| Ontario Health - Cancer Care Ontario's Data Book - 2021-2022 |
|
Updated in February 2015
Pathology Report Body Data
The body of the pathology report is coded into OBX segments. The narrative and synoptic portions of the report are divided and preceded by their own OBR segments. The preceding OBR segments are identical except for their Set Id (OBR-1).
The Synoptic section(s) are always coded first. The Narrative-text section is always the last.
MSH
PID
OBR – Set id 1 (for a primary cancer)
OBX – Set id 1 (1st CAP Checklist identifier & version)
OBX – Set id 2 (Question and answer 1)
OBX – Set id 3 (Question and answer 2)
OBX – .
OBX – .
OBR – Set id 2 (for a secondary cancer)
OBX – Set id 1 (2nd CAP Checklist identifier & version)
OBX – Set id 2 (Question and answer 1)
OBX – Set id 3 (Question and answer 2)
OBX – .
OBX – .
OBR – Set id 3 (for narrative text information)
OBX – Set id 1 (Section Id and text 1)
OBX – Set id 2 (Section Id and text 2)
OBX – .
OBX – .
Narrative Text Data
Narrative report observations are coded in OBX segments with data type „FT‟ (Formatted Text). The code indicating the section id is located in the OBX-3 field and the corresponding section text is contained in OBX-5. The section id is LOINC encoded.
Observation Result (OBX) Segment
|
Field |
HL7 Field |
Opt |
Description |
|
1 |
Set ID |
R |
Observation /Result Sequence |
|
2 |
Value type |
R |
„FT. indicates narrative section |
|
3 |
Observation Identifier |
R |
Section ID for narrative section id (LOINC encoded) – see Narrative Section LOINC Codes below. |
|
4 |
Observation sub-ID |
X |
(not-used by ePath) |
|
5 |
Observation Value |
R |
Narrative text for the specified section |
|
6 |
Units |
X |
(not-used by ePath) |
|
7 |
Reference ranges |
X |
(not-used by ePath) |
|
8 |
Abnormal flags |
X |
(not-used by ePath) |
|
9 |
Probability |
X |
(not-used by ePath) |
|
10 |
Nature of abnormal test |
X |
(not-used by ePath) |
|
11 |
Observation result status |
R |
The observation result status: F - Final C - Change If the Result Status (in OBR-25) is „F. (Final) then all of its Observations should have an Observation result status of „F. If the Result Status (in OBR-25) is „C. (change) then the Observations that are new or modified should have an Observation result status of „C. (in OBX-11) and the rest (that are the same as the original report) should have an Observation result status of „F.. If the LIS does not maintain distinct result status at the observation level (i.e. doesn.t record which observations are new or modified), then all the observations should have their Observation result status set to „F. |
|
12 |
Effective Date of Reference Range Values |
X |
(not-used by ePath) |
|
13 |
User defined access checks |
|
(not-used by ePath) |
|
14 |
Date/time of the Observation |
|
(not-used by ePath) |
|
15 |
Producer’s Reference |
|
(not-used by ePath) |
|
16 |
Responsible observer |
|
(not-used by ePath) |
|
17 |
Observation method |
|
(not-used by ePath) |
|
18 |
Equipment Instance Identifier |
|
(not-used by ePath) |
|
19 |
Date/Time of the Analysis |
|
(not-used by ePath) |
|
20 |
Reserved for harmonization with V2.6 |
|
(not-used by ePath) |
|
21 |
Reserved for harmonization with V2.6 |
|
(not-used by ePath) |
|
22 |
Reserved for harmonization with V2.6 |
|
(not-used by ePath) |
|
23 |
Performing Organization Name |
|
(not-used by ePath) |
|
24 |
Performing Organization Address |
|
(not-used by ePath) |
|
25 |
Performing Organization Medical Director |
|
(not-used by ePath) |
Narrative Section LOINC Codes
|
Section Id |
LOINC Section Coding |
|
1. Clinical history |
22636-5^Path report.relevant Hx^LN |
|
2. Tissue submitted |
22633-2^Path report.site of origin^LN |
|
3. Gross pathology |
22634-0^Path report.gross description^LN |
|
4. Microscopic description |
22635-7^Path report.microscopic observation^LN |
|
5. Final diagnosis |
22637-3^Path report.final diagnosis^LN |
|
6. Comments |
22638-1^Path report.comments^LN |
|
7. Supplemental Reports |
22639-9^Path report.supplemental reports^LN |
|
8. Addendums |
35265-8^Path Report.addendum spec^LN |
Synoptic-like Summaries
Hospitals may produce a textual synoptic-like summary (a formatted multi-line list of the synoptic fields and values) within a formatted text observation. This information should always be placed in the “Microscopic description” section (LOINC Section Code: 22635-7^Path report.microscopic observation^LN) of the narrative observations.
Escape Sequences
Any non-ASCII characters or formatting embedded in the narrative text sections must be replaced by the appropriate escape sequence from the table below.
|
Sequence |
Description |
|
\F\ |
“|” (Field separator) |
|
\S\ |
“^” (Component separator) |
|
\T\ |
“&” (Sub-component separator) |
|
\R\ |
“~” (Repetition separator) |
|
\E\ |
Escape character |
|
\.fi\ |
Begin word-wrap |
|
\.nf\ |
Do not (end) word-wrap |
|
\.br\ |
Line break |
|
\X0D\ |
Carriage return |
|
\X0A\ |
Line Feed |
|
\X09\ |
Tab |
Discrete Synoptic Data
Discrete Synoptic data is coded as separate OBX segments (one data-element) with a data type of „CWE‟ (Coded with Exceptions). The identifier is coded in the OBX-3 field and the data value in OBX-5.
Observation Result (OBX) Segment
|
Seq |
HL7 Field |
Opt |
Description |
|
1 |
Set ID |
R |
Observation /Result Sequence |
|
2 |
Value type |
R |
„CWE. indicates discrete synoptic data |
|
3 |
Observation Identifier |
R |
The discrete synoptic data element name - See Coding Checklists as Discrete Synoptic Data below |
|
4 |
Observation sub-ID |
RE |
Used to link “Fixed-list-fill-in” observations - See Coding “Fixed-list-fill-in” Answers) below |
|
5 |
Observation Value |
R |
Value for discrete synoptic data element – See Coding Checklists as Discrete Synoptic Data below |
|
6 |
Units |
RE |
ISO or ANSI encoded unit of measure, if applicable to the observation value Example: mm^millimeter^ISO+ mo^month^ANSI+ |
|
7 |
Reference ranges |
X |
(not-used by ePath) |
|
8 |
Abnormal flags |
X |
(not-used by ePath) |
|
9 |
Probability |
X |
(not-used by ePath) |
|
10 |
Nature of abnormal test |
X |
(not-used by ePath) |
|
11 |
Observation result status |
R |
The observation result status: F - Final C - Change If the Result Status (in OBR-25) is „F‟ (Final) then all of its Observations should have an Observation result status of „F‟. If the Result Status (in OBR-25) is „C‟ (change) then the Observations that are new or modified should have an Observation result status of „C‟ (in OBX-11) and the rest (that are the same as the original report) should have an Observation result status of „F‟. If the LIS does not maintain distinct result status at the observation level (i.e. does not record which observations are new or modified), then all the observations should have their Observation result status set to „F‟. |
|
12 |
Effective Date of Reference Range Values |
X |
(not-used by ePath) |
|
13 |
User defined access checks |
X |
(not-used by ePath) |
|
14 |
Date/time of the Observation |
X |
(not-used by ePath) |
|
15 |
Producer’s Reference |
X |
(not-used by ePath) |
|
16 |
Responsible observer |
X |
(not-used by ePath) |
|
17 |
Observation method |
X |
(not-used by ePath) |
|
18 |
Equipment Instance Identifier |
X |
(not-used by ePath) |
|
19 |
Date/Time of the Analysis |
X |
(not-used by ePath) |
|
20 |
Reserved for harmonization with V2.6 |
X |
(not-used by ePath) |
|
21 |
Reserved for harmonization with V2.6 |
X |
(not-used by ePath) |
|
22 |
Reserved for harmonization with V2.6 |
X |
(not-used by ePath) |
|
23 |
Performing Organization Name |
X |
(not-used by ePath) |
|
24 |
Performing Organization Address |
X |
(not-used by ePath) |
|
25 |
Performing Organization Medical Director |
X |
(not-used by ePath) |
Coding of CAP eCC Elements
CAP eCCs are coded as discrete synoptic data. As discrete synoptic data, each CAP eCC data element has a data element name or “question”; and a data value or “answer”.
Example: The first data element in the Checklist for Breast Excisions has a question: “Specimen Type”; which can have an answer of “Mastectomy”.
A checklist’s data elements (questions and answers) are coded in HL7 in successive OBX segments: the OBX-3 field contains the question; and OBX-5 contains the answer.
Each question is composed of two (primary and alternate) identifiers from different coding systems (Ckey and SNOMED CT - as suggested by CAP[1]). The primary identifier is always required whereas the alternate identifier is only required when available.
|
Identifier |
Seq |
Component |
Usage |
Data Type |
Len |
Example |
|
Primary |
1 |
Identifier (Ckey) |
R |
ST |
20 |
16272.1 |
|
2 |
Text (eCC entry descriptor) |
R |
ST |
199 |
Histologic Type of Invasive Carcinoma (Note H) |
|
|
3 |
Name of Coding System |
R |
ID |
20 |
CAPECC |
|
|
Alternate |
4 |
Alternate Identifier (SNOMED CT Concept Id) |
RE |
ST |
20 |
371441004 |
|
5 |
Alternate Text (SNOMED CT descriptor) |
RE |
ST |
199 |
Histologic type |
|
|
6 |
Name of Coding System |
RE |
ID |
20 |
SCT |
HL7 Data Types: ST – String data; ID – Code value for HL7 defined tables
Usage: R – Required; RE – Required (or Empty if it is unavailable)
The Ckey (Composite key) is a decimal number assigned by CAP as an identifier for each question (question id) in the CAP eCC definitions[2] (released by CAP as individual Checklist-specific XML document template files). The SNOMED CT Concept Id is a code mapped to the question Ckeys (mappings are also released by CAP as separate XML documents).
The SNOMED CT code must be optional because some may not be assigned at the time that the CAP eCC is released. Destination systems can assign the missing SNOMED CT codes to received checklists at a later time, when their mappings are released (as long as the Ckeys are retained).
CAP eCC data elements may come with a pre-defined set of values for its answers. Each of these potential answers will have an assigned Ckey (answer id).
Other data elements may require answers to be purely ad-hoc such as numeric or free-text information. These will not have associated answer ids.
There can also be a combination of these two conventions, where a set of pre-defined values are provided along with an option of specifying an “Other”-type answer which allows free-entry of an ad-hoc value. In this case the pre-defined values as well as the “Other” option all have answer ids.
Coding “Free-text”
Data elements that have “free-text” answers (such as comment fields) accept any text or numerical values as answers. In this case coding the alternate identifier (SNOMED CT Concept Id) is omitted as it is not applicable.
Example:
OBX|19|CWE|16784.1000043 ^Comment(s)^CAPECC||^smaller invasive carcinomas differ||||||F|
Numeric measurement values should always be stated in the unit of measure specified by CAP for the particular data element. The unit of measure for the numeric value should be specified in the OBX-6 field when applicable.
Example:
OBX|11|CWE|16246.1000043^Specimen Size (for excisions less than total mastectomy) (Note C)^CAPECC||^2.3|cm^centimeter^ISO+|||||F|
In past versions of the CCO Interface specification, numeric values were coded as left-zero-padded strings with implied decimal place (e.g. “023” for 2.3). This encoding is no longer required. Simply specify numbers as their string equivalent (i.e. “2.3”).
Coding “Fixed List” Answers
Questions that require “fixed list” answers have an associated set of pre-defined values. To code a “fixed list” answer specify the relevant answer id and descriptor as the primary identifier and the mapped SNOMED CT Concept Id and descriptor as the alternate identifier (if it exists).
Example:
OBX|2|CWE| 16272.1000043^Specimen (Note A)^CAPECC||16221.1000043^Partial Breast^CAPECC||||||F|
Coding “Fixed-list-fill-in” Answers
A “fixed list” answers may accept a “fill-in” answer which is an ad-hoc text response to the eCC element question.
Unlike the “free-text” answers, a “fixed-list-fill-in” answer has an associated Ckey (answer id). To code this type of answer, the answer id and the CAPECC coding system are coded in the answer (OBX-5 field). Coding the alternate identifier (SNOMED CT Concept Id) is omitted as it is not applicable.
The prefix-text of a “fill-in value” answer (e.g. “Other (specify)” is included in its own OBX segment along including the answer id. The filled-in text portion is coded in its own subsequent OBX segment with no answer id.
To link these two parts of the answer, the observation sub-id (OBX-4) component of each of these OBX segments is populated with the first (integer) part of the answer’s Ckey
Example:
OBX|26|CWE|16272.1000043^ Histologic Type of Invasive Carcinoma (Note H)^CAPECC^371441004^Histologic type^SCT|16292|16292.1000043^ Other(s) (specify)^CAPECC||||||F|
OBX|27|CWE|16272.1000043^ Histologic Type of Invasive Carcinoma (Note H)^CAPECC^371441004^Histologic type^SCT|16292|^Ductal carcinoma in situ with no microinvasion||||||F|
Coding Multi-value-selection Answers
When eCC element with a value-list allows multiple value selections in an answer (i.e. “check all that apply”), the multiple selections are coded in successive OBX segments each with the same coded question (i.e. identical OBX-3 fields).
Example: OBX|6|CWE| 16250.1000043^Tumor Site: Invasive Carcinoma (Note D^CAPECC^ 371480007^Tumor site^SCT||16254.1000043^Lower inner quadrant^ CAPECC^19100000^Structure of lower inner quadrant of breast^SCT||||||F|
OBX|7|CWE|16250.1000043^ Tumor Site: Invasive Carcinoma (Note D^CAPECC^ 371480007^Tumor site^SCT||16255.1000043^Central^ CAPECC^49058007^Structure of central portion of breast^SCT||||||F|
Coding the Checklist Identifier and Version
The Checklist Identifier and Version should be specified in the first OBX segment of the message with a CWE (Coded with exceptions) data type[3].
The CAP eCC Identifier for a particular checklist is its “template-id”. This is specified as an attribute within the particular CAP eCC definition XML document. This identifier is in the form of a Ckey (e.g. 189.1000043 for the “Carcinoma of the Breast: Complete Excision” checklist)
The version of a checklist defines its particular CAP eCC release (e.g. 2.000.011 for the April 2010 release of the CAP eCC). The CAP eCC Identifier for the checklist version is its “template-xml-version” (This attribute is only available in the CAP eCC XML from the May 2010 release and onward.
The Checklist Identifier and Version are concatenated together (delimited by a “:”) and coded into the OBX-5 component.
Example:
OBX|1|CWE|VERSION^Template Version Identifier^L||189.1000043:2.000.011^INVASIVE CARCINOMA OF THE BREAST: Complete Excision …^CAPECC||||||F|
This would represent the CAP eCC for the April 2010 release for “Carcinoma of the Breast: Complete Excision”.
Handling Multiple Checklists
To code multiple eCCs, the OBX segments for each set of checklists is preceded by its own OBR segment[4] (see § “Pathology Body Data”).
General Information regarding Transmission of Biomarker Templates
In order for CCO to be able to link all reports related to same specimen, please ensure the following referring facility information is always provided:
1. Referred from Accession Number in OBR-2
2. Referred from Master Number in PID-3
There is no HL7 specification change. Biomarker reporting follows the same HL7 message reporting instructions as submitting a consult report the only difference the consult report should be in synoptic format.
Use Case messaging for Transmission of Biomarker Template
Below are 3 examples of sample messages, which can be used to cover the above Biomarker Laboratory Flow Scenarios.
Example 1: Reporting of HL7 resection message
Hospital 1 signs off synoptic report (e.g. Invasive carcinoma) – report 1.
MSH|^~\&|PATHLAB_LIS|HSP1^1111^MOH|PIMS|CCO |…………………
PID|1||^^^^CMR^ Hospital 1&1111 &MOH~^^^^MRN^ Hospital 1&1111&MOH~9999999999&FT&ON^^^^JHN||patient^abcd………………
OBR|1||HOSP1-01|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L|||……………
OBX|1|CWE|VERSION^Template Version Identifier^L||189.1000043:2.005.001^INVASIVE CARCINOMA OF THE BREAST……………….
……………………
OBR|2||HOSP1-01|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L|||……………
OBX|1|FT|22636-5^Path report.relevant Hx^LN||Clinical history||||||F|
……………………
OBX|4|FT|22635-7^Path report.microscopic observation^LN||Microscopic description: the place for OBR 1 textual synoptic-like summary
…………………….
Hospital 1 sends a request to Hospital 2 for HER2. Hospital 2 performs HER2 studies and signs off report 2 (uses CAP Breast Biomarker Template) to Hospital 1 and to CCO.
MSH|^~\&|PATHLAB_LIS| HSP2^2222^MOH|PIMS|CCO|…………………….
PID|1||^^^^CMR^Hospital 1&1111&MOH~^^^^RMR^Hospital 1&1111&MOH~^^^^MRN^Hospital 2&2222&MOH~9999999999&ON^^^^JHN||patient^abcd………………
OBR|1|HOSP1-01|HOSP2-02|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L||……|Y|…………….
OBX|1|CWE|VERSION^Template Version Identifier^L||169.1000043:1.000.000^ BREAST: Biomarker Reporting Template……………….
OBR|2|HOSP1-01|HOSP2-02|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L|||…...|Y|………
OBX|1|FT|22636-5^Path report.relevant Hx^LN||Clinical history||||||F|
……………………
OBX|4|FT|22635-7^Path report.microscopic observation^LN||Microscopic description: the place for OBR 1 textual synoptic-like summary |||
…………….
Notes:
Synoptic consult
PID -3: collected and referred from = Hospital 1 master number 1111
OBR-2: referred from specimen number i.e. HOSP1-01 (accession number of original cancer case)
Consult (OBR-20 = Y)
Hospital 2 sends a request to Hospital 3 for HER2 FISH. Hospital 3 performs HER2 FISH and signs off report 3 (uses CAP Breast Biomarker Template) to Hospital 2 and to CCO.
MSH|^~\&|PATHLAB_LIS| HSP3^3333^MOH|PIMS|CCO|…………………….
PID|1||^^^^CMR^Hospital 1&1111&MOH~^^^^RMR^Hospital 2&2222&MOH~^^^^MRN^Hospital 3&3333&MOH~9999999999&ON^^^^JHN||patient^abcd………………
OBR|1|HOSP2-02|HOSP3-03|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L||……|Y|…………….
OBX|1|CWE|VERSION^Template Version Identifier^L||169.1000043:1.000.000^ BREAST: Biomarker Reporting Template……………….
OBR|2|HOSP2-02|HOSP3-03|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L|||…...|Y|………
OBX|1|FT|22636-5^Path report.relevant Hx^LN||Clinical history||||||F|
……………………
OBX|4|FT|22635-7^Path report.microscopic observation^LN||Microscopic description: the place for OBR 1 textual synoptic-like summary |||
…………….
Notes:
Synoptic consult
PID -3: collected = Hospital 1 (master number 1111), referred from = Hospital 2 (master number 2222)
OBR-2: referred from specimen number i.e. HOSP2-02
Consult (OBR-20 = Y)
Example 2: Centralized testing using same accession number
Hospital 1 sends a request to Hospital 1’s internal department for HER2. Hospitals 1 internal department performs HER2 studies and signs off report 2 – same accession number (uses CAP Breast Biomarker Template); both
reports are sent CCO.
MSH|^~\&|PATHLAB_LIS| Hospital1^1111^MOH|||201403151124……………………
PID|1||^^^^CMR^Hospital&1111&MOH~^^^^MRN^Hospital&1111&MOH~9999999999&&ON^^^^JHN||…………………..
OBR|1||HOSP1-01|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L|||20140308……………………|C|.………..
OBX|1|CWE|VERSION^Template Version Identifier^L||189.1000043:2.005.001^INVASIVE CARCINOMA OF THE BREAST : Complete ^CAPECC||||||C
OBX|2|CWE ……………………………..
…………..
OBR|2||HOSP1-01|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L |||20140308……………..……|C|….
OBX|1|CWE|VERSION^Template Version Identifier^L||169.1000043:1.000.000^BREAST : Biomarker^CAPECC||||||C|
OBX|2|CWE|29485…
………………
OBR|3||HOSP1-01|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L………………………………|C|….
……………..
OBX|4|FT|22635-7^Path report.microscopic observation^LN||Microscopic description: the place for OBR 1 textual synoptic-like summary ||||||C|
…………….
OBX|7|FT|35265-8^Path Report.addendum spec^LN||Addendum reports: the place for OBR 2 textual synoptic-like summary ||||||C|||
Notes:
• Synoptic addendum
• 3 OBRs: OBR|1| synoptic original cancer case; OBR|2| synoptic HER2 results; OBR|3| narrative with addendum segment
• OBR-3 = same specimen number i.e. HOSP1-01 (accession number of original cancer case)
• Result Status = C in OBR-25 and OBX-11
Example 3: Centralized testing using different accession number
Hospital 1 sends a request to Hospital 1’s internal department for HER2. Hospitals 1 internal department performs HER2 studies and signs off report 2 - different accession number (uses CAP Breast Biomarker Template); both
reports are sent CCO
MSH|^~\&|PATHLAB_LIS|HSP1^1111^MOH|PIMS|CCO |…………………
PID|1||^^^^CMR^Hospital 1&1111&MOH~^^^^MRN^ Hospital 1&1111&MOH~9999999999&FT&ON^^^^JHN||patient^abcd………………
OBR|1|HOSP1-01|HOSP1-02|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L|||……………
OBX|1|CWE|VERSION^Template Version Identifier^L|| 169.1000043:1.000.000^BREAST : Biomarker^CAPECC ……………….
……………………
OBR|2|HOSP1-01|HOSP1-02|11529-5^Surgical Pathology Study Report^LN^P^Pathology^L|||……………
OBX|1|FT|22636-5^Path report.relevant Hx^LN||Clinical history||||||F|
……………………
OBX|4|FT|22635-7^Path report.microscopic observation^LN||Microscopic description: the place for OBR 1 textual synoptic-like summary ||||||C|
…………….
Notes:
• Synoptic
• OBR|1| synoptic HER2 results
OBR-2: referred from specimen number i.e. HOSP1-01 (accession number of original cancer case)
[1] Oct. 16, 2009 CAP Webinar – “eCC conversation with the College of American Pathologists”
[2] Ckeys are also used to identify templates (template-id) fixed value answers for some questions (answer-id)
[3] NAACCR Standards for Cancer Registries Vol.5 - Pathology Laboratory Electronic Reporting Version 3 §3.2 Question 2
[4] NAACCR Standards for Cancer Registries Vol.5 - Pathology Laboratory Electronic Reporting Version 3 §3.2 Questions 6 & 8