2024-06-13 LabMCoP Meeting Notes

Nancy Cornish

CDC

Manjula Gama-Ralalage

CDC

Riki Merrick

APHL

Christina Gallegos

APHL

Amy Liu

Inductive Health / APHL

Raj Dash

Duke / CAP

John Snyder

National Library of Medicine (SNOMED CT)

Andrea Pitkus

UW

Kathy Walsh

Labcorp

Rob Hausam

Hausam Consulting

Doug York

APHL

Pam Banning

 3M

Sandy Jones

CDC

Upcoming OOO

 Yes

• Reminder: We are now using https://aphlinformatics.atlassian.net/wiki/spaces/LMCOPL/calendars and everyone can just keep it updated

  NOTE: you will need to use type “Event” if you do not have a confluence account

Previous Action Items

 No

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      • Nancy/Anne’s list is 10 years old - may not want to compare with this outdated list and use ARUP and Labcorp lists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

  • 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

    • Scott’s response: “When the SNOMED representative referred to the existence of “donor codes,” they might be referring to the ISBT-128 coding standard that’s managed by ICCBBA. Please see their website: ISBT 128 | ICCBBA, and navigate to view their technical documents: ISBT 128 | ICCBBA | Technical DocumentsFDA’s regulations for human cells, tissues, and cellular and tissue-based products (HCT/Ps) in 21 CFR part 1271 require assignment of a “distinct identification code” to facilitate tracking HCT/Ps (see 21 CFR 1271.290(c)) but I don’t believe this is relevant to your question.”

    • 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.)

• Amy follow up - check if she has all of these

  • nasal sinus fluid definition

  • surgical insertion site peritonealDialysisTunnelSite

  • surgical insertion site peritonealDialysisSite

• 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

• John:

  • 460621000124104 |Superficial surgical incision wound (morphologic abnormality)| - created in US extension in 2019. Is this needed? If so, then LabMCoP/APHL should promote it to SNOMED International to retain US SNOMED identifier. John submitted this to be promoted: https://request.ihtsdotools.org/#/requests/edit/959920?fromList=true

  • SNOMED guidance related to morphological abnormality: Morphologic Abnormalities vs. Findings - SNOMED CT Editorial Guide - SNOMED Confluence

Specimen CMT - review of terms with questions

 Yes

• Remove wound_postsurgical - duplicate to wound_Surgical

• Adding NHSN terms

  • adiposeTissue

    • use domain micro, since NHSN

    • partial - must have body site, nice to have laterality

    • also add to pathology domain

  • adrenal gland specimen

    • not sure why this is an NHSN term - usually only collected for neoplasm detection

    • fine needle biopsy with source site should cover

  • artery specimen

    • not sure why this is here for NHSN - maybe we shoudl get the current list to ensure we are only consdiering what is current

• Amy is reviewing

ADJOURNED

Yes

Specimen CMT pilot implementers

 No

• Review where we are: Vendor Connections

  • no update

Specimen CMT - Hosting Options

 No

• 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.

    • There will be a call Clinical Architecture on May 3rd to discuss moving specimen CMT to Symedical

    • Manjula will take a look at the concept map

Specimen CMT - education

 No

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

 No

Specimen CMT - Compare to NHS Medical Terminology testing

 No

LOINC to SNOMED CT mapping

 No

Future projects for this call after CMT

 No

• 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.)