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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
http://athena.ohdsi.org/search-terms/terms?vocabulary=LOINC&conceptClass=LOINC+Hierarchy&standardConcept=Non-standard&page=1&pageSize=15&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 )


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