2024-03-28 LabMCoP Meeting Notes

X

Nancy Cornish

CDC

X

Manjula Gama-Ralalage

CDC

X

Riki Merrick

APHL

X

Christina Gallegos

APHL

X

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

Upcoming OOO

Yes

• 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

• Cancel next week!

Previous Action Items

 Yes

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      • Nancy/Anne’s list is 10 years old - may not want to compare with this outdated list and use ARUP and Labcorp lists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

• 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:

  • 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

    • 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

Specimen CMT - review of terms with questions

• chorionic membrane - placental membrane - also forms the sac

  • need PHLIP preferred name = use the name of the specimen type, since fully specified

  • need to update the mapping to the correct SPM-8

• need to add another term for aminotic membrane tissue

  • definition in chat - need to abstract from that article https://mdpi-res.com/d_attachment/jfb/jfb-14-00531/article_deploy/jfb-14-00531.pdf?version=1697797445

• ChorionicVilliTissue

  • nice to have additional specification of collection method SPM-7 as either transabdominal or transcervical

• CombinedNP/Rectal/Eye

  • need to add reference neonatal-hsv-1_16_2020.pdf (http://hopkinsmedicine.org )

  • need to create APHL SCT extension code and submit to SNOMED

• Corneal Impression

  • should not be used for rabies testing - at least is not mentioned in CDC manual

  • says used to deterimne donor-host incompatibities - aybe dulicate as AP, though not not=rmally

• Genital vagina - too broad - do not use

• stool from ileostoma

  • need to ask why ileostomy stoma is mporphologic abnormality, since always result of surgery - shouldn’t it be acquired body structure

• wound fluid from ileostoma - same as above

• JP drain

  • update mapping to SCT extension term that is more speciifc

• lymphfluid drainage

  • map to Lymphe - that is fluid - maybe ask for another synonym

• NP Aspirate

  • do we need a reference for the definition, we have detailed specimen collection

• TUBES - HL70487 - do not uselist

• EXS from HL70487 - this must be the shunt removed

  • https://together.stjude.org/en-us/diagnosis-treatment/procedures/external-shunts.html - see if we can abstract a definition

  • there is a SCT code for this

  • must have source site

  • preferred specimen is sterile shunt tip

• Add new term for shunt tip

  • have SCT code

  • need to write out definition

• SHUNT from HL70487

  • must have source site

  • preferred specimen is sterile shunt tip

CALL ADJOURNED

 Yes

1:00 PM ET

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.

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

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