2023-09-21 LabMCoP Meeting notes

X

Nancy Cornish

CDC

Manjula Gama-Ralalage

CDC

Riki Merrick

APHL

X

Christina Gallegos

APHL

X

Amy Liu

Inductive Health / APHL

regrets

Raj Dash

Duke / CAP

X

John Snyder

National Library of Medicine (SNOMED CT)

Andrea Pitkus

UW

Kathy Walsh

Labcorp

Rob Hausam

Hausam Consulting

Doug Franklin

APHL

X

Pam Banning

 3M

Upcoming OOO

Y

• Riki OOO 9/29; 10/6; 10/20-11/5

• LOINC conference: 10/17-10/20 - cancel call on 10/19?

• SNOMED Business meeting 10/21-10/25 and Expo 10/26-10/27 = cancel call on 10/26?

• Christina OOO: 9/28

• John OOO 10/19 and 10/26

• Pam OOO 10/19

• Nancy - government shutdown

Previous Action Items

• 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 meatus (body structure)

    • which references: 78155005 |Structure of inferior nasal meatus (body structure)

    • Background info: Nasal Mid-turbinate (also known as deep nasal) swab placement location:

      The tapered swab is inserted through the anterior nasal aperture (one or sequentially both right and left) and is pushed along the floor of the nasal cavity through the inferior meatus which is the space between the inferior turbinate (also called concha )

      and the floor of the nasal cavity until resistance is met at the mid-point of the inferior meatus due to the size of the larger size of the swab tip or the length of the handle which stops further progress.

       Just to describe location; The mid-point between anterior nasal cavity and the posterior nasal cavity (nasopharynx ) of the inferior meatus, which is the space between the inferior turbinate (also called concha )and the floor of the nasal cavity,

       

       

      Open

      

       

      ENT surgeons are using them in their surgical reports. See link here The Nasal Cavity - Structure - Vasculature - Innervation - TeachMeAnatomy

• 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”

  • 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.

      • 105455006 | Donor for medical or surgical procedure (person) - or a descendant that is more appropriate for the speicmen type could be used in SPM-5 as a specimen type modifier when creating a prototype, since we cannot account for every possible organ or tissue type (would have to figure out how to represent that in the CMT)

      • or use specimen hierarchy term that is for the type of donated material - blood / organ / tissue and then require SPM-8?

      • Riki to write up a few examples and bring back next week

• 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

• EyeTissue_Lamella - we will need to create a SCT for anterior and posterior - from Nancy’s email post call:

  • The eyelid can be divided into two lamellae, namely, the anterior and the posterior. The anterior lamella consists of the skin and orbicularis, while the posterior lamella is formed by tarsus and conjunctiva.

    Anatomy | SpringerLink the picture below is the best I could find and I drew in the names for the structures not completely named.

  • Open

    

• definition for nasal aspirate and nasal wash - from Nancy’s email post call:

  • A Nasopharyngeal or a nasal aspirate is collected via a tube which is threaded through the nasal cavity to the back of the throat in the case of the Nasopharyngeal collection or inserted into the nostril a short distance, about 1 inch in the case of a nasal collection. Suction is applied which collects the fluid and mucous from the nasal cavity. This fluid is placed in transport media and sent to the lab for testing.

   

  2. A Nasopharyngeal or a nasal wash starts with several drops of sterile normal saline which is instilled in each nostril, the fluid is then retrieved via a tube which is threaded through the nasal cavity to the back of the throat in the case of the Nasopharyngeal collection or inserted into the nostril a short distance, about 1 inch in the case of a nasal collection, then suction is applied which collects the fluid and mucous from the nasal cavity. This fluid is placed in transport vial and sent to the lab for testing.

   

  https://www.cdc.gov/flu/pdf/professionals/flu-specimen-collection-poster.pdf

USCDI v5 comments are due Sep 22!

United States Core Data for Interoperability (USCDI)

• Riki submitted several comments - did a brief review

• Nancy will connect Riki with Maria Michaels

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

• ComboCytologicalMaterialfromEndocervixEctocervixVaginalFormix

  • specimen with two different body structure/site - how to handle this because only one is supported in HL7 v2? Which body site do we choose?

    • depends on whether you are collecting a biopsy, brush, etc.

    • may need guidelines for where you collect the specimen

      • Nancy to follow up with OB/GYN

• ComboCytologicalMaterialfromEndocervixEctocervixVaginalFormixSlide

  • pap smear sample

  • for SPM-5 should we be using cervical cytology microscopy slide or microscope slide?

    • use the microscope slide - since that doesn’t really change or is there something special about the slide? - Nancy to review

    • come back to review body site

• Pap Testing Liquid Sample

  • need reference to thin prep

  • need to request new term with parent cytology specimen container (physical object) for liquid-based cytology container --Nancy to look this up and ask the new cytologist at CDC

• Pap Testing Liquid Sample - different domain with same questions as above

• Pericardial effusion

  • need a path domain for the term

• Pericardium tissue_biopsy

  • added definition

  • micro domain

  • remove ‘biopsy’ from the term

• Pericardium tissue_biopsy

  • this has a different definition than the term above

  • added definition

  • micro domain

  • check to see if it is in the path domain

  • submit as tissue from pericardium, for specimen type comment

• 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

Specimen CMT pilot implementers

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

Specimen CMT - Hosting Options

• 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

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

Specimen CMT - Compare to NHS Medical Terminology testing

Future projects for this call after CMT

• 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