2023-05-04 LabMCoP Meeting notes

X

Nancy Cornish

CDC

X

Manjula Gama-Ralalage

CDC

-

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

-

Rob Hausam

Hausam Consulting

-

Doug Franklin

APHL

X

Pam Banning

3M

Upcoming OOO

Yes

• Riki 5/4 - 5/12 - what about the call on 5/4 and 5/11 - leave on the books - Christina to run and record

• John 5/17 - 5/25

• Raj week of 5/15

Question from CLSI

Yes

Working on a document for proper collection of respiratory specimens for microbiology testing and one of our member shared the coding below with us. https://aphlinformatics.atlassian.net/wiki/download/attachments/1915519082/How-To-Collect-NMT-Specimen-for-COVID-19.pdf?api=v2; https://aphlinformatics.atlassian.net/wiki/download/attachments/1915519082/NMT-Specimen-Collection-Infographic.pdf?api=v2

She has a number of concerns about the coding, the tests and what we are calling the specimen collection. Here is the link for SNOMED Coding: https://browser.ihtsdotools.org/?perspective=full&conceptId1=181203001&edition=MAIN/2023-03-31&release=&languages=en

Example: Anterior nares (both anterior nares) which makes sense since both sides should be sampled. - add synonym for anterior nasal cavity swab

Open

Example: middle turbinate instead of mid-turbinate - it is modeled to point to the middle turbinate - we need to update that to be a new term for the mid-section (on the anterior/posterior axis) of the cavity between hard palate and the inferior turbinate structure - it goes to the middle of it| Swab specmen from nasal mid-turbinate

Open

We also have description for NP Swab (along the top of the ):

Anterior nose swab (squamous epithelial vs respiratory epithelial (which is what is getting infected): https://www.cdc.gov/coronavirus/2019-ncov/testing/How-To-Collect-Anterior-Nasal-Specimen-for-COVID-19.pdf

add synonym for anterior nasal cavity swab)So we ned to update the modeling

Reporting Biomarkers to Cancer registries

Lab Test Naming Conventions

Andrea planning this

• SHIELD call topic (maybe June 13)

  • TRUU Lab

  • LOINC

Specimen CMT - review of terms with questions

• Cystic nodule vs nodule

  • SNOMED has these concepts in morphologic abnormality hierarchy

    • 367643001 |Cyst (morphologic abnormality

    • 27925004 |Nodule (morphologic abnormality)| with a subtype

      • 16217341000119101 |Cystic nodule (morphologic abnormality)

    • Cysts are always fluid filled, so can aspirate also fluid AND wall tissue

    • Nodule is always a mass = tissue only

    • when it is a cystic mass, it may contain fluid

      • so might need to add 367643001 |Cyst (morphologic abnormality as a parent to 16217341000119101 |Cystic nodule (morphologic abnormality)

• 5/4/2023:

  • Need to differentiate between Cyst fluid vs. cyst tissue/wall -currently have cyst tissue and cyst fluid for micro

  • Create rows cyst fluid and cyst tissue (instead of cyst tissue nodule and cyst fluid nodule) for pathology domain

  • SkinCyst -duplicates

    • WEN = pilar cyst

    • difference is for additional required fields

    • want to know collection method for pilar cysts (under both micro and pathology domain) - pilar cysts are one type of skin cyst

    • There are many different type of skin cysts so don’t want to discourage the term - maybe keep it open and let people enter the type of cyst?

      • SNOMED does not have individual morphological abnormalities for all different cyst types

      • synovial cyst term in SNOMED is used to model across different concepts

    • There may need to be a synonym for popliteal cyst fluid (Baker’s cyst)

    • SPM-4 (popliteal cyst fluid (specimen)) should be mapped to synovial cyst fluid 240008008 |Synovial cyst of knee (disorder)|

    • change PHLIP preferred name to popliteal cyst

    • create a generic Synovial Cyst specimen term and specify source site, laterality (nice to have) and collection method for micro related domain

    • John requesting synovial cyst specimen concept

  • PeritonealFluid - follow-up with Riki to handle term with everything is the same but multiple descriptions

  • Swab_boil - duplicate

    • Selected term with source site and spatial orientation required

  • Hair - duplicates

    • differences are the comments

    • Hair_clippings is discouraged because they are not ideal specimen

    • NHSN - Hair specimen term - domain changed to chemistry-related

    • micro-domain term - definition from hair-clippings copied over to micro-domain term

Specimen CMT - Hosting Options

• How can we publish the content in the dB?

  • Allow access somehow to query the dB

  • as access or excel

  • 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

No

Specimen CMT - potential pilot sites

Yes

• Goal is to have some implementers lined up by April - so who to reach out to?

  • Review where we are: https://aphlinformatics.atlassian.net/wiki/spaces/LMCOPL/pages/1863942201 - updated some notes there

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

No

• Setting baseline

Specimen CMT - Compare to NHS Medical Terminology testing

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