Computer-assisted Pathology Encoding and
Reporting System (CAPER)
An On-line Computer System Developed at the
Massachusetts General Hospital
RAYMOND D. ALLER, M.D., STANLEY J. ROBBOY, M.D., JAMES W. POITRAS, B.S., BARRY S. ALTSHULER, B.S.,
MARION CAMERON, B.A., MEREDITH C. PRIOR, B.A., SUSAN MIAO, B.S., AND G. OCTO BARNETT, M.D.
Alter, Raymond D., Robboy, Stanley J., Poitras, James W.,
Altshuler, Barry S., Cameron, Marion, Prior, Meredith C ,
Miao, Susan, and Barnett, G. Octo: Computer-assisted pathology encoding and reporting system (CAPER). An on-line
computer system developed at the Massachusetts General
Hospital. Am J Clin Pathol 68: 715-720, 1977. An on-line
computer-assisted pathology encoding and reporting system
(CAPER) has been developed by the Department of Pathology and Laboratory of Computer Science of the Massachusetts General Hospital for a department of surgical pathology that processes more than 25,000 specimens yearly.
CAPER performs clerical functions, including the accessioning of specimens, monitoring their state of completion,
production of log books, billing, statistics, and transfer of
diagnoses to other hospital departments. It also permits
instantaneous display of all diagnoses rendered within two
years, printout within 24 hours of all older diagnoses for
any patient, and retrieval of all specimens with any given
diagnosis, further defined by any data item (e.g., age)
stored in the computer file. (Key words: Computer system;
Coding; Report; Systematized Nomenclature of Medicine;
Information retrieval; Pathology.)
MOST COMPUTER SYSTEMS developed for surgical pathology have dealt solely with the storage and
retrieval of diagnoses. As the data files created have
been intended primarily for research and not patient
care, days to months often elapse between the time the
pathologist renders a diagnosis and its entry into the
computer.
Received November 1, 1976; accepted for publication November
29, 1976.
Dr. Aller's present address is: Department of Laboratory Medicine, University of California, San Francisco, California.
Address reprint requests to Dr. Robboy: Department of Pathology, Massachusetts General Hospital. Boston, Massachusetts
02114.
715
From the Department of Pathology, Harvard
Medical School, and the James Homer Wright
Pathology Laboratories and the Laboratory of
Computer Science, Massachusetts General
Hospital, Boston, Massachusetts
For a computer system to be useful in the daily
operation of a department of surgical pathology, it
must be designed to record and retrieve current
diagnoses on demand, be able instantaneously to
display prior diagnoses for long periods thereafter,
and be able to perform clerical functions, such as the
accessioning of specimens, monitoring their state of
completion, production of log books, billing, and statistics. For these reasons, an on-line computer system has been developed for the Department of Pathology in conjunction with the Laboratory of Computer Science, Massachusetts General Hospital. The
system has been named CAPER (Computer Assisted
Pathology Encoding and Reporting system), and its
principal goals are listed in Table 1.
Materials and Methods
The computer programs were written in MUMPS
(MGH Utility Multiprogramming System) 2 for a Digital
Equipment Corp. PDP-15 computer with three moveable-head disk drives and 48K words of memory.
The pathology system uses an average of two partitions and a maximum of five of the 30 available
on the machine at any one time. Each segment occupies about 1,000 words of memory. Four 1NFOTON
CRT Display Scopes serve as terminals, with an aver-
716
ALLER ETAL.
A.J.C.P. . December 1977
Table 1. Goals
A. Patient Care
1. Computerize the assignment of accession numbers, without duplication, for surgical pathology specimens received at multiple receiving
stations.
2. Consolidate different parts of the same operative specimen if various parts (e.g., frozen sections, uterus, pelvic lymph nodes, and
appendix) are received at different times and in different receiving stations.
3. Ensure the accuracy and consistency of patient identification, including name, hospital unit number (medical record number), age,
sex, and pathology accession number through automatic verification of these data and direct computer printing of them onto
all logs and pathology reports.
4. Provide the pathologist with diagnoses of all specimens from this patient previously examined by the department, despite changes
in name due to marriage, misspelling, or use of several different names.
5. Allow immediate access to the status or the diagnosis of a specimen for telephone inquiries by physicians given either the patient's
hospital unit number or name.
6. Provide an abbreviated final report for each hospital floor of all diagnoses rendered that day. This list will usually be available
prior to the actual pathology reports, which are not distributed until the early evening. (This feature is not yet implemented).
7. Ensure that all specimens are signed out in a timely fashion.
8. Ensure that reports on slides received from referring hospitals are in the patients chart when he is admitted to the MGH.
9. Automate the transfer to the MGH Tumor Registry of
a. All cases with a diagnosis of neoplasia or tumor-like condition.
b. All specimens received for patients already in the Registry, regardless of diagnosis of the current specimen (e.g., normal bone
marrow in a patient treated previously for leukemia).
10. Identify certain classes of specimens for review by the hospital tissue committee.
11. Identify all specimens to be given priority handling and those priority specimens not signed out within 48 hours.
B. Scientific
1. Provide a retrieval system with reliable data for use in retrospective studies, capable of generating lists of specimens with any
diagnosis, further narrowed when desired by any data item stored in the computer (e.g., sex, age, year, other diagnoses).
2. Facilitate retrieval of cases in which photographs have been taken, tissue deep-frozen, or electron microscopy performed.
3. Automatically prepare lists of patients whose diagnoses or case histories were specified to be unusual which should be further reviewed after follow-up history becomes available (the so-called "recurring file").
4. Automatically prepare lists of patients in the hospital with specific diseases. This permits persons with special areas of interest
rapidly to identify patients or specimens and monitor the cases.
C. Teaching
1. List all specimens and diagnoses for patients to be presented at interdepartmental conferences.
2. Retrieve cases for illustrative purposes.
3. Provide final diagnoses automatically to physicians who performed preoperative studies (e.g., radiologists).
D. Administrative
1. Generate complete and accurate daily logs of all specimens received.
2. Prepare statistical reports, including number of specimens examined, tabulated by type of specimen, hospital service submitting,
location of patient, and other items.
3. Automate the billing process.
4. Segregate and hold consult slides and specimens which cannot be accessioned without more detailed information.
age response time of less than 1 second. A DECWRITER terminal is used to print basic patient information on the pathology report form and various
other logs and lists. The computer is located in and
maintained by the Laboratory of Computer Science as
one part of a series of similar machines used for
Radiology, Chemistry, Microbiology, 4 Clinical
Laboratory (Hematology), Utilization Review, and Tumor Registry. A description of the overall MGH system, including back-up computers for periods of equipment failure, has been published in detail elsewhere. 1
Results
The basic flow of the computer system and the
programs (functions) used are outlined in Figure 1 and
Table 2. Upon receipt of a specimen, patient identification is established (Function ACCESSION). The
patient's hospital unit number (unique for each patient and identical for all admissions) is entered into
the computer, which responds by displaying the patient's name and relevant demographic information.
These data are then checked for accuracy against
those on the requisition slip. If the hospital unit
number has not been provided, the patient's name can
be searched in the computer's alphabetic file of names.
When necessary, a new hospital unit number is issued.
Before a specimen number is issued, the computer
lists all current specimens for this patient and allows
the user to specify that the present specimen represents a portion of one of these prior operations.
If it represents a new specimen, the computer assigns
a pathology accession number complete with a "check
letter" (Table 3). To ensure uniformity, the names of
the surgeon, pathologist whoxexamined the specimen
in the operating room, and the pathology resident
responsible for the specimen are selected from a computer-generated list. Additionally, the tissues received
and the operative procedure are entered via SNOMED
codes (Systematized Nomenclature of Medicine). 3,e
Vol. 68 . No. 6
SURGICAL PATHOLOGY ON-LINE COMPUTER
When outside slides are reviewed, the name of the
referring hospital, the number of slides, and their
pathology number are recorded. Finally, the priority
status of the specimen (e.g., rush handling) is entered
to complete the log-in protocol.
The resident then examines the specimen, prepares
it for paraffin embedding, and dictates the gross description. Meanwhile, the coding specialists enter the
diagnoses for each patient's older specimens that
have been maintained in a manual card file system
in use before the computer was introduced. The secretary then activates the program, PRINT-HEADER,
which prints all of the basic patient and specimen
identification, as well as the diagnoses of previous
specimens, directly onto the pathology report form
(Fig. 2). The dictated gross description is manually
typed onto this form by the secretaries. In certain
instances where only a gross diagnosis is made, e.g.,
tonsils in young people, the computer prints the entire report, including a standard gross description and
final diagnosis, and automatically records the case as
being "signed out."
After the histology laboratory has prepared the
slides, the pathologist and resident examine them and
render their final diagnoses. These are immediately
coded in SNOMED by the coding specialists and
entered (with appended qualifiers for certainty of diagnoses) through the SIGN OUT function, which responds with a display of the English translation for
verification. A provision has been made whereby in
instances of coder uncertainty, the diagnosis entered
is placed into a provisional status and cannot be inquired upon until approved by a staff pathologist. The
responsible staff pathologist's name, number of
hematoxylin and eosin-stained slides, data about special studies (e.g., electron microscopy and photography) and billing are necessary to consider the case
"signed out." Subsequently the diagnosis is typed
manually onto the Pathology Report form exactly as
rendered by the pathologist. After it is proofread and
the coded diagnosis compared with the actual diagnosis, the final report is distributed to the patient
floor.
Due to storage considerations, only selected data,
including patient name, unit number, pathology accession number, and diagnosis, remain on-line for two
years. All other data are moved to off-line files or destroyed seven days after the specimen is signed out.
Microfiche indices of all data, cross-indexed by name
and diagnoses, are planned and will be issued yearly
as cumulative volumes.
Numerous lists for patient care, scientific use, and
departmental administration are generated on a nightly,
weekly, monthly, and yearly basis (Table 2).
Operative
Specimen
.
717
Requisition
for exam
r
Computer lists
patients new to system.
Coding professional checks
card file ( 1 9 7 0 - 1 9 7 6 ) ,
Input previous diagnoses
Paraprofessionol accessions
Pathologist
/
Histology
Laboratory
Secretary
1. Requests printing of pathology
report form with prior diagnoses -*•
2 . Transcribes gross description
Slides
Report form and
requisition
/
Pathologist:
1. Proofreads gross description
2. Examines microscopically
3 . Renders final diagnosis
COMPUTER
Telephone inquiry
Printed logs
Billing
Final diagnosis
Coding Professional:
1. Checks for incomplete data i . e . ,
tissues received which lock
diagnosis, ambiguities
2 . Codes diagnosis
3 . Enters diagnosis Into computer
Secretary:
Types pathologist's diagnosis
onto report form
Pathologist:
Proofreads
Report lent to patient floor
FIG. 1. Flow of system.
Discussion
Several crucial features of this system deserve additional comment. Unstructured natural language is unsatisfactory for large-scale diagnosis retrieval, particularly when diagnoses are rendered by many different people over the course of years. Indeed, one
need only imagine the many ways of stating a single
entity to recognize the difficulties inherent in totally
free text. 5 A good coding scheme for pathology must
reflect a concept accurately in order that the diagnosis can be retrieved in the future. Therefore the
code must be detailed, complete, and specify precisely: Location (Topography), Appearance (Morphology), Cause (Etiology), Physiologic changes (Function), Entities comprising all of the above (Disease),
and Treatment (Procedure). In our system a diagnosis
must specify topography and morphology; the other
fields are optional. At the same time, the code should
permit statement of the certainty of diagnosis (e.g.,
probable, consistent with) and how it was made (e.g.,
electron microscopy). For these reasons, SNOMED,
718
ALLER£TA£.
A.J.C.P. . December 1977
Table 2. CAPER Functions
BASIC ROUTINES
ACCESSION—record patient demographic data, responsible clinician and resident pathologist, tissue submitted
and procedure.
RESIDENTS' INPUT—accession via an abbreviated program designed for use by residents at night and
during weekends.
SIGNOUT—record diagnosis, responsible staff pathologist, number of H&E slides, billing codes.
INQUIRY—inquire for patient's unit number, name, specimen number, pathologist, diagnosis; moreover, list
all data in the computer, if desired.
DAILY INITIALIZATION—specify resident examining specimens that day.
OLD UNIT NUMBERS TO BE LOOKED UP—list all patients for which pathology data may exist in manual
files predating the computer system and for which a check has not been made previously.
OLD SURGICAL NUMBER INPUT—accession old pathology diagnoses made prior to computer system.
PRINT HEADER—print computer-generated pathology report form with patient and specimen identification and
all prior pathology diagnoses (Fig. 2).
CODING VERIFICATION—list all diagnoses made since last listing arranged by specimen number and used
by pathologist to compare with manually typed pathology report as it is proofread.
END OF DAY—Print daily:
DAILY ACCESSION LOG.
MEEI ACCESSION LOG—subset of accession log for a specialty division.
OUTSIDE HOSPITAL ACCESSION LOG.
OPERATING ROOM CONSULTS.
RUSH HANDLING.
RUSHES NOT SIGNED OUT—rush specimens not signed out within two days.
TEMPORARY UNIT NUMBER—patients assigned fake control number rather than valid MGH unit number.
TUMOR REGISTRY—list of all specimens with diagnosis of cancer or patients previously known to have had
a cancer (regardless of current diagnosis).
(The following are printed weekly or at specified intervals)
HOLDING FILE—list outside slides received lacking critical data needed for processing.
SPECIMEN REFUSED FILE—list specimens originating in MGH that lack critical data needed for accession.
RESIDENTS' UNSIGNED OUT SPECIMENS—list specimens that lack diagnosis more than four days after receipt.
PENDING LIST—note specimens not in any of above lists that lack critical pieces of information after four days
(e.g., fake rather than valid MGH unit number, number of H&E slides prepared).
PATHOLOGIC CONFIRMATION OF X-RAY—list diagnoses of all pathology specimens that can be linked to
examinations performed by radiology department.
SIMILAR NAMES AND UNIT NUMBERS (>1 LIST)—list of all patients with similar last names whose MGH
unit numbers vary by no more than two digits (used to identify patients with possible unit number duplication).
PATIENT CARE AND RESEARCH
CONFERENCE LIST COMPILE—prepares or lists all diagnoses maintained on-line in computer for any patient
to be presented at conference.
CONFERENCE—each morning, lists each conference compiled the day before. The list contains all diagnoses ever
rendered on the patient, including all diagnoses stored off-line.
INVERTED FILES
SPECIMEN NUMBER COUNT—counts all cases with a particularfinding(e.g., tuberculosis).
LIST ALL SPECIMENS—lists above cases, giving patient's name, unit number, and all other diagnoses
associated with the specimens.
CROSS INDEX CODES—lists as above, but allows greater specificity of diagnosis, e.g., pulmonary tuberculosis.
SIGNED OUT SPECIMENS—lists a range of cases with diagnoses rendered.
OFF-LINE INQUIRY—inquire whether mountable disk pack is on-line for use with interactive program.
SNOMED
MICROGLOSSARY—printed abridged SNOMED dictionary adapted for anatomic pathology.
ON-LINE SNOMED CODES—list all SNOMED codes added on-line in addition to those listed in microglossary.
SNOMED DECODER—translate SNOMED codes into English.
ADD SNOMED CODE—add new SNOMED code to on-line dictionary.
MODIFIER CHANGER—edit modifiers of SNOMED (e.g., right, left, etc., grade of tumor, resection margins).
SEMANTIC QUALIFIER CHANGER—edit qualifiers of diagnosis (degree of certainty of diagnosis, e.g., probable
diagnosis, consistent with tumor arising in).
ADMINISTRATIVE AND MISCELLANEOUS
?—list all commonly used functions.
LIST—list all uncommonly used functions.
PHYSICIAN (BORROWER'S) LIST—list all MGH physicians with their resident or faculty status.
CORRECT—correct basic patient demographic data stored in hospital's master file.
MERGE—combine 2 patientfilesinto one (i.e., patient has duplicate valid MGH unit numbers, or a fake number to
be merged into valid unit number).
UNIT NUMBER DATA—list all laboratories with data on same patient.
CHECK LETTER—calculates check letter when unknown.
Vol. 68 • No. 6
SURGICAL PATHOLOGY ON-LINE COMPUTER
Table 2.
719
(Continued)
EDIT—directories used to verify input
HOSPITAL—name and address of hospitals that commonly refer slides to MGH.
RACE.
DOCTOR—list of Pathology residents and staff.
SPECIAL STAINS AND PROCEDURES.
STANDARD REPORTS—computer-generated gross dictation, currently used for tonsils.
BILLING—prepare and automatically transfer to the MGH administrative computer all billing information.
BILLING—permits accumulation of billing data at specified points during accession, signout or as a special function.
POST BILL—compiles all billing data after case is signed out and transfers it tofinancialcenter of MGH to be
posted on patient's hospital bill.
QUALITY CONTROL AND SAFEGUARDS FOR SYSTEM FAILURE
(NIGHTLY)
FILE COMPARE—Check the internal data base linkages between patients and specimens; also examine the data
for illegal conditions that indicate a programming error. Each night, an hour is devoted to checking successive
portions of the files.
(WEEKLY)
UPDATE LIST—update allfilesused for weekly printing in END OF DAY (see Basic routines).
GARBAGE—Copy data to an off-line file and reduce the on-line portion to "diagnosis" for all specimens signed
out more than seven days ago; also delete even the diagnoses from the on-linefilesonce the specimen is more
than two years old.
CRASH—reset allfilepointers and restart program at beginning of weekly lists if system fails during the special
weekly listing specified under END OF DAY (avoid reprinting of all daily lists).
(YEARLY)
MICROFICHE — prepares computer-generated cumulative index of all specimens arranged by patient hospital
unit number and cross-indexed by patient name, accession number, and diagnosis.
which is an updated and expanded version of SNOP
(Systematized Nomenclature of Pathology) was selected. Since the unabridged dictionary contains more
than 50,000 terms, we have devised a "microglossary"
for surgical pathology which is designed to list any
term used in anatomic pathology more frequently
than 0.002% of the time, grouped under the organ
systems in which the code typically occurs. 6 A further
abridged list of approximately 200 topography, 175
morphology, and 25 other terms comprises more than
80% of all diagnoses made in this department.
A major and all-too-often ignored problem in establishing any large data base is ensuring the quality of
the data collected. Procedures to ensure quality include:
1. Patient identification is cross-checked against the
hospital's master patient file.
2. All codes entered into the computer are translated into English phrases and displayed for the user
to verify.
3. The computer prints all patient and specimen
identification onto the report form.
4. The accession number, used throughout the system as a specimen identifier, incorporates a check
letter, which is computer-generated, to guard against
digit substitution and transposition during typing.
Whenever an incorrect accession number is entered, it
is rejected as invalid.
5. All diagnoses are coded immediately after the
Table 3. Calculation of Computer-Generated
Check Letter
Purpose: Method to detect erroneous transposition or substitution of
digits in the pathology accession number. At the time of
log-in, the computer assigns an accession number, e.g.,
S 75-M98346, complete with a check letter:
Multiplyfirstdigit by 1
Multiply second digit by 2
Multiply third digit by 3
Multiply fourth digit by 4
Multiplyfifthdigit by 5
Multiply sixth digit by 6
Multiply seventh digit by 7
Multiply laboratory number by 11
(S = lab number 14)
Add results
7x
5x
9x
8x
3x
4x
6x
1=
2=
3=
4=
5=
6=
7=
7
10
27
32
15
24
42
14 x 11 = 154
311
Divide result by 19, subtract the remainder from 19, and the result
"n" is used to assign the nth character of a list of letters where
A = 1, B = 2, . . . Y = 19, (omitting the commonly confused
letters, I, O, Q, S, U, V, Z)
16
19)311
19
121
114
Thus, 19 - 7 = 12, and the 12th check letter used is M.
Note: Each time a pathology specimen number is entered into the computer, it calculates
a check letter which is constant for any given sequence of numbers. When, for example,
the secretary errs and inquires about S75-M59346 instead of S75-M95346, the computer
calculates the check letter *'L" for S75-89346, notes the discrepancy with the letter
"NT" entered by the secretary, and immediately rejects the entry as invalid.
720
ALLERErAL.
A.J.C.P. • December 1977
PATHOLOGY REPORT
MASSACHUSETTS GENERAL HOSPITAL
Boston. MA. 02114 Tel. 617-726-2967
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half) with computer-printed patient
and specimen identification.
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pathologist has rendered them but prior to the time
when the secretaries type the final report. This procedure permits the coding professional to check the
reports; when the diagnosis seems to be incomplete,
incorrect, or lacking elements, the responsible staff
member can be immediately questioned. As the final
diagnosis is promptly entered into the computer, it
also becomes available for telephone inquiry before
the final report has reached the physician.
6. The accuracy of the diagnostic code is further
ensured by a staff pathologist who compares his
actual diagnosis with the English translation of the
SNOMED code at the time the final report is proofread.
Future extensions to this system lie in several
major directions. One area is the enlargment of the
system to include cytology and autopsy pathology.
A second area is increased communication with other
clinical laboratories in the hospital. For example,
the described system informs the MGH Tumor Registry
of all tumor diagnoses and the radiology department
of each pathology specimen that can be linked to an
appropriate x-ray on the same patient. These interfaces result in enhanced patient care. A third area is
computer generation of the entire report, including
gross description. Such a system exists for radiology
at another institution. 7 With improvements in terminal
and mass-storage equipment, reporting stations may
become a standard feature of the surgical pathology
department.
References
Barnett GO: The development of a modular information system at the Massachusetts General Hospital, Hospital Computer Systems. Edited by Collen MF. New York, John
Wiley and Sons, 1974, pp 517-545
Bowie J, Barnett GO: MUMPS—An economical and efficient
time-sharing system for information management. Computer
Programs Biomed 6:11-12, 1976
Cote R: Systematized Nomenclature of Medicine (SNOMED),
College of American Pathologists, Chicago, 1977
Kunz LJ, Poitras JW, Kissling J, et al: The role of the
computer in microbiology, Modern Methods in Medical
Microbiology: Systems and Trends. Edited by Prier JE,
Bartola J, Friedman H. Baltimore, University Park Press,
1972, pp 181-193
5 Pratt AW: Representation of medical language data utilizing
the Systematized Nomenclature of Pathology, Computers in
Laboratory Medicine. New York, Academic Press, 1975,
pp 42-53
6. Robboy SJ, Aller RD: Microglossary of Surgical Pathology:
Systematized Nomenclature of Medicine (SNOMED), College of American Pathologists, Chicago, 1978
7. Wheeler PS, Simborg DW, Gitlin JN: The Johns Hopkins
radiology reporting system. Radiology 119:315-319, 1976