2024-02-15 LabMCoP Meeting Notes

X

Nancy Cornish

CDC

X

Manjula Gama-Ralalage

CDC

X

Riki Merrick

APHL

X

Christina Gallegos

APHL

-

Amy Liu

Inductive Health / APHL

-

Raj Dash

Duke / CAP

John Snyder

National Library of Medicine (SNOMED CT)

Andrea Pitkus

UW

X

Kathy Walsh

Labcorp

Rob Hausam

Hausam Consulting

 X

Doug York

APHL

Pam Banning

 3M

Upcoming OOO

• Christina OOO: 2/29

• Riki OOO: 3/21

Previous Action Items

• Nancy Follow up

  • Can only have 1 bodysite in HL7, but these are from different sites - find out how often cervix + Fornix are collected together

    • ComboCytologicalMaterialfromEndocervixEctocervixVaginalFornix

    • ComboCytologicalMaterialfromEndocervixEctocervixVaginalFornixSlide

    • Labcorp allows multi-select - they use AOE question for this

    • We can’t have multiple sites in HL7

    • how to map for body site? - if there are multiple body sites - we decided that we will leave that body site field empty and require a comment in NTE segment to specify body site

  • We still need reference to thin prep (request new term with parent cytology specimen container (physical object) for “liquid-based cytology specimen container”) - we don’t want to use the trademarked name “ThinPrep”, but it can be done in US extension

    • We need to know what is in the thin prep liquid - this may be proprietary

      • Comprised of Hydrochloric acid >1.0% (CAS: 7647-01-0)

      • See document: Hologic Product Safety Data Sheet Library

      • The issue: is the same chemical used across all ThinPrep?

    • John could add “liquid-based cytology specimen container” to the US extension

      • …with liquid-based additive?

      • specimen cytology container with ThinPrep (or SurePath) liquid - will be in line with “cytology specimen container with ThinPrep liquid”

      • “cytology specimen container with SurePath liquid”

        • *composition of the liquid will change based on the purpose of cytology and use

      • Don’t want to combine the trademarked name in one SCT term

      • John will look into this

      • Decision: Keep the term generic -“liquid-based cytology specimen vial” and may include ThinPrep and SurePath as synonyms

        • ThinPrep vial and SurePath vial? (Vials are shorter and wider than the test tube) - “vial” is more preferred

        • “Vial” and “container” are not semantically equivalent – “vial” might be the preferred to use in the term

        • 2/1 update: John can work on this and send a CRS request - submitted

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

          • re-assigned to Riki

  • nasal sinus fluid definition - Amy to check

  • surgical insertion site peritonealDialysisTunnelSite - Amy to check

  • surgical insertion site peritonealDialysisSite - Amy to check

• Riki’s Follow up:

  • 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

    • 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 will submit this to be promoted.

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

• EDTA Stopper top

  • Amy to review this term

    • Q: For K2 or K3, do we need separate terms? Do different companies have different types of potassium? - Yes.

    • we will need to see what they are used for

    • Q: is 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

Modeling donor organs / parts

Yes

• Outreach out to Jane Pollack (jpollack@nmdp.org) at NMDP. was successful - schedule call for this topic - waiting for answer on what date will work

  • Nancy/Amy to reach out to Jane Pollack

  • Another contact: Scott A. Brubaker Division of Human Tissues, Office of Cellular Therapy and Human Tissue CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA - Nancy will reach out via email

    • Incomplete tissue product tracing during an investigation of a tissue-derived tuberculosis outbreak - ScienceDirect

• Should we make pre-coordinated terms, or support use of type modifiers?

SNOMED Submission follow up

Yes

Request to deactivate 119323008 | Pus specimen (specimen) was denied, so we need to write up some guidance that could be included for this term during mapping process into our comment for the pus specimen terms:

Note that pus and necrotic tissue cannot be distinguished by direct visual observation as differentiation requires a microscopic exam. This specimen concept does not include a declaration of how it has been evaluated or determined to be pus. Pus can certainly be found together with necrosis or with other pathologic processes. Medically lesions that contain pus are referred to as abscess. - John will take this text and modify to apply it to the term definition for 119323008, 258502009 for pus and then also add it to necrotic tissue 447407009 - making sure each of these texts only refer to the concept they belong to - we will use this text:

For 119323008, 258502009 = Pus cannot be identified by gross examination by a clinician. It may only be identified through microscopic examination.

For 447407009: Necrotic tissue cannot be identified by gross examination by a clinician. It may only be identified through microscopic examination.

Specimen type is not normally updated after the diagnosis.

Specimen CMT - review of terms with questions

 No

Specimen CMT pilot implementers

Yes

• Review where we are: Vendor Connections

  • no update

ADJOURNED

12:31 PM ET

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.

Specimen CMT - education

 No

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

 No

Specimen CMT - Compare to NHS Medical Terminology testing

 No

USCDI v5 draft

 No

United States Core Data for Interoperability (USCDI) has been published - comments due by April 5, 2024

LOINC to SNOMED CT mapping

 No

Reporting Biomarkers to Cancer registries

 No

National Program of Cancer Registries (NPCR) | CDC

Sandy will put together a one-pager

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