PubMed Health⌕ Search

Biomedical subjects

K H Cheung

Publications and source records attributed to K H Cheung.

10 recordsLinked to original sources
PubMed1998

A metadata approach to query interoperation between molecular biology databases.

MOTIVATION: Molecular biology databases have been proliferating rapidly. Their heterogeneity and complexity pose a great challenge to efforts in database interoperation. To minimize the efforts of interoperating heterogeneous databases, it is useful to develop a system that lets a user of a particular genomic database access another related database as if the latter is structurally similar to the former. RESULTS: We extend a structurally simple model-the entity-attribute-value (EAV) model-to describe uniformly metadata relating to individual databases. Such metadata, which are necessary for performing database comparisons, include descriptions of primitive database objects (including entities, attributes, domain values and entity relationships) and specification of correspondences among the database objects. We show how to decompose SQL queries and map them from one database to another based on the EAV representation of the basic database objects. A prototype system is implemented to demonstrate query interoperation between two chromosome map databases. AVAILABILITY: Freely available (Cold Fusion source code and an Access database containing the mapping knowledge) upon request from the author. CONTACT: kei.cheung@yale.edu

Chromosome Mapping↗
PubMed1998

Automatic query mapping among genomic databases: a pilot exploration.

As databases in the human genome project proliferate, it is important for users of one genomic database to identify similar or inconsistent data in other autonomously developed genomic databases. To do so, the user needs to issue the same query across multiple databases. We describe an approach that allows a query issued against one database to be automatically mapped to an equivalent query against another structurally different database. Our approach features two components: 1) a database designed to capture knowledge (metadata) that describes the correspondences among individual database components and 2) a module that utilizes the metadata to perform query mappings. As a demonstration, we apply our query mapping approach to two chromosome map databases (DB/12 and GDB).

Algorithms↗
PubMed1996

PhenoDB: an integrated client/server database for linkage and population genetics.

In this paper we describe PhenoDB, an Internet-accessible client/server database application for population and linkage genetics. PhenoDB stores genetic marker data on pedigrees and populations. A database for population and linkage genetics requires two core functions: data management tasks, such as interactive validation during data entry and editing, and data analysis tasks, such as generating summary population statistics and performing linkage analyses. In PhenoDB we attempt to make these tasks as easy as possible. The client/server architecture allows efficient management and manipulation of large datasets via an easy-to-use graphical interface. PhenoDB data (73 populations, 34 pedigrees, approximately 4200 individuals, and close to 80,000 typings) are stored in a generic format that can be readily exported to (or imported from) the file formats required by various existing analysis programs such as LIPED and Lathrop and Lalouel's Multipoint Linkage. PhenoDB allows performance of complex ad-hoc queries and can generate reports for use in project management. Finally, PhenoDB can produce statistical summaries such as allele frequencies, phenotype frequencies, and Chi-square tests of Hardy-Weinberg ratios of population/pedigree data.

Alleles↗
PubMed1996

DNA workbench: a database package to manage regional physical mapping.

DNA Workbench (DW) is a client-server database to manage physical mapping data that will form the basis for sequencing and efforts in biologically interesting regions of a chromosome. DW draws maps at different levels of resolution in either of two modes: proportional, when the sizes of objects and the physical distances between them are known accurately or approximately, and nonproportional, when most physical distance information in a region is not available, but order information is. DW interacts with the user primarily through the map graphic. Selection of individual objects on the graphic lets the user inspect and modify the underlying data. DW also manages dependency tracking between map objects and has a rudimentary form of version control. It is currently used to manage information on the DRD2 region on chromosome 11, and on the HOX region of chromosome 17.

Chromosome Mapping↗
PubMed1995

SQLGEN: a framework for rapid client-server database application development.

SQLGEN is a framework for rapid client-server relational database application development. It relies on an active data dictionary on the client machine that stores metadata on one or more database servers to which the client may be connected. The dictionary generates dynamic Structured Query Language (SQL) to perform common database operations; it also stores information about the access rights of the user at log-in time, which is used to partially self-configure the behavior of the client to disable inappropriate user actions. SQLGEN uses a microcomputer database as the client to store metadata in relational form, to transiently capture server data in tables, and to allow rapid application prototyping followed by porting to client-server mode with modest effort. SQLGEN is currently used in several production biomedical databases.

Computer Communication Networks↗
PubMed1992

Fuzzy classification of hemodynamic trends and artifacts: experiments with the heart rate.

Fuzzy set theory allows one to map inexact data, concepts, and events to fuzzy sets via user-defined membership functions. This paper describes a method for (1) robustly estimating the mean and slope of an arbitrary number of data points, (2) developing a set of fuzzy membership functions to classify various properties of heart rate trends, and (3) finding the longest consecutive sequence of heart rate data that fit a particular fuzzy membership function. Preliminary results indicate that fuzzy set theory has significant potential in the development of a clinically robust method for classifying heart rate data, trends, and artifacts.

Data Interpretation, Statistical↗
PubMed1992

A parallel implementation of a multi-state Kalman filtering algorithm to detect ECG arrhythmias.

Detecting arrhythmias from the electrocardiogram (ECG) is of great importance for the continued development of intelligent cardiovascular monitors (ICM). An ICM's main goal is to present to the clinician a 'high-level' analysis of the patient's condition (e.g., the patient is slightly hypovolemic) based upon 'low-level' physiologic signals (e.g., blood pressure, heart rate, etc.). This paper reports on a parallel implementation of a multi-state Kalman filtering algorithm, within a prototype ICM, to help detect ECG arrhythmias. Preliminary test results show that the parallel, multi-state implementation performed exactly as the original sequential version. Several different rhythm disturbances were correctly identified after 3-5 beats. We conclude that our parallel implementation of the multi-state Kalman filter provides a faster and still reliable means of accurately detecting ECG arrhythmias in real-time.

Algorithms↗
PubMed1992

Online bibliographic information: integration into an emerging IAIMS environment.

The Medical Library at Yale University has developed an online free-text database containing Current Contents citations. The database was designed to be integrated into an emerging campus-wide information environment. To this end Current Contents at Yale was designed with a user interface familiar to the Yale community, an alerting service based on electronic mail, and search expansion using the National Library of Medicine's Meta-1 metathesaurus.

Consumer Behavior↗