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MICROCOMPUTER-BASED GENETICS OFFICE DATABASE SYSTEM
James H. Cutts III, M.Sc., Joyce A. Mitchell, Ph.D.
Information Science Group, 605 Lewis Hall University of Missouri - Columbia, Missouri 65211
Abstract A database
information, and (4) review past clinical experience as a diagnostic and research tool. The
management system (Genetics Office Automation System, GOAS) has been developed for the Medical Genetics Unit of the University of Missouri. The system, which records patients' visits to the Unit's genetic and prenatal clinics, has been implemented on an IBM PC/XT microcomputer. A description of the system, the reasons for implementation, its databases, and uses are presented.
GOAS is amenable to expansion.
Implementation of the Genetics Office Automation System The minimum hardware requirements for GOAS are 256K bytes of RAM and a hard disk on an IBM PC (or compatible) computer. A method for backing-up the data is necessary, usually floppy disks. The hard disk is essential since GOAS uses 93 files, all of which must be available continuously. This tremendous disk storage requirement precludes the use of floppies. Any memory above the 256K minimum can be used by other programs designed to be executed from within GOAS.
Introduction A prime ability of modern computers is management of large amounts of data and extraction of the
specific information of interest from a large collection of related facts. In the field of Medical Genetics, large volumes of data are collected for each patient. For these data to become useful information, they must be accessible in an timely and orderly fashion.
Two software packages are required to run GOAS in the Genetics Clinic office: dBase III and Incremental Backup Utility (IBU). GOAS was written in dBase III. IBU backs-up only those files that have been changed since the last back-up. It differs from the PC-DOS BACKUP in the way that it determines which files need to be copied. It uses special flags, stored in the directory entry of each file, which are set each time the file is modified and reset when backed-up. IBU compares the dates of the file modification with the dates on the backup disk. Use of IBU allows two alternating backup disks, each of which has all the new data since the last time they were used for backup.
Most information management systems developed for Genetics offices and 5linics require the use of With the advent of mainframe computers ' .
increasingly powerful desk-top microcomputers, complete database management systems have been developed to operate within the Genetics office. Some of these packages are designed for3specific purposes, such as pedigree management , while others arfe more generalized but require special equipment . The GOAS described here is designed to run on an IBM PC/XT with a minimum of 256K Random Access Memory (RAM), a ten megabyte hard disk and one floppy disk drive. GOAS is written in the procedural language of a commercially ava+able database management software (dBase III ). The system is designed to meet the needs of the Medical Genetics Unit at the University of Missouri, but the basic design is readily adaptable to similar environments .
Databases of the Genetics Office Automation System Each of the 24 databases in GOAS can be defined as either a Primary or a Reference database (Figure 1). The primary databases contain patient data. Reference databases contain information which is referred to by. records in the primary databases. Every record in each database is assigned a unique, six digit number. These record numbers index the database to allow quick and efficient access to any record and link the various databases together. Since the record number is stored in the primary database and is used as a "pointer", the reference record can be found easily but requires only six bytes of storage in the primary database. Furthermore, records in a primary database do not need to repeat information
The basic motivation in system design was to organize patient data into useful information. Specific goals were to (1) collect statistical data for internal use and for reports to funding
agencies, (2) facilitate follow-up on patients by generating reports that contain the latest patient information, (3) ease record management by providing a single central location for
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Figure 1. Databases of GOAS
Principle Databases The database, "Patient", contains basic descriptive information about each patient in the system including name, sex, date of birth, date of first visit, financial information and any other data used to describe an individual. Pointers are included to permit access of all records associated with the patient. There are two pointers to the "Visit" records, one indicating the record of the first visit, the second being used to locate the record of the most recent visit.
and need only to point to the same reference database record. Thus the storage required in the primary databases can be reduced without decreasing the amount of information stored. example of the space savings is the interaction between the primary database "Visit" and the reference database "Reason". Each visit made by a patient is stored in a record in the "Visit" database. Five reasons can be stored for each visit. By establishing a basic set of reasons and putting them in a reference database, it is possible to indicate the reasons for the visit using only 30 bytes of storage in the This space is primary "Visit" database. equivalent to the storage required to store one textual description of the reason for the visit. One
Each visit by a patient is represented by a record in the "Visit" database that contains the initials of the Medical Geneticist and Genetic Associate who saw the patient, where the patient was seen, and the date of the visit used to calculate the patient's age. A maximum of five reasons for the visit and three descriptions of the services provided to the patient are recorded as pointers to reference databases. The reasons and services are selected from a list stored in their respective databases. There are two "Reason" and two "Service" databases, one each for the Medical Genetic or Prenatal clinic. To determine which set of reference databases to use for a visit, the type of visit is stored in the record, allowing visits to more than one clinic to be stored in the system.
Primary Databases There are eight primary databases. Except for "Visit", "Diagnosis" and "Test", each database has one record for each patient in the system. There is a record in the "Visit" database for each visit made by a patient and one record per test per visit. One "Diagnosis" record is assigned to each patient and to as many as three relatives who are not already patients in the clinic.
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In each visit record, a field points to the first record in a chain of records that describe the tests performed during a visit. The records in the "Tests" database contain a pointer to the patient's main record in the "Patient" database and a pointer to the test performed. The latter are stored in "Test Matrix", a database that describes all the tests acceptable as input to GOAS. The records for the tests performed during (or as a result of) a single visit are stored as a chain of tests. This is accomplished by a pointer in each "Tests" record that points to the next test performed. The pointer in the last record of the chain has a special value to indicate the end of the chain.
Data
Security
Neither the IBM PC nor dBase III has a security Since GOAS contains personal system built-in. information, some measure of security is necessary to prevent casual unauthorized use of the system. The first step of GOAS is to disable the break key, preventing a user from stopping the system and gaining direct access to the data. Before the main menu is displayed the user is requested to enter his/her initials. The initials are checked against a list of authorized users. If the person requesting access to the system is not authorized, then the system will exit GOAS and suspend operation of the computer, requiring the machine to be reset before the computer can be used again. Authorized persons have various levels of access assigned, and the specific tasks available are all dependent on the access level. Although passwords are not implemented, they could very easily be added. There is not any defense against a knowledgeable "hacker" who wants to get to the system's data.
Record Keeping Databases The "Number" database contains the numbers associated with each patient and includes the hospital number assigned by the UMC Hospital, the Missouri Genetics Disease Program identifier and the Great Plains Genetic Service Network number. Each number is unique to each patient and duplication is prevented by the system during entry of the various numbers.
To secure the data against data loss all modified databases are backed up to floppy disk when GOAS is exited. The system displays and backs up all database files which have been modified since the last GOAS session. Two alternating floppy disks are used for backup. By using two floppies, even if the most recent backup disk is damaged, the most data that can be lost is the data entered in the two previous sessions.
The "Contact" database contains the names and addresses of the persons to be notified about the Each record in the progress of the patient. "Patient" database is permitted two related contact records, of which the first is assumed to be the address of the patient.
Diagnostic Databases
"Diagnosis" database contains the current diagnoses of the patient. Included in the record is the relationship of the person described in the diagnosis, since the diagnosis may not be for the patient, but for a relative. The date of the initial diagnosis and of the most recent change in The diagnosis are stored in the database. diagnosis is stored under three different categories: Chromosome Abnormalities, Mendelian Disorders, Other Common Disorders. An additional field is provided for entering a free-form description that cannot be described by one of the above categories. Associated with each category is a indicator of the degree of confidence in the diagnosis - Definite, probable or conceivable.
The
Current Status of the system
(V.2) has recently been installed in the Child Health office, and the first patients are being entered. Version 1 was used to enter the initial values into reference databases and no patient data were entered. For example, the reference database for referring physicians was entered so that as patient data referred to a specific physician, GOAS automatically fills in the address and phone number. The current problem is acquisition of the information requested by the system for patients seen before the system was implemented. Data are collected from patients at the various clinics around the state, transcribed onto data forms and the forms given to the data Problems arise when the data entry personnel. forms are not filled out completely and in the differences between the notations and terminology used on the data forms and the choices available It is not always possible for in GOAS. non-medically trained entry personnel to make the necessary adjustments.
GOAS
"Findings" database stores the seven most significant findings in the patient's physical examination. These are stored as pointers into the "Finding" database that contain a character description of the observation and the code number for the finding.
The
The "Family Name" database contains the surnames of paternal and maternal grandparents and space for four other surnames, two maternal and two paternal. Other fields include consanguity in the pedigree of the patient and high-risk ethnic background.
Output from GOAS GOAS is routinely used to generate a patient visit summary of all visits, tests and diagnoses made on This report allows the a patient (Figure 2). genetics staff to trace the patient's progress. Whenever information is added which modifies this report, a flag is set which indicates that a new
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Patient
Visit Summary for: Factitious Hospital Number: 99-00-00-5
Date of Birth: 12/31/34 Contact: Mary Patient Contact: John Smith Referring Physician: Boris Family Physician: Bearnard
Date of Visit: 02/13/85 Bearnard Freelander
Genetics Visit Summary: Dates Who Saw Reason 02/13/85 JAM ED Diagnostic Evaluation Affected Relative Counseling 02/13/85 JAM ED Follow-up Date 02/13/85 02/13/85 02/13/85
Age: 50.1 Years Relation: Mother Relation: Uncle
Service Diagnostic Evaluation Counsel i ng Fol low-up Counseling
Result Abnormal Abnormal Normal
Tests Chromosome Analysis Fragile-X Blood Chromosome Analysis G-Banded Skin Biochemical Studies Urine
Provisional Diagnosis for Patient: Self Date(s) of Diagnosis:Initial 02/13/85 Mosiac Abnormalities: Fragile X Trisomy 21 ISCN: 46,XY,FRA(X)/47,XY,FRA(X),+21 Certainty: Definite
McKusick No. 16220
Description Neurofibromatosis
Certaintv Definite
Other Common Disorders: Hearing Loss
Figure 2. Example of Output from GOAS
wordprocessing system to form personalized letters quickly and efficiently.
report should be printed. This provides the genetics staff with the latest information at all times.
A standard use of databases is generation of statistical reports that summarize the information stored in the database. The system can quickly (1) summarize the number of patients per county to determine service use rates; (2) list the number of patients with various dysmorphic features associated with their diagnosis; (3) list patients with specific diagnoses or anomalies; (4)determine patients with various combinations of anomalies. Three backlog reports list the various data fields that need to be filled in before patient data are complete.
The Missouri Genetics Disease Program requires a form to be filled out for each visit of every patient seen for a genetics disease. All the necessary information requested is available in GOAS. Permission has been obtained for GOAS to transmit electronically the data for the state form directly to the mainframe on which the state database resides. The report for Great Plains Genetic Service Network will be handled in the same manner, with the data being transmitted directly to the mainframe computer. The GOAS, in information addition to containing all the required for the Missouri Genetics Disease Program and the Great Plains Genetic Service Network, conforms to the national minimum dataset as specified by the Center for Disease Control.
future goal is to provide a method of integrating the data contained in the system with Some packages king other software packages. a considered for integration are MulitMate word processing system; Personal Ancestral File , Crunch a genealogical management system.ji and Statistical Package ; Interact4je a graphics package. ChartStar
A
Another useful feature of GOAS is the ability to generate mailing labels from the "Doctors" and "Contact" databases. This aids the office staff in sending notices to patients and informing doctors of a patient's progress. Data can be extracted from the database into a file used with an office
,
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References 1) Tross KD: The design and implementation of a computerized data management system for a genetic center. (Unpublished masters thesis) Pittsburgh, PA: University of Pittsburg; 1984.
2) Mitchell JA, Loughman WD, Epstein, C: GENFILES: information a computerized medical genetics network. II. MEDGEN: the clinical genetics system. Am J Med Genet 1980; 7(3):251-266 3) Gersting JM, Conneally PM: MEGADATS-3M: a human pedigree database management system (Abstract). Am J Hum Genet 1984 Jul; 36(4):52S.
4) Ash SR, Ulrich DK, Laxton DE: The TOTAL RECALL program: a relational office database interfacable with briefcase computers. In: Cohen GS. Symposium on Computer Applications in Medical Care; 1984; Washington. DC. New York, NY: IEEE; 1984: 429-432.
5) McKusick VA: Mendelian inheritance in man, 6th ed.Baltimore, MD: Johns Hopkins University Press, 1983. Trademarks: - Ashton-Tate; IBU - Mike Hodapp; MultiMate - MultiMate International; Personal Ancestral File - The Church of Jesus Christ of Latter-day Saints; Crunch Interactive Statistical Package - Crunch Software; ChartStar - MicroPro dBase
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International Corporation
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