edits.seer.internal.rules.IFN7040.xml Maven / Gradle / Ivy

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Java implemenation of the SEER edits.
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        <rule id="IFN7040" name="Primary Site, Morphology-Type, Beh ICDO3, 2024 (SEER)" tag="N7040" java-path="lines.line" category="inter-field" depends="Year_of_Diagnosis">
            <expression><![CDATA[if (line.dateOfDiagnosisYear == null || line.dateOfDiagnosisYear < '2024')
    return true
if (line.primarySite == null || line.histologicTypeIcdO3 == null || line.behaviorCodeIcdO3 == null)
    return true

Integer siteNum = Functions.asInt(line.primarySite.substring(1))
Integer histNum = Functions.asInt(line.histologicTypeIcdO3)
Integer behNum = Functions.asInt(line.behaviorCodeIcdO3)

Map<String, Map<String, Map<String, String>>> naaccrPathChartTable = (Map<String, Map<String, Map<String, String>>>)Context.IFN7040_NAACCR_PathCHART_Table
Map<String, Map<String, String>> siteMap = (Map<String, Map<String, String>>)naaccrPathChartTable.get(siteNum);
Map<String, String> histMap = (Map<String, String>)siteMap?.get(histNum)
String status = histMap?.get(behNum)

if (status == null || status == '2')
    return line.overRideSiteType == '1'
else if (status == '1')
    return line.overRideSiteType == null
else if (status == '3')
    return false
return true
]]></expression>
            <message>Conflict between Primary Site, Histologic Type, and Behavior</message>
            <description><![CDATA[This edit checks on primary site, histologic type, and behavior combinations based on the PathCHART tables starting with 2024.  The edit checks for valid, unlikely, and impossible combinations.

1. This edit is skipped for any of the following:
    a. Diagnosis date blank (unknown), invalid, or before 2024.
    b. Any of Primary Site, Histologic Type ICD-O-3, or Behavior Code ICD-O-3 is blank


The SEER Site/Histology Validation List (see SEER web site) has traditionally designated all histologies/behaviors that do not require review for each site.
Any site/histology/behavior combination not in the Site/Histology Validation List was accepted only if the case was reviewed, accepted as coded, and
Over-ride Site/Type set to 1. Beginning with 2024, the SEER Site/Histology Validation List has been replaced by PathCHART, a database designating the status
for each site/type/behavior combination as valid ("1") or biologically impossible ("3"). The status for any site/histology/behavior combination not in PathCHART
is considered unlikely ("2"). The PathCHART database resulted from an extensive pathologic review of sites and histologies undertaken by NCI SEER, implemented
over the 2024 and 2025 diagnosis years.

The PathCHART table is imported into EditWriter from the PathCHART database.  The table includes all site/type/behavior combinations as they were evaluated in
existing edits through 2023, plus any site/type combinations with a change in status based on the PathCHART review beginning with 2024.  This edit will pass all
site/type/behavior combinations designated as "valid" ("1") in the corresponding table. This edit will fail all site/type/behavior combinations designated as
"impossible" ("3"). This edit will fail all site/type/behavior combinations not included in the table ("2"); Over-Ride Site/Type can be set for these cases to
allow them to pass the edit. Over-ride Site/Type should not be set for status "1" cases; Over-ride Site/Type cannot be set for status "3" cases.

Review of unlikely or rare combinations often results in changes to the primary site and/or morphology and/or behavior, rather than a decision that the
combination is correct.  The over-ride flag should not be set to 1 if the primary site, histologic type, and behavior is changed to a combination that will pass
the edit.  However, if upon review the site/type/behavior combination is found to be accurate and in conformance with coding rules, it may be left as coded and
the Over-ride Site/Type flag coded to 1.


Additional Information:

This edit forces review of atypical site/type/behavior combinations.  Combinations not requiring review are presented, by primary site, in the PathCHART database.
This edit does not imply that there are errors but rather that the combination of  site,histology, and behavior is so unusual that it should be checked to ensure
that it correctly reflects what is in the medical record.  Resolution of discrepancies may require inspection of the abstracted text, review of the original
medical record, or consultation with the pathologist or diagnosing physician.

Review of these cases requires investigating whether a) the combination is biologically implausible or unlikely, or b) there are cancer registry coding
conventions that would dictate different codes for the diagnosis.  The following resources can be checked:

    SEER PathCHART database
    Current oncology and pathology textbooks
    Current medical journal articles, e.g., via MEDLINE
    Pathologist advisors to the registry
]]></description>
            <history>
                <event version="SE24-024-03" user="beverung" date="2024-04-04" ref="69439">Edit created.</event>
                <event version="SE24-024-06" user="beverung" date="2024-06-21" ref="69477">Updated PathCHART table.</event>
            </history>
        </rule>