2023-11-16 LabMCoP Meeting Notes

X

Nancy Cornish

CDC

-

Manjula Gama-Ralalage

CDC

-

Riki Merrick

APHL

X

Christina Gallegos

APHL

-

Amy Liu

Inductive Health / APHL

-

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

-

Pam Banning

 3M

Upcoming OOO

Y

• Riki 11/13 - 11/16 and 12/20 - 12/22

• Amy 12/15-12/20 and 12/25-12/29

• Nancy 12/18 - 1/1

• APHL closed 11/23 & 11/24 (Thanksgiving)

• APHL Closed 12/27 - 1/1 - will cancel the call for 12/28

Previous Action Items

Y

• Nancy Follow up with Jane (will CC Riki)

  • Modeling donor organs etc) - reach out to Jane Pollack (jpollack@nmdp.org) at NMDP. She is the SME for standard vocabularies and terminologies for stem cell transplantation.

  • ComboCytologicalMaterialfromEndocervixEctocervixVaginalFornix

  • ComboCytologicalMaterialfromEndocervixEctocervixVaginalFornixSlide

  • need reference to thin prep (request new term with parent cytology specimen container (physical object) for liquid-based cytology container) - John will have to work with Riki to do this

    • could use this: ​https://hologicwomenshealth.com/products/thinpreppaptest/Open

  • Scotchtape prep (scotch tape swab from Mike Miller’s book) - what is needed for this term?

    • 258664003 |Scotch tape slide specimen (specimen)|

    • Mike Miller’s Book - do not use invisible scotch tape, collect early in the AM

      • Nancy has a diagram of the prep

      • What's the difference between Scotch® Magic™ Tape and Transparent Tape? Transparent Tape has a glossy finish, while Scotch® Magic™ Tape is frosty on the roll, but invisible on paper making it perfect for writing on in pen or pencil.

  • nasal sinus fluid definition - not sure if the definition was sent already?

    • no nasal sinus fluid specimen term in SCT (this would be an aspiration)

    • 430238007 |Specimen from nasal sinus (specimen)| (this could be interpreted as fluid or tissue)

    • 16223051000119101 |Nasal sinus contents specimen (specimen)|

    • 433861002 |Specimen from nasal sinus obtained by fine needle aspiration biopsy (specimen)| → does not specify ‘nasal sinus fluid’ as part of modeling for the concept

    • may need to know which sinus the fluid comes from (not currently in SCT) ​https://breathefreely.com/pasha-chamber-of-sinuses/Open

      • frontal sinus, maxillary sinuses (in your cheeks; one of four paranasal sinuses), ethmoid sinus (one of four sets of sinuses that drain into the nasal cavity), sphenoid sinus (between eyes and behind the nose)

      • There is a fronto-ethmoid sinus term in SCT: 306868000 |Frontoethmoid sinus structure (body structure)|

  • surgical insertion site peritonealDialysisTunnelSite - discuss with Jim Case on modeling

  • surgical insertion site peritonealDialysisSite - discuss with Jim Case on modeling

  • Riki to reach out to cytologist for the endocervix/ectocervix/vaginal fornix?

  • Need to figure out what to do with these terms

• Riki’s Follow up:

  • modeling exposure (wounds) - check if Jim Case can join 11/20 (11/30?) or 12/7

  • work with John

    • new term for pacemaker insertion site sample

      • in SCT there are only swabs for insertion sites (line, drain, chest tube, vascular catheter) - this should be fixed

      • we should model it after 435971000124108 | Body fluid specimen from peritoneal dialysis insertion site (specimen) and require method, which should be aspirate

  • 2 Stamey procedures in SCT - 2 glass (midstream / post-massage = ​https://emedicine.medscape.com/article/1948091-technique?form=fpf#c3Open ) and 4 glass (dirty catch = first void / mid-stream / prostatic massage fluid / post-prosthetic massage urine = ​https://emedicine.medscape.com/article/1948091-technique?form=fpf#c2Open ) - Do we want to have SCT codes for type that say ‘stamey’?

    • inactivate the urine specimen for stamey (445383006) once we have requested the new SCT code for post-prosthetic massage urine

  • submit a code for formalin10

  • Riki and John discussed modeling of this term last call - Riki will need to submit this term

• Open homework EDTA Stopper top - Riki item?

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

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

      • can’t use color of the top, but can use the additives, percent of additives

        • glass, plastic, size/volume of tubes

        • additives aren’t sold independently = challenge

        • 706049005 |Blood tube (physical object)|

    • 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

NHSN organism terms / PH domain reference WG

Y

• There is a database for organisms - these are all SCT coded

• Need to make sure to go through the proper channels at either APHL / NLM or IHTSDO

• From CDC, NNDSS (I don't know of a person) and Sandy Jones at Cancer are also submitting to SNOMED when required

• CDC is working on creating a standards division that should be the conduit for vocab work

• Discussion about setting up a SNOMED PH clinical reference group (Desiree, Laura Conn, several others)

LOINC to SNOMED CT mapping

Y

• How will this affect the speicmen SMT work

• released alpha package during the confernece - available here: loincsnomed.org and there is a browser

  • programmatically converted 25,000 LOINCs to SCT codes in a namespace extension

  • looking for feedback by ???

  • for US perspective this will probably end up being more used in research

  • some terms will be primitive - example multi-system terms

  • allows for use of single terminology based terminology

  • some use cases for translation in C-CDA or FHIR content between LOINC and SCT

  • extension is NOT going to be part of the US edition - so terminology server systems will need to resolve any dependencies when they add this extension

  • assume this will be available via the LOINC FHIR terminology server

• purpose is to have a 1:1 representation of LOINC to SCT concepts

  • for cross-border interoperability

  • for use in countries that don't use LOINC

  • for those terms that have the fully defined attributes, you can then use the SCT reasoning power for LOINC aggregating etc

USCDI v5 comments

 N

United States Core Data for Interoperability (USCDI)

• Had call with Maria Michaels, Nancy and Manjula - working on better coordination within CDC and with partners - will set up recurring calls well prior to next comment period

• Nancy talked to leadership and we have experienced scientist available (understands lab workflows and what issues exist with LIS and EHR-s)- may pull her into the Data Standardization Lab subgroup; USCDI is one of the topics; currently working on minimum data set for surveillance Desiree is running this there is also the CSTE work: (​https://cste.sharepoint.com/:x:/g/EQdpo_BqId1Ih6EE0C1vKYIB0tkA4elCABwDA8Rn47xluQ?rtime=QO7JLK7F20gOpen )

• this might re-org as part of the CDC re-organization - so might be a hiatus until all figured out

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

•  sublungual scraping - add PHLPName

• Epitheilial cell tissue

  • can we get a vet extension term promoted to international (791000009104 - Epithelial tissue sample from vesicle (specimen)

  • this is very specific to VTM for transportmedium - can also be submitted using UTM or saline, should we drop the transport medium?

    • as long as we have these different transport media availabe as products / substances in SCT so that we can mark these as nice to have and make this a prototype

• SerumThrombinGel

  • we don’t have enough information about the gel to submit - lok for Nancy’s email related to clotactivator

• ToeJointSynovialFluid

  • this is probalby used for Dx of gout (crystal analysis) - found SCT code and mapped

• tumor tissue

  • should be using massTissue instead of this

  • make this discouraged

• ulcer

  • from definiton this sounds like Gi, but it is a chronic wound that can be anywhere

  • adjust griupr to be wound

• vaginalIntroitusSwab

  • same as low vaginal swab?

  • there are 2 SCT codes for these:

    • 472899007 Swab from vaginal introitus (specimen)

    • 258522008 Low vaginal swab (specimen) - already pointing to the vaginal canal - per definiton is for patient collected swab

    • treat as 2 separate specimen, though having both may lead to confusion

    • if you need that much detail, then much more detail about the precise location (clockface and potentially distance from a landmark, which cannot be done

Specimen CMT pilot implementers

 N

• Review where we are: Vendor Connections

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