Swapna Abhyankar

Forum Replies Created

Viewing 15 posts - 1 through 15 (of 19 total)
  • Author
    Posts
  • in reply to: Missing mappings between LoincNumber and RPID? #466803
    Swapna Abhyankar
    Participant

    Hello,

    The RPIDs included in the LoincRsnaRadiologyPlaybook are all from the RadLex Core playbook. A decision was made early on in the collaboration between RSNA and Regenstrief to only include concepts from the Core playbook and not from the Complete playbook. RPID602 is not in the Core playbook, which is why it isn’t included in the file.

    All of the entries that do not have any information in the RPID column are radiology concepts in LOINC that have no corresponding concept in the Core playbook. Many of these LOINC terms existed before the Regenstrief/RSNA collaboration, and some have been added since then based on user requests. Because RSNA is no longer updating the playbook and new concepts will only be added to LOINC, over time the percent of LOINC codes that have corresponding RPIDs will decrease.

    Hope this helps!

    in reply to: Inconsistencies with LOINC codes. #455959
    Swapna Abhyankar
    Participant

    Hi Jess,

    To add to what Pam said, LOINC codes are made based on user requests. Many inconsistencies stem from the original requests, for example, where a user may have only requested a code for the right side and not the left. In recent years, when we spot these inconsistencies we follow up with the user and recommend creating a complete set of codes, but that did not happen as consistently in the earlier years of LOINC.

    Hope this helps!

    Swapna Abhyankar
    Participant

    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
    Participant

    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    In addition to “Body fld”, we also have a System “Asp”, which represents the fluid withdrawn during an aspiration procedure from an abnormal collection of fluid, such as from an abscess or cyst.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
    Participant

    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
    Participant

    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
    Participant

    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
    Participant

    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
    Participant

    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
    Participant

    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
    Participant

    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
    Participant

    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
    Participant

    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
    Participant

    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
    Participant

    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!

Viewing 15 posts - 1 through 15 (of 19 total)