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United States Government Work, uncopyrighted, public-domain,
DRAFT COPY ONLY. This document does not necessarily represent the views
or policies of any United States Government agency.
This document is provided "as is", without warranty of any kind,
express or implied, including but not limited to the warranties
of merchantability, fitness for a particular purpose and
non-infringement. In no event shall the authors be liable
for any claim, damages or other liability, whether in an
action of contract, tort or otherwise, arising from, out of,
or in connection with the document or the use or other dealings
made with the document.
PRINCIPLE OF THE TEST.
It is important to understand the structure
of the surgical pathology computer software.
SPECIMEN REQUIRED.
Tissue Specimen and filled-out
Tissue Examination Form (USSF515).
REAGENTS, INSTRUMENTATION.
1. Not Applicable.
STEP-BY-STEP DESCRIPTION.
1. Every pathology report begins as pieces of human tissue,
submitted to a pathology laboratory with accompanying paperwork. In the
simplest case, there is one piece of tissue, obtained from one surgical
procedure, arriving in one container, from one appropriately identified
patient, with one accompanying page of paper that contains matching
identifiers, and a relevant medical history in plain English, with correct
spelling and grammar. Roughly half the specimens received in a typical
pathology department conform to this description. Furthermore, this model
can serve as the basis for understanding the more complex situations,
in which an accessioned case arrives in the pathology laboratory with
multiple specimens from one or more procedures performed on the patient.
2. When the specimen and paperwork arrives in the laboratory,
an accession clerk verifies the paperwork, and assigns a unique accession
number to the specimen-and-paperwork ensemble, known as an accession.
A sample surgical pathology report is illustrated in Table 1. The format
for this pathology report is United States Government
Tissue Examination Form, Standard Form 515.
All U. S. Government installations use the same form, and academic
and community hospital tissue examination forms contain essentially
the same information, although details differ. Different institutions
enforce the completion of these forms with different degrees of strictness.
For example, at the Baltimore VAMHCS, a form with a patient-name
not recognized in the hospital database, a form without a physician-name
or unsigned by a physician, or a form without a patient-history,
are not accepted, and an effort is made to resolve any problems with
the submitting physician. These procedures are minimum requirements
set by the College of American Pathologists.
3.
There are four general classes of data
in an anatomic pathology report:
Assigned numbers (accession number, procedure number, etc.).
Date/time stamps (date obtained, date received, date released).
Person (patient, submitting physician, pathologist).
Clinicopathologic information (brief clinical history, gross description, microscopic diagnosis).
4.
Accession numbers are assigned
by the pathology laboratory, and are used
to keep track of what specimens arrived in the laboratory. This accession
number assignment is ideally carried out in one physical location, using
a computerized Laboratory Information System (LIS) with a parallel offline
accessioning system (logbook). The LIS assigns the accession number, which
should be sequential and non-duplicated. If specimens are accepted and
accession numbers are assigned at more than one physical location,
then great care must be taken to keep numbering assignments at all the
physical locations in synchrony. This requirement is trivial as long as
the LIS is always functioning everywhere, but may become very convoluted
when different accession areas have dyssynchronous periods
of computer downtime.
5.
Date/time stamps
include: date obtained, date received, date released.
The LIS should not accept date/time information that is inconsistent,
such as a specimen obtained at a date/time later than specimen received.
On the other hand, reality is unpredictably complex, and there must be
mechanisms to override apparent inconsistencies in the usual
sequence-of-events in a pathology report. For example, what if the exact
date of a particular event is not known? When a patient cannot recall
the appearance of a particular symptom; or, for some older patients,
birthdate.
6.
There must be a
formalism for managing inexact dates.
In the VistA®
computer system used by Veterans Affairs Medical Centers, date/time
is denoted by seven decimal digits, followed by a decimal point, followed by
six decimal digits. The first digit denotes century (0=1700, 1=1800, 2=1900,
etc.). Thus, U. S. Veteran George Washington (born 1732) has a century digit
of 0; and U. S. Veteran George Bush (born 1924) has a century digit of 2
(DeGregorio, 1997). Digits two and three denote year; digits four and five
denote month (01=January, etc.); and digits six and seven denote day.
The first and second post-decimal digits denote hour (24-hour clock);
the third and fourth post-decimal digits denote minute; and the fifth and sixth post-decimal digits denote second. Missing values in the date/time are denoted with zero. Thus, an event happening during an unknown month in 1999 is denoted 2990000.000000; and an event happening at an unknown time on August 27, 1908 (birthdate of U. S. President Lyndon B. Johnson (DeGregorio, 1997)) is denoted 2080827.000000. The VISTA date/time numbering system is ideally suited for managing patient confidentiality on in a public data mine resource. All events can be rounded off to year-of-occurrence, simply by replacing all digits past the third digit with zero; or to decade-of-occurrence, by replacing all digits past the second digit with zero.
7.
Each person named on the report
(patient, submitting physician, pathologist)
must match up to a person on a list, who can be reached as necessary for
purposes of notification, billing, and followup. It is critical that the
paperwork reliably identifies the patient and the submitting physician,
and unambiguously links the paperwork to the specimen. Correct
identification is not easy to achieve, but is not an idle luxury.
A misidentification could mean the failure to assign a serious diagnosis
to a patient, or assigning a diagnosis to the incorrect patient. Patient
injury and legal action could ensue.
8.
Unusual names
must be spelled correctly, and common names must be
distinguished for different actual patients. For example, a thousand-bed
U. S. hospital can expect to add one new Mary Smith every week to its
patient identification system. The U. S. Social Security Number is not an
acceptable method for distinguishing among all the Mary Smiths, since there
is a known error rate in the social security system (about one percent), and
the immediate consequence of a misidentified patient is far more serious than
that of a misplaced social security payment. It is not acceptable to assign
Mary Smith a new identification number each time her physician submits a new
specimen to the pathology laboratory, because the certain knowledge of a
patient's prior diagnoses is critical toward understanding each subsequent
diagnosis. Finally, uncommon names with unusual spellings must be spelled
consistently for each entry into the LIS, and aliases (i.e., different names
used by the same patient) must be known and managed appropriately by the LIS.
9.
Clinicopathologic information
includes: brief clinical history,
gross description, microscopic diagnosis, and typically appears on a
pathology report as free-text. This free-text is the most unstructured part
of the pathology report, and is difficult both to enter correctly and to
recover satisfactorily in data mining investigations. Clinical histories
are received from other departments, so that one makes the effort to clarify
an unintelligible clinical history only if the clinical information
is perceived as critical to the final diagnosis on the pathology report.
In many cases, medical histories replete with misspellings, nonsequiturs,
and missing information are accepted. Gross description and microscopic
diagnosis are under the administrative control of the pathology laboratory,
but there is typically little motivation to achieve standards of spelling
and punctuation beyond those necessary for a presentable report.
10.
The microscopic diagnosis field
contains the final result of the anatomic
pathology examination. The microscopic diagnosis is referred to by a number
of different names, including diagnostic impression, diagnosis, microscopic
evaluation, and even report. The lack of consistent terminology for common
data elements poses yet another obstacle for data mining efforts using stored
pathology reports. In our experience, approximately half the microscopic
diagnosis fields from anatomic pathology reports must be copyedited before
the reports are optimally suitable for data mining investigations. In some
cases, this copyediting might consist of little more than inserting
appropriate sentence terminators. In other cases, major revision might be
necessary to correct misspellings, and to reconstruct sentences into a
grammatically correct and unambiguous text.
11.
Converting Parts of a Report into Object Domains.
In the Laboratory Information System (LIS), the report database
is separated into fields, and certain minimum standards are enforced
by the system. For example, the date/time that the specimen was removed
from the patient must precede temporally the date/time that the specimen was
received in the pathology laboratory; and in turn, the date/time that the
specimen was received in the pathology laboratory must precede the date/time
that a final report was issued by the pathology laboratory. The name of the
patient must correspond to an identifier recognized by a third-party-payer
(insurance carrier); the name of the submitting physician must correspond
to an identifier to whom the report can be sent (in order to receive
payment); and the name of the attending pathologist must correspond
to an identifier who can be disciplined if the report is tardy. The
advantage of such a LIS is a level of managerial control over workloads,
turnaround times, and billing that a simple word processor system cannot
offer. An important byproduct of this enforced structure is that such
systems contain data that are usable in data mining projects. However,
in the commercial setting, there is always a tradeoff between strict
enforcement of standards and offending the customer, so that optimal data
standards are not always achieved.
12.
In complex cases,
the submitting physician may submit multiple pieces
of tissue from the same patient, taken during a single outpatient visit
or inpatient encounter. For example, Table 1 describes two containers taken
at the same encounter from the patient, and consecutively numbered by the
submitting physician. The final pathology report must reproduce the
numbering produced by the submitting physician. All discrepancies
in the actual containers received and their descriptions on accompanying
paperwork must be resolved in the final report.
13.
There are two other natural divisions
in a multi-container anatomic pathology
accession: procedure and bodysite. Many multi-part pathology reports do not
unambiguously reflect these divisions; and in our conversations with
colleagues, we are convinced that some of our colleagues do not clearly
understand these divisions. However a correct assignment of these divisions
is essential for making sense of the data in any anatomic pathology data mine
resource, and for many quality assurance surveys.
14.
For example, suppose that a surgeon performs a total laryngectomy on a patient with previously diagnosed squamous cell carcinoma of the left true vocal cord. The patient has hard, palpable lymph nodes (probable metastatic cancer) on both sides of the neck, so the surgeon performs a bilateral radical neck dissection in the same operative session. The surgeon also notices two small, irregular black macules (i.e., flat skin discolorations), one over the right clavicle, the other over the left scapula, and removes them for diagnosis. The laryngectomy specimen arrives in the pathology laboratory in container #1. Ten surgical margin specimens arrive in containers #2 through #11. The right radical neck dissection arrives in container #12, and the left radical neck dissection arrives in container #13. The right clavicular skin excision arrives in container #14, and the left scapular skin excision arrives in container #15.
15.
These fifteen containers separate logically into five surgical procedures,
namely, laryngectomy, right radical neck dissection, left radical neck
dissection, right clavicular skin excision, and left scapular skin excision.
The laryngectomy procedure subdivides into at least sixteen bodysites; the
right and left radical neck dissections subdivide into nine bodysites apiece;
and each of the skin excisions and their surgical margins subdivide
into five bodysites apiece (Rosai and Ackerman, 1996; Hruban et al, 1996;
Association of Directors of Anatomic and Surgical Pathology, 1997).
The structure of the mined database must capture these divisions and
subdivisions, in order to be optimally useful to epidemiologists
and tissue resource specialists.
16.
Sometimes the submitting physician does not even accurately identify
the site of origin of a specimen, omitting such details as left versus right,
medial versus lateral, or superior versus inferior. Sometimes the anatomical
orientation is resolved in such a convoluted manner that only an expert can
reasonably understand what is intended. In any event, no commercially
available LIS enforces the correct disambiguations from carelessly composed
pathology reports. Ensuring that reports can be automatically parsed into
data elements that accurately represent the concepts included in the
free-text report is one of the greatest impediments (and challenges)
to the advancement of pathology informatics.
Table 1. Surgical Pathology Sample Report.
U. S. Government Standard Form 515
U. S. Government Standard Form 515
MEDICAL RECORD | SURGICAL PATHOLOGY
PATHOLOGY REPORT
Laboratory: BALTIMORE VAMHCS Accession No. BSP 99 8888
Submitted by: J SURGEON MD Date obtained: Jan 14, 1999
Specimen (Received Jan 15, 1999 10:32):
1. LARYNGECTOMY.
2. LEFT RADICAL NECK DISSECTION.
Brief Clinical History:
SQUAMOUS CARCINOMA, LEFT TRUE CORD.
Preoperative Diagnosis:
SQUAMOUS CARCINOMA, LEFT TRUE CORD.
Operative Findings:
SAME.
Postoperative Diagnosis:
SAME.
Surgeon/physician: J SURGEON MD
Gross description:
PATIENT IDENTIFICATION AGREES WITH REQUISITON AND TWO CONTAINERS.
1. THE SPECIMEN IS RECEIVED FRESH, LABELED WITH THE PATIENT'S NAME,
AND ADDITIONALLY LABELED "LARYNGECTOMY".
THE SPECIMEN CONSISTS OF A LARYNGECTOMY RESECTION, MEASURING
10.5 X 5.5 X 3.5 CM. THE LARYNX IS EDEMATOUS. THE LARYNX IS OPENED
POSTERIORLY, TO REVEAL AN IRREGULARITY OF APPARENT TUMOR, ON THE SURFACE
OF THE LEFT TRUE VOCAL CORD, MEASURING 3.0 X 1.5 CM. THE TUMOR DOES NOT
APPEAR TO INVOLVE THE SUBGLOTTIS, NOR THE ANTERIOR COMMISSURE. THE SUPERIOR,
INFERIOR, ANTERIOR, AND POSTERIOR MARGINS ARE GROSSLY UNINVOLVED BY TUMOR
REPRESENTATIVE SECTIONS OF TUMOR ARE SUBMITTED, AS WELL AS THE SURGICAL
MARGINS, AS FOLLOWS:
SUMMARY OF SECTIONS:
1-1, 1 PIECE. TRACHEAL MARGIN.
1-2, 1 PIECE. BASE OF TONGUE MARGIN.
1-3, 1 PIECE. RIGHT PYRIFORM SINUS MARGIN.
1-4, 1 PIECE. LEFT PYRIFORM SINUS MARGIN.
1-5, 1 PIECE. ANTERIOR SOFT TISSUE MARGIN.
1-6, 1 PIECE. POSTERIOR SOFT TISSUE MARGIN.
1-7, 1 PIECE. LESION OF THE LEFT TRUE CORD.
1-8, 1 PIECE. LESION OF THE LEFT TRUE CORD.
1-9, 1 PIECE. LESION OF THE LEFT TRUE CORD.
1-10, 1 PIECE. EPIGLOTTIS.
2. THE SPECIMEN IS RECEIVED FRESH, LABELED WITH THE PATIENT'S NAME,
AND ADDITIONALLY LABELED "LEFT RADICAL NECK DISSECTION". THE SPECIMEN
CONSISTS OF A LEFT RADICAL NECK DISSECTION, MEASURING 25.0 X 15.0 X 5.0 CM.
THE SPECIMEN IS DIVIDED INTO LEVELS 1, 2, 3, 4, AND 5. IN LEVEL 1,
THE SALIVARY GLAND AND ONE PROBABLE LYMPH NODE ARE SUBMITTED.
IN LEVEL 2, SIX PROBABLE LYMPH NODES ARE SUBMITTED.
IN LEVEL 3, TWO PROBABLE LYMPH NODES ARE SUBMITTED.
IN LEVEL 4, ELEVEN PROBABLE LYMPH NODES SUBMITTED.
IN LEVEL 5, FIVE PROBABLE LYMPH NODES ARE SUBMITTED.
REPRESENTATIVE SECTIONS ARE SUBMITTED, AS FOLLOWS:
SUMMARY OF SECTIONS:
1-1, 1 PIECE. LEVEL 1.
2-1, 5 PIECES. LEVEL 2.
3-1, 5 PIECES. LEVEL 2.
4-1, 4 PIECES. LEVEL 3.
5-1, 3 PIECES. LEVEL 3.
6-1, 6 PIECES. LEVEL 3.
7-1, 5 PIECES. LEVEL 4.
8-1, 5 PIECES. LEVEL 4.
9-1, 4 PIECES. LEVEL 5.
Microscopic exam/diagnosis:
1. SQUAMOUS CELL CARCINOMA OF LEFT TRUE CORD, WELL-DIFFERENTIATED, INVASIVE.
SURGICAL MARGINS OF RESECTION ARE FREE OF TUMOR.
2. RADICAL NECK DISSECTION. SALIVARY GLAND WITH NOEVIDENCE OF MALIGNANCY.
ELEVEN OF TWENTY-THREE LYMPH NODES WITH METASTATIC SQUAMOUS CELL CARCINOMA,
AS FOLLOWS.
LEVEL I: SALIVARY GLAND AND ONE LYMPH NODE WITH NO EVIDENCE OF MALIGNANCY.
LEVEL II: THREE OF FIVE LYMPH NODES WITH METASTATIC SQUAMOUS CELL CARCINOMA.
LEVEL III: ONE OF TWO LYMPH NODES WITH METASTATIC SQUAMOUS CELL CARCINOMA.
LEVEL IV: SEVEN OF TEN LYMPH NODES WITH METASTATIC SQUAMOUS CELL CARCINOMA.
LEVEL V: FIVE LYMPH NODES WITH WITH NO EVIDENCE OF MALIGNANCY.
JOHN Q PATHOLOGIST MD xyz| Date Jan 16, 1999
VETERAN,JOHN Q. STANDARD FORM 515
ID:123-45-6789 SEX:M DOB:12/01/1940 AGE:58 LOC:ENT J SURGEON
Table 2. XML File for Surgical Pathology
Sample Report
<?xml version="1.0" ?>
<!DOCTYPE path_report
<path_report>
<accession> BSP 99 8888
<lab_identifier> BALTIMORE VAMC SURGICAL PATH </lab_identifier>
<time>
<time_obtained> Jan 14, 1999 14:18 </time_obtained>
<time_received> Jan 15, 1999 10:32 </time_received>
<time_reported> Jan 18, 1999 09:18 </time_reported>
<time_amended></time_amended>
<time_supplemented></time_supplemented>
</time>
<submission>
<submitting_physician> J SURGEON MD </submitting_physician>
<submitting_service> SURGERY </submitting_service>
</submission>
<pathologist> JOHN Q PATHOLOGIST MD </pathologist>
<patient>
<patient_name> VETERAN,JOHN Q. </patient_name>
<patient_identifier> 123-45-6789 </patient_identifier>
<date_of_birth> 12/01/1940 </date_of_birth>
<patient_gender> M </patient_gender>
<patient_ethnicity> WHITE </patient_ethnicity>
</patient>
<procedure> LARYNGECTOMY AND LEFT NECK DISSECTION
<procedure_cui> C0023065, C0205091, C0034542
</procedure_cui>
<specimen> LARYNX
<specimen_cui> C0023078 </specimen_cui>
<unique_specimen_identifier> 9876543
</unique_specimen_identifier>
<container>
<container_number> 1 </container_number>
<label> LARYNGECTOMY </label>
<gross>
<gross_description> THE SPECIMEN IS RECEIVED FRESH,
LABELED WITH THE PATIENT'S NAME, AND ADDITIONALLY LABELED "LARYNGECTOMY".
THE SPECIMEN CONSISTS OF.... </gross_description>
<lesion_size> 3 cm </lesion_size>
</gross>
<diagnosis>
<diagnosis_number> 1 </diagnosis_number>
<disease_concept> SQUAMOUS CELL CARCINOMA </disease_concept>
<disease_concept_cui> C0280324, C0007137
</disease_concept_cui>
<disease_modifiers> WELL DIFFERENTIATED SQUAMOUS CARCINOMA
OF LARYNX </disease_modifiers>
<disease_modifiers_cui> C0205615 </disease_modifiers_cui>
<diagnosis_number>2</diagnosis_number>
<disease_concept> MARGINS FREE OF TUMOR
</disease_concept>
<disease_concept_cui> C0332648 </disease_concept_cui>
<disease_modifiers></disease_modifiers>
<comment> </comment>
</diagnosis>
</container>
</specimen>
<specimen> LEFT NECK
<unique_specimen_identifier> 9876544
</unique_specimen_identifier>
<container>
<container_number> 2 </container_number>
<label> LEFT </label>
<gross>
<gross_description> THE SPECIMEN IS RECEIVED FRESH,
LABELED WITH THE PATIENT'S NAME, AND ADDITIONALLY LABELED
"LEFT RADICAL NECK DISSECTION". THE SPECIMEN CONSISTS OF....
</gross_description>
</gross>
<diagnosis>
<diagnosis_number>1</diagnosis_number>
<disease_concept> METASTATIC SQUAMOUS CARCINOMA
</disease_concept>
<disease_concept_cui> C0334246, C0280399
</disease_concept_cui>
<disease_modifiers></disease_modifiers>
<disease_modifiers_cui></disease_modifiers_cui>
<comment> METASTATIC SQUAMOUS CARCINOMA
FOUND IN 11 OF 23 EXAMINED LYMPH NODES </comment>
<diagnosis_number>2</diagnosis_number>
<disease_concept> NO EVIDENCE OF MALIGNANCY
</disease_concept>
<disease_concept_cui> C0391857 </disease_concept_cui>
<disease_modifiers></disease_modifiers>
<disease_modifiers_cui></disease_modifiers_cui>
<comment> SALIVARY GLAND </comment>
</diagnosis>
</container>
</specimen>
</procedure>
</accession>
</path_report>
REFERENCES.
1.
Rosai J.
Ackerman's Surgical Pathology. Eighth Edition.
St. Louis: C. V. Mosby. 1996.
2.
Westra WH, Hruban RH, Phelps TH, Isacson C.
Surgical Pathology Dissection. An Illustrated Guide.
Second Edition. With a Forward by Askin FB.
New York: Springer. 2002.
ISBN 0-387-95559-3, 258 pages.
3.
Lester SC.
Manual of Surgical Pathology.
New York: Churchill Livingstone. A Harcourt Health Sciences Company. 2001.
ISBN 0-443-07918-8, 336 pages.
4.
Sinard JH.
Outlines in Pathology.
Philadelphia: W.B.Saunders Company.
A Harcourt Health Sciences Company. 1996.
ISBN 0-7216-6341-9, 229 pages.
5.
American Joint Committee on Cancer.
AJCC Cancer Staging Manual. Sixth Edition.
New York: Springer. 2002.
ISBN 0-387-95271-3, 421 pages.
6.
Moore GW, Berman JJ.
Anatomic Pathology Data Mining.
Chapter 4. In: Cios KJ.
Medical Data Mining and Knowledge Discovery.
"Studies in Fuzziness and Soft Computing",
Physica-Verlag Heidelberg, a Springer-Verlag Company.