2023-08-24 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

X

Raj Dash

Duke / CAP

X

John Snyder

National Library of Medicine (SNOMED CT)

X

Andrea Pitkus

UW

X

Kathy Walsh

Labcorp

X

Rob Hausam

Hausam Consulting

Doug Franklin

APHL

Pam Banning

Upcoming OOO

Y

• John OOO at HL7 WGM 9/10-9/14

• Riki & Christina OOO at HL7 WGM 9/8-9/15

• Christina 9/18-19 and 9/28

• Rob at HL7 WGM 9/8-9/15

• Raj OOO 9/14-10/5

Previous Action Items

Y

• Mid-turbinate Nasal swab:

  • SCT International will make new body structure

  • is looking for evidence that this is used in the wild to access impact of changes:

    • https://www.cdc.gov/csels/dls/livd-codes.html provides the mapping to the SCT code

    • CDC has collection image of how it should be - provided already

    • Look at ARUP, Mayo, Labcorp, Quest to see if they list SCT codes for specimen - those are not normally published in on-line compendium

    • We could check COVID data at CDC

  • we will update the LIVD file with the new SCT code, once assigned and then explain in the revision log why the change including a link to the collection image on CDC website

• Anterior Nares ticket was accepted

• Modeling exposures on wounds

  • Nancy reached out to Bob Milius and Joel Schneider - no answer also reached out to UNOS - Maya Webber - have sent explanatory email - Nancy will forward email to Riki and Andrea - she mentions “we collect laboratory data per OPTN specifications”

• Updates on Specimen CMT pilot implementers

  • Review where we are: Vendor Connections - nothing new since last week

  • CDC is updating the one-pager

  • Riki estabished that we could download CMT content via SQL script (Manjula would have to write that) in csv format - maybe by lab domain?

  • we need more input on what format vendors would find useful

Reporting Biomarkers to Cancer registries

Y

This is a future topic.

Nancy worked with Sandy Jones works for Division of Cancer National Program for Reporting Cancer Registry (NPCR) who would be interested in this. She will be at the CAP’s annual summit in Chicago October 8th

https://www.cdc.gov/cancer/npcr/index.htm

works on synoptic reporting

Sandy will put together a one-pager

We could share the CMT one-pager with her

Lab Test Naming Conventions

 Y

• SHIELD#2 call topic presentation to SHIELD on August 29

Specimen CMT - review of terms with questions

Y

• Open homework EDTA Stopper top

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

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

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

    • Need to check on completeness against the Anne/Nancy list

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

    • K1 or K2 might be important to differentiate

    • More homework

    • see more links for references in the chat below

  • Ileal fluid

    • Do we have small intestine fluid?

      • Yes 2 terms, both for micro, one preferred, one do not use

      • Make preferred, partial, need to have collection method – make the more detail nice to have

      • Mapping:

        • 309199003 |Gastrointestinal fluid specimen (specimen)| - and specify ileum

          • Definition – copy from gastrointestinal fluid – specific to iluem

        • 258462005 |Ileostomy fluid specimen (specimen)| - this is something different, so create separate term?

          • What tests would be done on this kind of sample

          • micro

          • jejunal tissue

            o   map to small intestine tissue sample and add jejunum as source, so rename to smallIntestineTissue_Jejunum

            o   make preferred, partial, require collection method

Specimen CMT - Hosting Options

 N

• 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 https://build.fhir.org/conceptmap-example-specimen-type.html - based on this profile: https://build.fhir.org/conceptmap.html

  • @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 https://build.fhir.org/conceptmap-example-specimen-type.xml.html . 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

 N

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

N 

Specimen CMT - Compare to NHS Medical Terminology testing

 N

Future projects for this call after CMT

 N

• 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