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Improve LOINC representation in OMOP Vocabulary (Athena) (link parts to lab tests)

(Chris Knoll) #21

I don’t know what you mean by this: clinical drugs roll up to ingredients via the concept_ancestor hierarchy.

(Denys Kaduk) #22

Hi all, I have a propose to add a new concept class for LOINC attributes - “GENE”, we can find link between measurement and this attribute in

Some examples:

loincnumber longcommonname partnumber partname parttypename
44606-2 ALOX3+ALOX12B gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal LP288622-6 ALOX3 gene GENE
44606-2 ALOX3+ALOX12B gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal LP288621-8 ALOX12B gene GENE
42712-0 AML/MDS gene 7q31 deletion [Identifier] in Blood or Tissue by Molecular genetics method Nominal LP288623-4 AML gene GENE
42712-0 AML/MDS gene 7q31 deletion [Identifier] in Blood or Tissue by Molecular genetics method Nominal LP288634-1 MDS gene GENE

If we do this, it will become easier for researchers to work with genomic data.
@Vojtech_Huser @Christian_Reich @Dymshyts @Polina_Talapova @Alexdavv @zhuk What do you think about this?

(Christian Reich) #23

It would. We may not call it “GENE” though. More like “Genetic aberration”

(Alexander Davydov) #24

@Denys_Kaduk, with a new class ‘Gene/Genetic aberration’ you will get just a full set of associated genes for each test. You won’t even know whether it’s searching for an alteration/mutation or just gene detection analysis. Also, you cannot distinguish between single genes and gene combinations (just 2 links are created for the latter).

For now, we’re planning to have the following:

loincnumber longcommonname partnumber partname relationship_id
44606-2 ALOX3+ALOX12B gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal LP227586-7 ALOX3+ALOX12B gene targeted mutation analysis Has component
42712-0 AML/MDS gene 7q31 deletion [Identifier] in Blood or Tissue by Molecular genetics method Nominal LP227622-0 AML+MDS gene 7q31 deletion Has component

As a Component, you have a gene/gene combination + type of analysis in a single attribute concept. Unfortunately, LOINC doesn’t use ‘targeted mutation analysis’/ ‘deletion detection’, etc. as precise ‘Molgen’ METHODs, so you need to sort out all these components in any kind of genomic analysis anyway.

Also, we are thinking about adding the hierarchical links between test COMPONENTs and more general COMPONENTs derived from ‘DetailedModel’ and ‘SyntaxEnhancement’ model (what you probably need as Genes).

partnumber partname relationship_id partnumber partname
LP227586-7 ALOX3+ALOX12B gene targeted mutation analysis Is a LP36747-1 ALOX3+ALOX12B gene
LP227622-0 AML+MDS gene 7q31 deletion Is a LP36196-1 AML+MDS gene 7q31

@Vojtech_Huser @Christian_Reich @rimma @Denys_Kaduk What option is preferable? Or we can implement both.

(Oleg Zhuk) #25

We need one more community advice for Loinc Parts incorporation into CDM for the upcoming LOINC release.

Should we make them Standard?

There are a few options:

  1. Make them standard. LOINC Parts can be helpful in the mapping process but are not extremely necessary. There are a lot of possibilities to perform mapping to SNOMED or other vocabularies without mentioning LOINC Parts.
  2. Make them non-standard.
  3. The best option would be to make it all classification concepts so users can query concept ancestor to get Lab tests with any specified method, scale, property, component, etc. as our initial plan was. BUT since we’ve decided to use the same relationships for SNOMED and LOINC, making parts ‘C’ concepts will require complete SNOMED rearrangement and have a lot of consequences. That’s why not the best decision, unfortunately.

@Christian_Reich @Vojtech_Huser what do you think?

(Christian Reich) #26

Agree with 3

(Alexander Davydov) #27

Impossible solution is always the best solutions :slight_smile:

SNOMED attributes are Standard concepts so how can they be ancestors of SNOMED tests?
Relationships between tests and attributes become vertical hierarchical, right?

Otherwise, we need to split back SNOMED and LOINC relationships for attributes and build different logic for SNOMED and LOINC.

(Chris Knoll) #28

Question about this approach: using a concept ancestor using for a higher level class of measurement may lead to the lower-level measurement concepts being selected, but you may get different units for those different children. So, what would a query look like where you search on a parent concept, but then need to find the appropriate unit/measure for the possible children?

(Vojtech Huser) #29

Ad making parts standard: I don’t know enough about all the rules Athena team is using when doing changes to the vocabulary. And also which LPs were even now made into concepts and which were not. I was looking at LOINC in order to map HIV viral load data. E.g., at methodless codes in LOINC and how often there are such codes. (if interested, my ugly code is here https://github.com/vojtechhuser/project/blob/master/lab/loinc-parts-v002.Rmd )

I looked at result of this current query

(but no major conclusions from reviewing it)

One bonus remark

e.g., LP for methods should probably not be standard. e.g. LP6464-4 | Probe.amp.tar

and currently it is not even a concept. (this should become one but not a standard one)

(the LP example is taken from https://raw.githubusercontent.com/vojtechhuser/project/master/lab/LoincPartLinkPrimary.csv )

(Vojtech Huser) #30

at LOINC upcoming conference, I see the following on agenda

Automated hierarchical crosswalk between LOINC Laboratory tests and SNOMED CT Measurements
Photo forthcomingPhoto forthcoming

Polina Talapova, MD
Odysseus Data Services
Eduard Korchmar
Odysseus Data Services
It is known that the purpose of the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) is to standardize the representation format of healthcare data. It has been adopted by the Health Data Sciences and Informatics (OHDSI) collaborative, a multi-stakeholder, to create open-source solutions that bring out the value of observational health data through large-scale analytics.

In the OMOP CDM, such ontologies as SNOMED CT and LOINC are used as Gold standards for the transformation of raw Observations and Measurements into the standardizes ones. Moreover, Regenstrief Institute and SNOMED International have formed a long-term collaborative relationship with the objective of developing coded content to support order entry and result reporting.

Material and methods: the LOINC-SNOMED collaborative has provided a mapping from LOINC Terms to SNOMED pre-coordinated concepts. Using this, we have built a hierarchical crosswalk that embeds more granular LOINC Laboratory tests into the SNOMED CT Hierarchy of Measurements. The approach is based on both sophisticated logic and an automatic match of common attribute combinations via SQL. Hierarchical links are represented by “Is a” relationship that implies that the LOINC Term semantically resides below the SNOMED CT concept.

Results: We have obtained more than 12,000 hierarchical links from the LOINC Laboratory Tests to SNOMED Measurements. This approach gives the opportunity to reproduce the automatic mapping with respect to every LOINC update.

@Polina_Talapova - can you comment on if those will be released (or have been released) in OMOP Vocab ?

I understand that the mapping the abstract references was done few years ago (and not sure if there is commitment to keep it updated) and newest LOINC terms may not have this mapping. (so OHDSI would have to “maintain it”)

(Polina Talapova) #31

@Vojtech_Huser, the hierarchical mapping has not released yet (but I am looking forward to this).

I plan to map more LOINC Parts to SNOMED attributes. This will help to build more links between LOINC Laboratory tests (including new Terms) and SNOMED Measurements.

(Ana Szarfman) #32

Curious: How are you going to deal with the many-to-many valid mapping outputs that LOINC generates?

(Eduard Korchmar (Terminologist @ Odysseus Vocabulary Team)) #33

Since we do not neccessary look for equal mappings in all cases and OMOP CDM allows for multiaxial hierarchy, our main concern is that all LOINC concepts become descendants of all SNOMED concepts they should be descendants of. It is absolutely expected that LOINC concepts will have multiple SNOMED parents and that some SNOMED concepts may have multiple LOINC descendants.

(Vojtech Huser) #34

Also of note is this call by LOINC (effort to update top2000 tests). https://loinc.org/usage/obs/

In addition, LOINC effort for groups is relevant and was mentioned in conversations I had with various folks.

(Ana Szarfman) #35

How will you handle the multiple valid mappings that LOINC generates within LOINC itself that are not interoperable? LOINC urgently needs high level terms.

(Vojtech Huser) #36

I am pleased to see that as of May 2020 (and probably earlier) - OMOP Vocab now has implemented the Loinc Part inclusion as I suggested.

See example here

This component is now an Athena concept
https://athena.ohdsi.org/search-terms/terms/40796255 for ‘HIV1 RNA’

and has relationships such as ‘component of’