2023-05-04 LabMCoP Meeting notes

Date

May 4, 2023

Attendees

Present	Name	Organization
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

Discussion topics

Topic	Discussed?	Notes
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 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 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 - based on this profile: @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 . 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: - 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

Recording:

FROM CHAT:

last week we added a domain of chemistry because we had a chemistry test listed under microbiology. Do we want to continue to work on chemistry terms now or later?

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