POLARS: A pathology on-line logging and reporting system

COMPUTERS

AND

BIOMEDICAL

POLARS:

R. C. PLATT, Department

7, 83-99

RESEARCH

(1974)

A Pathology and Reporting

On-Line System*

Logging

R. L. WONG,~ K. W. LANTNER, AND P. S. GAYNON of Pathology,

Abraham Lincoln Uniaersity of Illinois

School

of Medicine,

Received July 17, 1973 A system has been established to collect medical data and produce reports, logs, and retrieval files. On-line data entry programs allow for entry of both fixed-length and free-text data through remote terminals. This data is then collected to allow retrieval based on its natural language contents. The system is currently implemented for surgical pathology and cytology applications.

1. INTRODUCTION A systemhas been designedand implemented to improve the efficiency of medical data management in a pathology department. This project, named the Pathology On-Line Logging and Reporting System (POLARS), is a component of an ongoing effort designedto construct a retrieval systemfor a pathology library of educational resources based on clinical histories, autopsy reports, and surgical pathology reports (I). The total system, when in full operation, will integrate the service, education, and research functions of the department of pathology in a university hospital. This project’s potential rests on its capability to integrate and utilize various narrative data sources.Surgical pathology reports and their corresponding requests for tissue examination occupy an important position in a patient’s medical record. Surgical pathology reports are usedasa progressnote in the patient’s chart providing a tissue diagnosis, and as a document to verify the removal of the patient’s tissue, organ, or a foreign body. The accompanying request for tissue examination, authored by the clinician, provides a concise source of background information including the operation performed and a summary of the patient’s illness. This information can be collected to monitor the activities of the clinical departments as well asthe pathology department itself. Such information also provides a meaningful context for the study of the specimens,slides, kodachromes, and photographs that are preserved for their teaching and researchpurposes. * This project is supported by the Department of Pathology and a Norval Pierce Research grant from the University of Illinois College of Medicine. P Send reprint requests to: Ruth L. Wong, M.D., Pathology Department, Abraham School of Medicine, University of Illinois, 1853 West Polk. Chicago, Illinois 60612 Copyright in 1974 by Academic Press, Inc. All rights of reproduction in any form reserved. Printed in Great Britain A

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A surgical pathology report must serve dual functions as a communication and as a medical document. Since the clinician frequently depends on the tissue diagnosis in order to plan the patient’s therapy, rapid transmission of the clinician’s request and the pathologist’s report is essential for efficient patient management. To fulfill the documentation function, a pathology department must keep a log of requests and reports. These logs also serve both administrative and statistical purposes. 2. DATA ENTRY

The two types of data usedin this project poseddifferent data entry requirements. Patient identification data are fixed length and are conventionally handled by filling in blanks on forms designedfor typewriters. Error correction usually occurs while the field is being typed and rarely involves the manipulation of a large number of characters. In contrast, correction of free-text data, such as a patient’s clinical history or the content of a pathology report, requires the ability to insert or delete characters independent of their relative position in a line of text. In addition, representation of separate lines of text and compressionof multiple blanks become problems in free text as a result of greater length. In order to meet these different requirements, two on-line data entry programs, DISPLAY and WY LBUR, are used. 2.1. Entry Methods DISPLAY,’ which is used to enter fixed-length data, allows a typist to fill out a form projected on a cathode-ray-tube screen. When the typist fills in the fields, characters are transferred to a buffer in the terminal. A tab key is used to move from one field to the next, and control keys allow the cursor to be positioned anywhere on the screenwithout deleting text. When all fields have been filled correctly, the typist enters a “Q” in a validation field and transmits the contents of the terminal memory buffer to the computer. If the transmission was successful, the form is cleared and the typist may proceed to the next case.If a transmissionerror occurred, then the form is reproduced and the typist is instructed to retype the case. Once a record has been successfully transmitted, incorrect entries can only be revised by retyping the entire record. DISPLAY does not have facilities for insertion or deletion of individual characters. WYLBUR’ is an on-line text editor which allows free-text files to be processed. It has commands for both intraline and interline editing, which are used for error correction. WYLBUR’s data set managementfacility allows data files to be created, modified, listed, or destroyed and permits control of the entire system from a secretary’s desk through remote job entry. WYLBUR also permits retrieval of individual casesand automatic expansion of certain abbreviations to assisttypists. ’ DISPLAY is a terminal data-entry program written by the Research Resource Laboratory of the University of Illinois at the Medical Center, Chicago, IL. ’ WYLBUR is available from Stanford University, Palo Alto, CA.

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REPORTING

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2.2. Data Types The data originates from two separate sources. When a specimen is submitted for pathological examination, a request for a surgical pathology examination form accompanies it. This form contains two types of information. One type, the identification information, is fixed-length data and is therefore entered through DISPLAY. The DISPLAY blanks are arranged in the same order as the blanks on the form for ease of transcription of data. Information entered through DISPLAY includes the requesting doctor’s name, the pathologist’s name, the patient’s name and other identification data, the date the specimen was received, previous biopsies if any, SURGICclL

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the type of examination desired, and, finally, a description of the specimen (see Fig. 1). After all cases have been entered, the DISPLAY data are processed by POLARS. The second type of information on the form is the clinical history information. This clinical data is entered through WYLBUR (because of its free-text nature), with conventions seen in Fig. 2. A dollar sign “!I? in the first column marks the start of cases and also separates a description of the surgical procedure from the 1. 2. ?. 4. F. 6. 7. 8. cj. 10.

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remainder of the free text that is on the request form. This separation allows later retrieval methods to distinguish between key medical terms on the basis of their free-text source. The seconddata source is the surgical pathology report authored by a pathology resident. Its important portion is the pathological diagnosis which summarizes the nature of the case without including more descriptive writing. POLARS’s 1. 2. 3. 4. 5. 6. 7. 6. 9. 10. 11. 12. 13. 14. 15. 16.

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FIG. 3. A resident’s worksheet showing the pathology accession number and gross description (flagged by “$GROSS :“) for each case.

flexibility allows the separate sections of this report to be entered at three different times, in order to conform to the needsof the pathologist. Upon receipt of a specimen, a pathology resident dictates a grossdescription. The dictation is transcribed

87

PATHOLOGY LOGGING AND REPORTING SYSTEM

using WYLBUR, and the text is saved as an on-line WYLBUR data set. A listing of this text serves the resident as a worksheet upon which to write the diagnosis and the microscopic description (see Fig. 3). At the sametime, corrections to the transcription of the dictation can be indicated by the resident on the worksheet. Each day, the resident returns the worksheet to the typist, regardlessof the number of casescompleted. A second WYLBUR sessionis used to enter the changesand additional material such as diagnosis and microscopic description supplied by the 1. 1.1 1.2 2. 3. 4. 5. 6. 7. 8. 8.1 8.7 8.3 8.4 8.5 P.6 8.7 9. 10. 11. 11.1 12. 13. 14. 15. 15.1 15.2 16.

873503312Y 1. RDNF MARROW WITH INCKE4SE CIF IMMATURE ATYPICAL CELLS. 2. ND ACID FAST QACILLI OR FWNGI FOUNO. 6GRflSS: SPFCIMFN IS SUBMITTED IN TWO CONTAINERS. CONTAINER “A” IS 1 ABELED AS “RDNF BIOPSY”, CONTAIYER “8” IS LABELED AS “BONE MARROW PSPICATE”. SPECIYEN “A” CCINSISTS TlF ONE FRAGMENT OF YELLOWISH TISSUE SUBYITTED IN S@UIN’S SOLUTIUN MEASURING 1.2 X 0.3 X 0.2 CM. FNTIRE SPECIMEN IS EMBEDDED. SPECIMEN “B” CUNSISTS OF MULTIPLE FPAGYFNTS riF sRnwNISH-YELLOd TISSUE YFASURING Ibi AGGREGATE 1.5 X 1.3 X 0.5 CM. ENTIQC SPECIYEN IS FMBEDDED. wIcRn: SECTIONS PEPRESENTIYG A HIOPSY AhD AN ASPIRATION SPECIMCN OF PARRQW REVFAL SLIGHTLY INCREASED CELLUL4RITY. %FGAKARYnCYTES ARE INORMAL. FRYTHRDPDIESIS IS N1RMOSLASTIC. THERE IS A YARKED INCREASE IN-\/FRY IMMATIJRE AND ATYPICAL CELLS WICH ARE. OISTKIbUTED UNEVENLY THRDUGH?UT THE MARROW. THESE ARE SIMILAR T O THE CELLS SEEN IN THE PRFVI71IS BI?PSY, BUT HERE THEY D1 NOT FJPM A OISCRETE NOUULE AS 1N s-1153-73. PF. GPOYA

LYYPtiilCYTlC LiiJKEflIA INVOLVING BflNE MARROW. IGRDSS: SPECIIE’J iS SUBMITTED AS “HARRIIW CLDT”. SPECIMEN IS SIIBMITTED IN ,L1l!JIN’S SOLUTI@h! AN3 CONSISTS UF MULTIPLE FRAbMENTS Thlh’, HRDiiNISH-YELLDU, SOFT TISSUE MEASURING 1-L X 1 X 0.5 CM. tYTI°F SPECIYEN IS ~MREDUEC. PIG??: THE ASPIF4TE CIF MARROW CONSISTS SOLFLY i:F CLUSTERS OF IMYATURF AND’ ATYPICAL LYMPHCCYTES. iJa. GROYA

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FIG. 4. A listing from a WYLBUR file of completed cases. Note that the pathologist’s diagnosis has been entered between the pathology accession number and the gross description. The microscopic description has also been appended to the case.

pathologist. A new listing of caseslacking a diagnosis and/or a microscopic description (incomplete cases)will again serve as a worksheet, while the listing of the completed cases(Fig. 4) are proofread with corrections added during a third WYLBUR session. The correct, complete cases are flagged by the typist, and POLARS automatically removes them from the file and produces the output described below. 3. COMPUTER FACILITIES POLARS usesthe computer facilities of the Research ResourcesLaboratory of the University of Illinois Medical Center Campus. The installation offers an IBM 370 Model 155 with HASP-II and with a 250 K partition available for batch processing.Telecommunications through a Hazeltine 2000 remote terminal located

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in the departmental office are supported by the DISPLAY data entry program and WYLBUR, an on-line text editor. Software includes a standard utilities package, a PLjl level F compiler, and an information retrieval system. All POLARS programs were coded in PLjl and are compatible with IBM 360’s.All listings are produced by an IBM 1403high-speedprinter. 4. REPORTS Two general types of listings are produced by POLARS. One type consists of three listings which are produced daily. The other is a status listing produced as needed. Further utilization of the data is made in the creation of a research and teaching file, which will index the existing pathology library file (1). (Also refer to Section 4.4 below.) 4.1. Dailv Output Three listings are produced on a daily basis to serve the reporting and logging needs of the pathology department. The first is the “specimen log”, produced from the DISPLAY data entry sessions(seeFig. 5). One line is generated for each specimen, and the log is currently sorted both by pathology accessionnumber and by patient’s last name. (Tf needed, the log can be sorted on any of its fields.) A second log, the “diagnosis log”, is produced from the completed casesfile (see Fig. 6). This is a cumulative log, containing all of the information recorded in the specimenlog as well as the pathology diagnosis. The diagnosis log is also sorted in two ways-by pathology accessionnumber and by patient’s last name. The two logs serve several functions. First, they provide a clear, convenient record for surgical pathology to usein keeping track of the status of cases.Second, they provide the telephone answering service of the pathology department with an easy-to-usereference for answering inquiries from other departments. The formal pathology report is the third listing produced daily (see Fig. 7). It contains tissue diagnosesand corresponding descriptions of gross and microscopic findings. This is a medicolegal document and must be signed by the attending pathologist for the patient’s chart. Carbon copies are made for the pathology department and the attending clinician. The last copy is a file card for the existing name file kept in the pathology department. 4.2. Status Listing One other listing may be obtained when needed in order to check on the actual status of casesin the system. This listing, called “waiting cases”, is a printout of the waiting-casesfile by pathology accessionnumber and indicates which of the three data entry sessionshave been completed for each case(seeFig. 8). The three types of data are identification data (ID) from DISPLAY, clinical data (CL) from the surgical pathology request form, and pathology diagnosisdata (PA).

SURGICAL

PATHOLOGY PART 1 OF 2

LOG

PATHOLOGY

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REPORTING

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This status reporting has proven itself to be quite useful. The pathology data will not be reported by the system if the ID data from DISPLAY has not been entered. When the program to produce the pathology report is run, it generates a list of cases processed as well as cases dropped due to a lack of ID data. When a case is dropped, it is saved in a special file. By using the current listing, missing ID data can be entered for those dropped cases. The next time a current-cases listing is

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FIG. 7. Final pathology report. This output is added to a patient’s chart. Compare its contents with the contents of Fig. 4.

produced, a check can be made to ensure that the former dropped cases are now listed as complete cases. 4.3. Retrievals

Once a case has been completed, a final pathology report is printed (Fig. 7) and forwarded to the patient’s chart and requesting clinician. In addition, the patient’s FIG. 8. A listing of cases which require further processing. Three codes indicate data present in the system for each case: CL, clinical data from the surgical pathology request forms; ID, identification information from DISPLAY; PA, pathology diagnosis data.

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identification data and diagnosis are placed on a WY LBUR data set to allow simple retrievals. Figure 9 shows a sample retrieval from this file based on a patient’s chart number. As this search technique is inefficient for large files, it is intended to provide retrieval of cases only until they can be added to the research file and catalogs described below. COMMAND? C~IUY4ND? 2477. CUMM4Yil? 2477. 2478. 2479.

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FIG. 9. A sampleretrievalfrom a WYLBUR data set. A patient’s chart number @receded by the code“U=“) retrievesthe corresponding pathologyaccession numbersand WYLBUR line numbers.A listingof the followingline producesthe case’s diagnosis. Retrievalcan also be made on thetext of the diagnosis itself. 4.4. ResearchFile and Catalogs

Another important output is a fixed-length record file produced from the patient identification data, the text of the clinical history, and the preoperative and pathological diagnoses. This file is used to generate catalogs and an on-line retrieval data base for research and educational functions. (The organization of this retrieval system was described in detail in another paper (I).) The design of the record format is independent of the data entry device in order to allow cases entered by this system to be merged with a 2600-case data base entered by a key-to-tape machine3 and a 6000-case data base entered with an optical character reader.S The file is organized into identification information, written on fixed fields, and free-text information. The free-text fields are divided into the following sections: (1) a description of the surgical procedure performed and the specimensubmitted supplied by the clinician, (2) the clinician’s preoperative diagnosisand brief clinical history of the patient, (3) the pathologist’s

diagnostic summary.

Each word in these fields is looked up in a dictionary (Lexicon) in order to retrieve codesthat determine whether the word is an entry in the catalog or is accessiblein the on-line retrieval system. The dictionary also provides for standardization to noun forms, substitution of preferred synonyms, spelling correction, and insertion of implied terms. The dictionary hasa frequency of occurrence count for each word. Words new to the system are automatically added to the dictionary. The frequency count is maintained to decide which words are to be placed in core for economy 3 Model R 30 Recording Typewriter by Data Instrument Co. 4 Scan Data Model 200.

PATHOLOGY LOGGING AND REPORTING SYSTEM

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purposes, sincea major part of the cost is for disk I/O’s. Furthermore, the frequency count might have research potential for analysis of medical English. The printed keyword-in-context catalogs are produced separately for three sections corresponding to the three free-text fields described above: operation, clinical, and pathological. These catalogs serve as a permanent index to the slide and kodachrome collection based on the casesprocessedby the system. Requestsfrom the on-line data baseare entered through an information-retrievalsystem user’s language5 which can produce tables or the full text of the source documents (Fig. 10). Pertinent casesare located by specifying any logical combination of medical key words or identification fields. To assistin the formulation ;----r

722732 61 W F 73533312 053073 BONE MARROW ASPIRATE. np: h?NF RIOPSY, 2. FUCJ, R/O TUBERCULOSIS, FUNGI. 1. RFTICULUY CFLL SARCOYA. CL: POSITIVE CYMPH N,lOE YIUPSY IN PAST. NOW ON P0SITIVk RONF, MAKROW, CL: HAS HAD lO*OhY HISTOQY OF FEVEh, C?JLD BE DUE T O CL: CHE’4OTHERAt’Y. INcREASFT) nISrASF Sii TUREQCULCSISIFUNGI. :L: HAPF!(l’,i WITH IhlC?,tASp !lF IMMATlJQE ?TYPICAL CELLS. L’ 4 : +ti,r;F “A: Nl-: AC19 FAST BACILLI OH .FUNGI c-lU”IO. ____________________-----------------------+3b**t6~4tfft*4*6ftr~~~~~~~8~~~~~~*~~~~’~~~~*

FIG. 10. A sampleIRS retrieval.Compare this case with Figs. 2, 3,4, and 7. of retrieval requests, a natural-language retrieval preprocessor which uses the dictionary to standardize and optimize natural language requestsis being planned. (A more efficient process under consideration is accessingthe data base directly without generating complete user’s-languageprograms.) 5. PROGRAMSAND

DATA STORAGE REQUIREMENTS

The flow chart in Fig. 11 shows how the data are transformed and sorted to produce the logs, reports, and files described above. The most important factor in determining the structure of the system is whether the data must be available at all times in an on-line environment or whether the data can be stored off-line with accessconfined to brief periods of time. In general, the amount of on-line storage is limited and is at an economic premium. This results from the limited number of input/output devices at any given installation and the need for a core resident program to control the on-line files as well as the data entry terminals. This problem is reduced by having only two common data entry routines service all the installation’s data entry applications. This, a lo-cylinder IBM 2314 disk file, meetsthe storage needsof all DISPLAY users.(A day’s output of pathology records 5TheIRS User’sLanguageispart of the ComputerCorp. of America’sInformationRetrieval System Series 200 Model 203, Cambridge, MA.

PLATT ET AL. !?;;NlClAF, 1 SENDS 1 REOUEST

LOG :_ .__.’ /

/‘-

70

PATIENT’S CHART

FIG. 11. System flow chart.

usually fills only one track of that file.) All WYLBU R-created data setsare stored on-line and are allocated as needed from two 2314 disk packs reserved for this purpose. Our experience has shown an average of 18 tracks are required at a given time, with each file being allocated a minimum of one track. This is kept at a minimum by prompt deletion of unnecessary data sets and by the compressedinternal format used by WYLBLJR. The DISPLAY records are copied to an off-line data set at the end of each day. The ENTER program then validates the contents of each record. calculates the

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patient’s age, produces the daily log of specimens submitted, and adds records to the waiting cases file. This off-line file is a PLjl environment (regional (1)) directaccess data set with a capacity of 4000 cases held in 8 cylinders. It is keyed by the pathology accession number assigned during the use of DISPLAY. This pathology accession number is necessary because the final reports will be produced independent of the order in which the specimens were received. A special program is used to produce a log of waiting cases when necessary. The clinical-history WYLBUR files are reformatted on an off-line research file as soon as all corrections have been entered. Rough drafts of the surgical pathology report are kept on-line to allow correction and insertion of diagnoses at the secretary’s convenience and to permit on-line retrieval if needed. The REPORT program searches these on-line files for complete cases, and the contents combined with the information in the waiting cases file are reproduced in a hard copy form to allow low-cost long-term storage as well as to function as a medicolegal document. The information is also transferred by REPORT to the research file and to the short-term retrieval file. The REPORT program creates an updated on-line file of incomplete cases. 6. RESULTS POLARS has been in full operation since March I, 1973, and had been functioning in parallel to the existing surgical pathology system for 5 months prior to that date. Approximately 5000 cases have been processed to date. The first 500 cases have been successfully incorporated into the research file catalog. The first three months of full operation required an average of 7594 min of terminal connect time, 7.19 min of WYLBUR edit time, and 11.06 min of CPU time to process a monthly average load of 699 cases. However, several of these parameters will vary from user to user. For example, terminal connect time is a function of typist’s speed, or skill, and amount of text to be entered per case. 7. DISCUSSION A WYLBUR-based retrieval system has previously been shown to be a convenient short-term retrieval system (2). However, POLARS has the added advantage of interfacing with a long-term, and more efficient, data-base management system. Unlike some systems using visual-display terminals (3, 4), POLARS is designed to be operated by a typist rather than by clinicians. Therefore, liberties were taken in requiring operators to learn conventions and standardized procedures. POLARS offers several advantages over manual handling of surgical pathology data. First, it eliminates retyping complete drafts of surgical pathology reports and, hence, encourages residents to strive for more precise reports without fear of causing an undue secretarial burden. Next, it allows the current status of a patient’s pathological examination to be readily retrievable for inquiry. The various logs, because

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they are sorted on several fields, greatly aid the telephone-answering service of the pathology department and enable telephone inquiries to be handled at several stations. The logs also help the staff to utilize material for conferences and the “Living Museum”, an educational resource project now being planned for the University Hospital. POLARS has the added advantage of minimizing transcription errors and systematizing proofreading. POLARS is best suited for producing quickly updated status logs and nontrival revisions between report drafts. Subdepartments that do not have these requirements can use a manual system that produces final reports in a form compatible with an optical character reader. The machine output from these reports is added to the researchfiles and catalogs. From the user’s point of view, POLARS’s best feature is its adaptability to a traditional system while providing the neededflexibility for future growth. The easy acceptance of POLARS by medical and clerical staff is attributed to the fact that this system utilizes the ordinary medical typist’s skill for data input and provides ample opportunity for manual editing and error correction by the medical staff, which are necessaryin free-text data entry. Even though POLARS presently applies only to surgical pathology and cytology records, the utilization of this data through retrievals will extend to patient care and to the long-range functions of education and research. Furthermore, procedures and techniques employed by POLARS can easily be adapted to other types of free-text medical documents. Free-text medical information systemshave been proven to be feasible and of significant value (‘5~-8). and techniques similar to POLARS can be a solution to their data-entry problems. In the absenceof a totally integrated medical information network (9-111, a workable component such as POLARS, serving well-defined yet limited goals. can be a contribution toward the construction of a total system serving the patient care education, and research functions of a university hospital complex in the future, REFERENCES

I.

P., AND WONG, R. L. A retrievalsystem for a library of pathologyreports,slides andkodachromes. Methods Infbrm. Med. 11,152-l 62 (1972). 2. HOROWITZ, DAVID L. Analysisof biomedical data by time-sharing computers,II. An on-line tissue bankgraft registry. Research Report No. 1, Project No. M4305.03.3009, Naval Medical GAYNON,

Research Institute, Bethesda, MD, 1971. 3. SINGER, SAMUEL J. Visual display terminals in a hospital information system (HIS). C;)I)I/I. Biomed. Res. 3,510-520 (1970). 4. SLACK, WARNER, V.. VAN CURA, LAWRENCEJ., AND CKEIST, JOHN H. C’omputers and doctorsUse and consequences. Comput. Biomed. Res. 3,X-527 (1970). 5. WONG, R. L., AND GAYNON, P. An automated parsing routine for diagnostic statements of surgical pathology reports. Methods Infotw. Med. 10,169.-l 75 (I 971). 6. LAMSON, B. G. AND DIMSDALE, B. A natural language information retrieval system. h.clC.. IEEE 54,1636-1640 (1966). 7. BROSS,

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G. AND BECKER, H. Klartextanalyse pathologischer biopsiebefunde mit bildschirmabfrage. Methods 1form. Med. 12,10-16 (1973). 9. WHITE, D. Information processing of medical records-state of art: Report on the IFIP-TC4 Working Conference, Lyon, April 6-10, 1970. Methods Inform. Med. 9, 189-193 (1970). 10. DELAND, E. C. AND WAXMAN, B. D. Review of hospital information system. Special Publication of Rand Corporation, Santa Monica, CA, 1970. II. DAVIS, L. S. A system approach for medical information. Methods Inform. Med. 12,1-6 (1973). 8. GELL,