2023-09-07 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)

Andrea Pitkus

UW

X

Kathy Walsh

Labcorp

X

Rob Hausam

Hausam Consulting

Doug Franklin

APHL

Pam Banning

Upcoming OOO

Y

• Riki OOO 9/2-9/10 vacation

• 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

• Nancy - 9/14-9/15

• Cancel Call on Sep 14 - Riki to send out

Previous Action Items

Y

• Mid-turbinate Nasal swab:

  • new body structure will be added SNOMED to describe the replacement concept for Mid-turbinate. It is:

    1290369003 | Structure of middle region of inferior nasal turbinate (body structure)| - is that correct?

    • could we say Structure of middle region between hard palate and inferior nasal turbinate (body structure)?

    • we could add that as the definition?

    • Structure of inferior middle region below inferior nasal turbinate (body structure)|

    • Nancy will create the definition / text to explain this location a little better - may keep this in the US edition, if SNOMED International is not taking it - this will display as additional description on the concept (4 sentences max)

    • No updates from SNOMED International

  • 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

• Modeling exposures on wounds (organ donors)

  • 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” - Still no updates this week (9/7)

    • Nancy to follow-up one more time with Bob and Joel

    • Need SCT for liver, kidney potential transplant biopsies - sometimes it is wedge biopsy

    • Do we need SCT code that delineates donor before transplant is in the recipient?

    • There is allowance for donor in pre-coordinated concept in SNOMED

    • Identify donor organs that are transplanted (identify the donor organ before it is transplanted)

      • “Organs that have been successfully transplanted include the heart, kidneys, liver, lungs, pancreas, intestine, thymus and uterus. Tissues include bones, tendons (both referred to as musculoskeletal grafts), cornea, skin, heart valves, nerves and veins” including bone marrow

      • will need additional information, reference material, use case, etc.

      • 444464007 |Recipient of biological material from subject (person)|

      • Ask Riki for input

• Share CMT one-pager with Sandy Jones - Manjula to do, once we have the updated version (will also have it for the SCT Expo) - she will need to have it before Oct 6

  • No update yet - hopefully by the end of the week

USCDI v5 comments are due Sep 22!

Y

​https://www.healthit.gov/isa/united-states-core-data-interoperability-uscdiOpen

• CDC and has been meeting with CAP around USCDI and USCDI+ submissions for new concepts - Nancy and Maria Michaels (liaison between the different divisions at CDC)

  • Maria shared document with CAP (Helena Duncan) for their input

• Difference between specimen ID and accession number - it is not a 1:1 relationship (accession number depends on the way the lab operates)

  • It could be the specimen ID

  • It could be the number of all specimen collected from the same patient on the same date/time (aka requisition number)

  • it could be the order number

• Specimen Collection method

• Specimen Collection date/time - promote from level 2

• Laboratory Date/Time stamps - needs more detail - just as a meta-data element - should identify the minimum dates that MUST be collected:

  • specimen collection date/time

  • specimen received date/time

  • test result released date/time

• Observation Date/time - needs clarification against others listed in USCDI

  • Laboratory Test Performed Date - current definition is NOT a good one for this name - see ​https://www.healthit.gov/isa/comment/11646Open

• Specimen Condition Acceptability - this made it into V4 - but is comingling 2 concepts:

  • condition (on the specimen)

  • acceptability (for a test - does the specimen condition affect being able to perform the test)

  • reject reason - when the test was not performed CLIA requires that the lab provide the reason

Reporting Biomarkers to Cancer registries

N

National Program of Cancer Registries (NPCR) | CDC

Sandy will put together a one-pager

Specimen CMT - review of terms with questions

Y

• 9/7/2023

  • EyeTissue_Lamella

    • Generic lamella structure SCT code is inactivated and no replacement.

    • which body structure term should be used? There are more specific terms available - we will need to create a SCT for anterior and posterior

  • Meconium

    • domain not finalized - Are there other domains you would see meconium? No, just micro

  • Mycobacerial isolate

    • missing PHLIPPrefName

    • need to update the definition to be specific for “mycobacteria” instead of just “bacteria”

    • Nancy to send this to Amy

  • Aspirate_Nasal

    • not a synonym for nasal wash

    • Nasal aspirate vs. nasal wash

    • will need definition for nasal aspirate - Nancy to send to Amy

    • Comment: specimen type is used for pertussis - yes, confirmed by Nancy

  • Oropharyngeal and Nasopharyngeal Swab

    • How best to model source site since SPM-8 does not repeat in HL7 messages? Right now, there is no way to add two different source site

    • Usually take the samples and put it in the same tube to save resources

    • For now, can map it to “combined nasopharyngeal and oropharyngeal swab (specimen)”

      • it is technically a pharyngeal swab (one is from the mouth and the other is from the nose)

      • will use “pharyngeal structure (body structure) for SPM-8

• 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

Specimen CMT pilot implementers

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

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 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

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