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Speicmen CMT presentation for SHIELD

Presentation on September 10, 2024 went welll - here is the link to the recording: 2024-09-10 SHIELD Topic#2 Call Meeting Notes

HL7 FHIR Profile: Skin and Wound Assessment, Release 1 (For Comment)

Background in the Proposal:  Skin and Wound Assessment - FHIR - Confluence (hl7.org)  There was a vendor that created a FHIR App that apparently is used.

While not specific about pathology there was much discussion on how to document "landmarks" on the body like moles, tattoos, etc in relation to wound location.  Conceivably, if a wound culture was performed, the specimen source site info would overlap with wound details.  Pathology specimens would have similar needs.   There are various refsets, value sets and SCT extensions listed.  It was mentioned it should align with laboratory and pathology specimen information, but I haven't reviewed the codes/terms.  Not sure if anything they developed would fill any CMT gaps or already contained therein?   Mitre did a lot of the work on this too.  

Discussion:

specimen condition and reject reason work

Here is the confluence page where OO is tracking this project: https://confluence.hl7.org/display/OO/Specimen+Condition+and+Specimen+Reject+Reason+Vocabulary

Next step is to review against the concepts in

#1 Standard PREanalytical Code Version 4.0 - (version 3.0 is here: https://cdn.ymaws.com/www.isber.org/resource/resmgr/isber_2019/pdf/standard_preanalytical_code_.pdf) maybe consider using this (if so, HL7 would need joint copyright or something) and also

#2 international standard for biobanking: the ISO 20387:2018 - is anyone member and has access?

• Annex A lists some requirements regarding documented information during sample acquisition (see A.2 Acquisition)

• Annex B gives a list of examples for the respective requirements mentioned in Annex A (see B.2 Acquisition). Based on the acceptance criteria 'reject reasons' can be deduced.

#3 ISBER BP5 for information regarding 'Specimen Reject Reason'

Previous Action Items

• Nancy Follow up:

  • EDTA Stopper top

    • EDTA sufficient or do we need to specify K2 or K3?

    • Nancy can review the list in SNOMED from John

    • Need to check on completeness against the Anne/Nancy list (compare with ARUP)

      • Nancy/Anne’s list is 10 years old - may not want to compare with this outdated list and use ARUP and Labcorp lists

      • Raj: I found this at a phlebotomy certification course website: What Color Tubes Are Used for Which Tests in Phlebotomy – PhlebotomyU

        • Here's a nice one-pager (University of Colorado Health): https://www.testmenu.com/universityhospital/TestDirectory/SiteFile?fileName=sidebar\CLNLAB-2020-03-13-Blood-Tube-Color-Chart.pdf

        • Cleveland Clinic: Blood Collection Tubes - Collection | Cleveland Clinic Laboratories

    • https://phlebotomygeeks.yolasite.com/resources/PRINT OUT COMMON TUBES.pdf

      • but color is manufacturer dependent, which is why we named the tubes by the additives

      • there are container types in SNOMED under 706049005 |Blood tube (physical object)|

      • Have a start here: https://aphlinformatics.atlassian.net/wiki/download/attachments/2018312270/ContainertypesListRikiEmailed20171013.xlsx?api=v2

      • K1 or K2 might be important to differentiate

    • We should leave the top color out of it, since that is manufacturer specific

    • Nancy will see, if their fellow has time to review and complete the list for us (she is a phlebotomist )

  • Contact United Network for Organ Sharing for input on donor terms (pre-coordinated or not?) = Contact - UNOS

    • Riki filled out the form - No repsonse

    • ISBT 128 | ICCBBA | Technical Documents

      • https://www.isbt128.org/_files/ugd/1a7593_edfd176861c94dca94c34eff8fa3ad0d.pdf - for organs

    • Might be a topic for SNOMED International

      • We may need to reach out to laboratories/industry to see if the donor codes are needed (we need to show that these codes are needed.)

    • Riki has some contact now with European bloodbank and biobanks = Home - BBMRI-ERIC working with the folks that define their minimum data set: MIABIS - BBMRI-ERIC

• Riki’s Follow up - none of these got done yet 😞

  • liquid-based cytology specimen vial = https://us-request.ihtsdotools.org/#/requests/preview/354843?fromList=truehttps://request.ihtsdotools.org/#/requests/edit/786429

  • submit a code for formalin10

  • work with John

    • new term for pacemaker insertion site sample

      • in SCT there are only swabs for insertion sites (line, drain, chest tube, vascular catheter) - this should be fixed

      • we should model it after 435971000124108 | Body fluid specimen from peritoneal dialysis insertion site (specimen) and require method, which should be aspirate

    • For wound modeling (see 2023-11-30 LabMCoP Meeting Notes ) create a few pre-coordinated specimen terms

      • to cover the wound causes as children under: 119365002 | Specimen from wound (specimen)

      • another child term for aspirate under 445611000124106 | Specimen from bite wound (specimen), since that is preferred over the existing swab

    • IDSA has a guidelines for wound cultures (deep and superficial - related to surgical wounds) - link sent to Amy

Specimen CMT - review of terms with questions

Specimen CMT pilot implementers

• Review where we are: Vendor Connections

  • no update

Specimen CMT - Hosting Options

• How can we publish the content in the dB?

  • Allow access somehow to query the dB

  • as access or excel or csv

  • Using FHIR conceptMap similar to Conceptmap-example-specimen-type - FHIR v6.0.0-cibuild - based on this profile: ConceptMap - FHIR v6.0.0-cibuild

  • riki.merrick to ask Eric if he still has that or how he built it:

  • ANSWER FROM ERIC:

    • if you look in the xml source Conceptmap-example-specimen-type.xml - FHIR v6.0.0-cibuild . you can see how it is mapped. 

    • I am not sure if you mean the table rendering or creating the concept map from a spreadsheet or CSV file.  The FHIR build tool did the table rendering for that mapping, I think I entered the data by hand, or Grahame did it. It would not be hard to create a script to create a concept map from an excel or csv file if needed.  The table needs to be large enough to make it worthwhile though. you could even create formula cells in the spreadsheet to generate the XML or json for each item. and then copy to a text editor and append to the Metadata fields.

    • Manjula will take a look at the concept map

Specimen CMT - education

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

Specimen CMT - Compare to NHS Medical Terminology testing

LOINC to SNOMED CT mapping

Future projects for this call after CMT

• In general the call is intended as a forum for ANY messaging related issues to work out.

• In the past we have

  • reviewed containers re-vive that - and how does that interact with devices (UDI identification?)

  • review code systems around additives (HL70371 and SCT substance and product hierarchies)

  • started work on cross-mapping between HL7 method codes and SNOMED CT procedure / technique concepts

    • American College of Surgeons is working on procedure protocol and synoptic data elements / surgical synoptic reports - we could work with them together on that

  • Look at other HL7 tables that we would want to migrate SCT (i.e., Specimen Condition table, etc.)