Swapna Abhyankar

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Viewing 15 posts - 1 through 15 (of 17 total)
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  • Swapna Abhyankar
    Moderator

    Hi Alla,

    Consumer names are available as a separate downloadable csv file (https://loinc.org/consumer-names/). They are still in Alpha status, so if you use them, use them with caution. And we would appreciate any feedback you might have.

    We do not currently publish Part descriptions.

    Thanks!

    in reply to: Body fluid #454601
    Swapna Abhyankar
    Moderator

    Hi everyone,

    In addition to “Body fld”, we also have a System “Asp”, which represents the fluid withdrawn during an aspiration procedure from an abnormal collection of fluid, such as from an abscess or cyst. “Asp” is used for abnormal fluid collections that are aspirated, while “Body fld” is used for named body fluids, such as synovial fluid or peritoneal fluid, that are not inherently pathologic.

    in reply to: PD-L1 TC vs. IC #448018
    Swapna Abhyankar
    Moderator

    Hi Philipp,

    Please submit a request using the values you have in your message above, and we will work with you to make sure the terms are modeled correctly. Don’t worry about having all of the pieces correct in your initial submission, and it will be easier to work out the details through our submissions process rather than through Forum posts.

    The most important thing we need with the submission is de-identified lab reports or clinical notes as you mentioned in your original email, or any other information you can provide about the types of results that you need new LOINC terms for.

    Thanks,
    Swapna

    Swapna Abhyankar
    Moderator

    Hi Samuel,

    The best source to get LOINC codes for SARS-CoV-2 tests approved by the FDA is the LIVD file published by the CDC – https://www.cdc.gov/csels/dls/sars-cov-2-livd-codes.html. The LOINC team helps maintain this file and it’s updated each week. Can you please check the file and see if the test kit you are using is included?

    We also have more information on choosing LOINC codes on our webpage dedicated to SARS-CoV-2 – https://loinc.org/sars-coronavirus-2/.

    Thanks,
    Swapna

    in reply to: Cardiac Catheterization #447961
    Swapna Abhyankar
    Moderator

    Hi Marc,

    The meaning of a single LOINC term is based on the 5 or 6 major Parts (Component, Property, Timing, System, Scale, +/- Method).

    When comparing 80234-8 and 8583-7, you will see that the first one has a Method of cardiac catheterization, while the second is methodless, meaning that it represents Right atrial A-wave amplitude as measured by any method. The first code is more specific.

    https://loinc.org/80234-8/:
    A wave amplitude:Pres:Pt:Heart.atrium.right:Qn:Cardiac catheterization

    https://loinc.org/8583-7:
    A wave amplitude:Pres:Pt:Heart.atrium.right:Qn:

    Thanks,
    Swapna

    in reply to: PD-L1 TC vs. IC #447960
    Swapna Abhyankar
    Moderator

    Hi Philipp,

    I want to clarify several issues in addition to the information Pam provided –

    1. LOINC Parts should not be used to represent lab tests or lab test results. The Parts together define a single LOINC term, so for example, there are several different Parts related to PD-L1, including LP221212-6, that, in various combinations with other Parts, result in 9 different LOINC terms (https://search.loinc.org/searchLOINC/search.zul?query=programmed+ligand+1) that represent various lab tests. Some of those terms have an ordinal scale, meaning they would be used to represent tests that have positive/negative results, but they all specify various clones.

    2. In your example: “PD-L1 tumor cell (TC) staining: LOW POSITIVE, PD-K1 immune cell (IC) staining: POSITIVE”, there are 4 pieces of information – two test names (PD-L1 tumor cell (TC) staining and PD-K1 immune cell (IC) staining), and two results (LOW POSITIVE and POSITIVE). The two test names would be candidates for mapping to LOINC codes (not Part codes), and the two results would be mapped either to SNOMED CT codes (preferred) or LOINC Answer (LA) codes.

    Unfortunately we don’t have generic PD-L1 codes that don’t specify the clones, so you would either have to get more information about the specific testing being reported, or potentially request new generic LOINC codes.

    3. As documented in the LOINC terms of use, LOINC Part (LP) codes are non-semantic identifiers and can only be used to organize LOINC terms or link to other ontologies. They should not be used as a stand-alone terminology. Here is the text from Section 5 of the license:

    The LOINC parts and LOINC part hierarchies shall not be used in any manner except as they are presented in the Licensed Materials (and/or in other formats of distribution approved by Regenstrief Institute, Inc.) to organize, categorize, and be constituents of LOINC terms, and provide links to external terminologies. The LOINC parts and LOINC part hierarchies are subject to change, addition, modification, or deletion, without notice, and are not strictly managed under the same policies as LOINC terms.

    Thanks,
    Swapna

    Swapna Abhyankar
    Moderator

    Hi Malar,

    To add to John’s reply, the Multiaxialhierarchy.csv file does not contain a separate field for LOINC term status. However, the names of the deprecated terms in the file are still prefixed with “Deprecated” as you can see in John’s first screenshot above. They might have moved from the LAB.NOTYETCATEG node, but they should still have the prefix.

    Also, 2019AB and 2020AA are version numbers for the UMLS. Are you looking at LOINC content in the UMLS? I wonder if that is why you are seeing different information. UMLS 2020AA contains LOINC content from our 2.67 release published in December 2019 – see https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/LNC/metadata.html.

    The latest release of LOINC is 2.68 and was published a few weeks ago, but that content is not currently available in the UMLS.

    in reply to: Covid Groups #435889
    Swapna Abhyankar
    Moderator

    Hi Peter,

    We will have SARS-CoV-2 Groups in the upcoming release in June. I’m planning to include the individual Groups shown below:

    1. SARS-CoV-2 virus detection (including molecular, antigen, and culture codes)

    2. SARS-CoV-2 molecular detection

    3. SARS-CoV-2 antibody tests

    For virus detection, we only have one code each for antigen and culture so far, so those won’t have individual Groups. Also, I don’t think more specific antibody Groups would make sense, because we have a mix of IgG, IgA, IgM, IgG+IgM, and any antibody (IgA+IgG+IgM), so there are no clear breakpoints.

    I would welcome your feedback about other Groups that might be useful.

    Thank you!

    in reply to: SARS-CoV-2 codes discussion #435453
    Swapna Abhyankar
    Moderator

    We have generic codes – “SARS Coronavirus 2 RNA” as well as specific codes for different targets. If you haven’t already, please check out our special SARS-CoV-2 FAQ page: https://loinc.org/sars-coronavirus-2/

    These codes will be added to our Groups content for the June release, but at this time, we are not planning to release temporary Groups or Parts before then.

    Swapna Abhyankar
    Moderator

    Hi Dirk,

    I don’t have an exact number, but over the last five years I would estimate 5-10, and the actual number is probably even lower than that.

    Thanks,

    Swapna

    Swapna Abhyankar
    Moderator

    Hi Marc,

    We never reuse LOINC codes. In the rare case that codes are published on the pre-release page but never get officially released, they still persist in our internal database and will not be used again.

    Thanks,

    Swapna

    in reply to: Point of care testing (POCT) #24248
    Swapna Abhyankar
    Moderator

    Hi Pavan,

    RELMA is using your test name, specimen, and units of measure to find the correct code. You can find more information about how it works in the RELMA manual (https://loinc.org/download/relma-manual/).

    The reason there is an appropriate LOINC match for “Leukocytes bld  x 1000/ul” and not for “Glucose -124” is because the first one includes information about the specimen and units, as well as the analyte, while the second only includes the analyte.

    Thanks,
    Swapna

    in reply to: Call for Feedback on LOINC Groups #22599
    Swapna Abhyankar
    Moderator

    Hi Rebecca,

    Regarding the best way to view and consume clinical observables data, that will depend on your local implementation of the Groups and your EHR system. And please keep in mind that the LOINC Groups must be reviewed and validated for your specific use case.

    Looking at the Parent Groups should help you decide which ones might be useful for your particular use case because the Parent Group name will tell you whether the individual Groups are related to laboratory, radiology, vital signs, etc.

    We were creating Groups based on our clinical experience and feedback we have received from the LOINC Community over time. It is still a work in progress, and we haven’t deliberately excluded any particular types of LOINC codes, such as challenge terms, except maybe from specific existing Group definitions where including the challenge terms did not seem useful for that particular Group.

    If there are Groups that you think would be useful, such as a broader vital signs grouping, please submit your ideas through our Groups Community submission portal (https://loinc.org/groups/community/).

    You can search by any of the 6 major LOINC Parts (as well as many other fields) in both RELMA and search.loinc.org. So for example, if you are looking for ejection fraction codes, use Component:”Ejection fraction”. This search will return radiology codes for cardiac studies as well as ejection fraction measurements. If you want to restrict by the measurements, add the scale to the search, e.g., Component:”Ejection fraction” Scale:Qn.

    If in general you want to exclude all laboratory terms, you can add -Type:1 to all of your searches. The RELMA and online search help both have a lot of information about search strategies, including which fields you can search on and how to include and exclude terms from your search.

    Thanks again for your interest in the LOINC Groups!

    in reply to: Call for Feedback on LOINC Groups #22465
    Swapna Abhyankar
    Moderator

    Hi Rebecca,

    Thank you for your interest and comments about the LOINC Group work.

    I completely agree with you that having the same ID over time is essential, and starting with the December 2017 Group release, the Group IDs (LG numbers) have been stable, so that the LG numbers for a Group in the December release is the same as the LG number for that Group in the new June (2.64) release.

    The file you originally looked at (LOINC_2.61_GroupFile_Alpha_1_grouped_with_counts) was not part of our official release package, though it did contain content from our initial alpha release. It was created by our colleagues at NLM and posted by Dan Vreeman in this same thread on July 5, 2017. Because the counts file wasn’t part of our official release, it did not come with the Readme and Release notes, which specifically said that users should expect the contents of the file to change. Given that it was the first release of the Group work, we did not know what feedback we would get or how the structure or contents of the file would change, so we wanted to be able to change any part of it for the next release.

    For the December 2017 release, we significantly changed the structure of the Group release artifact (from one CSV to several) in order to decrease data redundancy and make the contents more computable. In the Release notes for that release, we said that starting with that version, the LG numbers would persist.

    The version of the file with the counts is not part of our official release package because given its formatting, subtotal functions, and hidden rows, it cannot easily be uploaded into a database or used for data analysis, and similarly, creating the file is a manual effort.

    I hope this information helps, and be assured that going forward (starting with December 2017), the LG numbers are stable.

    Please let me know if you have any questions.

    in reply to: Mappings for Pulmonary Function Tests #21600
    Swapna Abhyankar
    Moderator

    Hi Malar,

    I just did a quick search and also could not find the pulmonary function concepts you mentioned in your post.

    Nearly all of our terms are created based on submitted requests, and nobody to date has requested these pulmonary tests.

    You are welcome to request new LOINC codes for these concepts. We have detailed instructions on how to submit requests and the information we need as part of the request on our website: https://loinc.org/submissions/new-terms/.

    Thanks,
    Swapna

    Swapna Abhyankar, MD
    Associate Director for Content Development
    LOINC and Health Data Standards

Viewing 15 posts - 1 through 15 (of 17 total)