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bzkf / obds-to-fhir

This project contains a Kafka Stream processor that creates FHIR resources from oBDS-XML data and writes them to a FHIR Topic.
GNU General Public License v3.0
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bodysite: add ICD-O-3-Topography mapping #63

Open jasminziegler opened 1 month ago

jasminziegler commented 1 month ago

as of now, we map the oBDS bodysite to SCT with this mapping table: <html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns="http://www.w3.org/TR/REC-html40">

ADT Code | ADT Text | SCT Code | SCT Text -- | -- | -- | -- L | links | 7771000 | Left R | rechts | 24028007 | Right B | beidseitig (sollte bei bestimmten Tumoren 2 Meldungen ergeben) | 51440002 | Right and left / Both sides M | Mittellinie/Mittig | 260528009 | Median T | trifft nicht zu (Seitenangabe nicht sinnvoll, einschließlich Systemerkrankungen) | 396360001 | Tumor site not applicable (finding) U | unbekannt | 87100004 | Topography unknown

Lübeck created a concept map that maps ICD-O-3-Topography to Snomed-CT, see MII Zulip MII-Onko "Coding der bodySite in Onkologie Diagnosen"

It might be interesting to map this - to be discussed.

jasminziegler commented 1 month ago

could be difficult for UKER, we dont have ICD-O-3-T in our oBDS as of my current knowledge, but maybe other locations do?

edit: i checked again - we do have it in "Meldeanlass diagnose":

C80.9 32
pcvolkmer commented 1 month ago

In Würzburg, we have a body side entry (XPath: //Tumorzuordung/Seitenlokalisation) in almost every oBDS for the year 2022.

ICD-O-3-T is also present in many oBDS for 2022 (XPath: //Primaertumor_Topographie_ICD_O), but seems to be missing in some oBDS, even if ICD-O-3-T is present (today) in the documentation software.

At this point, I don't know if this is caused by missing documentation at the time of oBDS generation/export, a bug in the software or intentional in these cases.

As for Onkostar, oBDS can be checked using SQL:

SELECT with_body_side, with_icd_o_3_t, COUNT(*) FROM (
  SELECT
    EXTRACTVALUE(xml_daten, '//Tumorzuordung/Seitenlokalisation') <> '' AS with_body_side,
    EXTRACTVALUE(xml_daten, '//Primaertumor_Topographie_ICD_O') <> '' AS with_icd_o_3_t
  FROM lkr_meldung_export
  # change year or comment out for all entries
  WHERE YEAR(STR_TO_DATE(EXTRACTVALUE(xml_daten, '//Diagnosedatum'), '%d.%c.%Y')) = 2022
) sub GROUP BY with_body_side, with_icd_o_3_t
jasminziegler commented 2 weeks ago

https://simplifier.net/packages/de.dktk.oncology/1.1.1/files/405254

must support in new profiles: https://www.medizininformatik-initiative.de/Kerndatensatz/Modul_Onkologie/MIIIGModulOnkologie-TechnischeImplementierung-FHIRProfile-Diagnose-Diagnose-Condition.html