent of the patients on conventional antipsychotics received dosages below the recommended range, 5 percent were above the range, and 53 percent were within it. In contrast, of the 53 patients who received clozapine or risperidone, 87 percent received prescriptions within the recommended dosage range. As for the recommendation to offer a trial of clozapine to patients who do not respond to adequate trials of two different classes of conventional drugs, 10 percent of patients who were switched from conventional regimens to clozapine were receiving dosages of conventional medications below the recommended range. CONCLUSIONS: Patient prescription data can provide preliminary measures to cost-effectively assess conformance with treatment. However, the approach has several limitations, and complementary analyses would enhance its usefulness.

Aged↗

PubMed2000

Informatics issues in the national dissemination of a computer-based clinical guideline: a case study in childhood immunization.

IMM/Serve is a computer-based guideline that provides patient-specific recommendations regarding childhood immunization. IMM/Serve is currently installed at an estimated 75 sites within the US Indian Health Service (IHS), with plans to extend its use to roughly 150 additional sites nationwide by the end of the year 2000. The dissemination of IMM/Serve within the IHS provides a case study with concrete examples that illustrate the diverse informatics issues that arise in the widespread dissemination of a computer-based clinical guideline.

Child↗

PubMed1999

Olfactory Receptor Database: a database of the largest eukaryotic gene family.

The Olfactory Receptor Database (ORDB) is a WWW-accessible database that stores data on Olfactory Receptor-like molecules (ORs) and has been open to the public since June 1996. It contains a public and a private area. The public area includes published DNA and protein sequence data for ORs, links to OR models and data on their expression, chromosomal localization and source organism, as well as (i) links to bibliography through PubMed and (ii) interactive WWW-based tools, such as BLAST homology searching. The private area functions as a service to laboratories that are actively cloning receptors. Source laboratories enter the sequences of the receptor clones they have characterized to the private database and can search for identical or near identical OR sequences in both public and private databases. If another laboratory has cloned and deposited an identical or closely matching sequence there are means for communication between the laboratories to help avoid duplication of work. ORDB is available via the WWW at http://crepe.med.yale.edu/ORDB/HTML

Animals↗

PubMed1999

Using semantic constraints to help verify the completeness of a computer-based clinical guideline for childhood immunization.

The paper describes Commander, a prototype computer program designed to help verify the completeness of a computer-based clinical practice guideline built using if then rules. It also describes the application of Commander to a guideline for childhood immunization. Commander is designed to help identify incomplete rule sets, where there are clinically meaningful conditions to which the guideline does not respond. To allow this, the user defines semantic constraints, in the form of if-then statements, which indicate combinations of conditions which are not meaningful. In an iterative process, Commander takes the guideline rules, together with an increasingly refined set of constraints and helps focus in on any combinations of conditions to which the guideline does not respond. When applied to the clinical guideline for childhood immunization, Commander was able to dramatically reduce the number of potential combinations of conditions for consideration and also identified several areas of incompleteness in the rules.

Child↗

PubMed1999

Measuring the effects of street pole banners on consumer awareness and preference.

The authors used a relatively new advertising medium to increase public awareness of their children's hospital. They found that street pole banners, a form of outdoor advertising, made a measurable, positive impression on consumer consciousness. Banners effectively supplemented a product awareness campaign that included more traditional media. This study is the first documentation of the use of banners to market health care services. Using a two-phase approach, respondents were surveyed via telephone before and after exposure. Results of the follow-up survey show significant increases in levels of awareness and preference. The authors hope their report on the successful use of street pole banners will spur further research on the use of this innovative media.

Advertising↗

PubMed1999

Exploring three approaches for handling incomplete patient histories in a computer-based guideline for childhood immunization.

A significant problem faced by immunization registries is that the dates of a patient's previous vaccinations may not be known. These incomplete histories can pose a problem when attempting to use a computer-based guideline to produce patient-specific immunization recommendations automatically. This paper describes an overall approach, together with 3 specific strategies, developed to help deal with this problem. The paper then describes our experience applying the approach to a database containing over 400,000 immunization histories. The paper also discusses a number of the issues raised in adapting a computer-based guideline to accommodate incomplete patient data of this sort.

Child↗