While reviewing the LOINC release content, I’ve noticed that some components still leverage outdated organism names. I was wondering whether it might be possible to review the bacterial content and update it to reflect current naming conventions. A good starting point would be organisms that were formerly classified within the genus Mycoplasma. A few examples are listed below, though the list could be expanded further by leveraging basionyms or the homotypic synonym relationships identified by LPSN.
Example: Mycoplasma hominis is now Metamycoplasma hominis
Thank you for raising this. We plan to update the affected LOINC Components and associated term names to reflect the newer organism names, while retaining the former names as synonyms. These are nomenclature-only changes, so the existing LOINC codes will remain unchanged; no deprecation or replacement mapping is needed.
I will begin editing the affected Components soon, with the updates planned for the next LOINC release.
I am looking forward to further dicussion on this topic. Given the presence of the LOINC ontology and the significant amount of work done in the organism hierarchy over the last several years by SNOMED, it might help if we align with this work. The use of SNOMED CT is required for state reportable laboratory results for communicable diseases in the United States.
This is a huge topic that we will likely want to break down into several steps as follows:
Phase 1: Idenitify and adopt authoritative sources for organism names for LOINC. The following are the list of sources recognized by SNOMED International as well as the US National Release Center (NRC) for SNOMED CT for organism names:
For example: ( I was going to provide the entire list of URLS from SNOMED CT, but the LOINC forum is restricting me to 2 URLS)
Please note that NCBI taxonomy is typically not considered an authoritative source for organism names. The NCBI website explicitly states:
Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information.
Phase 2 to “N”: Update Names by domain (i.e. Bacteria, Virus, Eukarya, etc.)
Phase “N+1”: Update bacterial and viral DNA names for PCR testing
Of special interest is bacterial and viral DNA for PCR testing. These are treated as substances by SNOMED and not as organisms. I am currently working with the Australia National Release Center (NRC) for SNOMED CT to create an attribute relationship that will link the substance concept to the organism concept that will help to resolve this linkage for the LOINC ontology. We are in the testing phase of the new attribute so we hope to get this into production in the near future.
We will likely want to build in a process to feed any naming corrections that have not made it into SNOMED CT International Edition back into that terminology in order to keep the two terminologies in sync.
Where there is a test that identifies an organism (e.g. Culture), LOINC is expected to mapped to the test order and result and SNOMED CT Organism hierarchy codes to the organism identified.
Most tests for infectious disease DNA, serologies, serotypes, etc. do not actually identify the organism itself as John notes. Rather it’s a biomarker, such as an Antigen, Antibody, DNA or RNA, toxin, resistance gene, etc. that is either on or produced by the organism or in response to the organism. Some may be concurrent with infection with the organism, but in other cases it may signify exposure and immunity to the organism. Hopefully, it’s clear especially with the latter that the test is not of the organism like with culture based identification.
In SNOMED CT, while there is the substance category, US response values usually for these tests often use the SNOMED qualifier hierarchy codes as many are ordinal or qualitative response values. (Some may be semi-quant too.) US LISs do not typically have functionality to map to SCT substance hierarchy codes as the dictionary for qualitative response values is set to only map to a single SCT hierarchy, which would be the qualifier hierarchy as the responses are used for other lab result values too. There is typically a separate Organism dictionary in US LIS builds, which is set to map terms to the SCT organism hierarchy.
A PCR test for an organism’s DNA may likely return either positive/negative or detected / Not detected from the qualifier value hierarchy.
In the case of the detected / positive result, adding an attribute in SNOMED CT will allow implementers to programmatically make the jump from the DNA substance back to an Organism concept.
The business logic path would look like this:
LOINC Code for results links to the LOINC Part for Component
LOINC part for Component represents the Organism’s DNA which is mapped to a Substance concept in the mapping used to create the LOINC ontology
DNA Substance Concept linked to Organism concept via attribute named “Has material source”
Initially, only data warehouses will likely be able to traverse this business logic path, HOWEVER, LIS system should be able to put this on their roadmap for implementation because it will remove their customer’s mapping burden and replace it with a curated product.
Granted, this is all dependent on getting the testing done and the attribute implemented and populated in the International Edition of SNOMED CT. (I know…no pressure right!)
Thanks for mentioning the linkage between the substance and organism. Is this only for DNA? Does this include linking toxins to the organism with which they are associated or are they excluded as they are different from the organism? Will all DNA tests associated with an organism be linked? Including those for different markers? See https://loinc.org/115082-0 for an example. It may be identifying different parts of the elephant in the room as the saying goes.
As discussed on other calls, US LISs (and likely a number globally) do not have functionality for SCT substance hierarchy mapping especially in the data dictionaries where the terms are built and originate. For lab results, the functionality is to map to LOINC. For organisms, the dicitonary is set to map them to the SCT orgnanism hierarchy. It’s unlikely this will change as it can be handled downstream in data warehouses, EHRs, and research systems, if needed and since labs don’t need the functionality. Many laboratory professionals are not even aware of the substance hierarchy in SCT.
It would also require LIS and LIMS vendors to do product development to support what is outlined in the business logic. It was very painful for customers of a major US LIS vendor in a jurisdiction just to get the vendor to support the LOINC Long Name for public health reporting needs. The vendor refused to add the functionality even with public health, customers and LOINC team members requesting. They only added to their development roadmap after Regenstrief decided to extend all LOINC fields to the 212 characters and they had to support for all their customers. Not sure if this impacted all their global customers as well. It took several years to get this functionality rolled out for their US customers.
Certainly after the work is done as you mentioned in SCT, then it will be available for those who can use it.
