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"patient-friendly" descriptions of LOINC/SNOMED/etc codes. #46
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Both https://github.com/IHTSDO/snomed-database-loader and https://github.com/IHTSDO/snowstorm look like good SNOMED options, provided by https://github.com/IHTSDO |
We know that snomed content is licensed - we are not sure how it is for open-source, but commercial usage of it definitely requires the vendor to have a license |
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From the Fasten discord....
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Also from @AnalogJ in the Discord.....
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That post can be found here. |
From Carol Macumber In reply...
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@AnalogJ#3506 my UMLS License was just Approved.... I will take a look at the data they provide in a little bit.... |
I think we want Value Set Authority Center (VSAC) and/or SNOMED CT RxNorm could also be useful to integrate. |
The full object body for that, is {
"pageSize": 25,
"pageNumber": 1,
"pageCount": 1,
"result": [
{
"rootSource": "MSHCZE",
"value": "Zlomeniny některé kosti/kostí v kotníku. Bimaleolární fraktura = fraktura obou kotníků, trimaleolární zlomenina = fraktura obou kotníků a zadní hrany tibie.",
"classType": "Definition",
"sourceOriginated": true
},
{
"rootSource": "NCI",
"value": "Traumatic or pathological injury to the ankle joint in which the continuity of an ankle bone is broken. Symptoms include pain, swelling, and difficulty moving the affected leg and foot.",
"classType": "Definition",
"sourceOriginated": true
},
{
"rootSource": "MSH",
"value": "Fractures of any of the bones of the ANKLE.",
"classType": "Definition",
"sourceOriginated": true
},
{
"rootSource": "HPO",
"value": "A fracture or multiple fractures of one or more of three bones in the ankle joint: the tibia (shinbone), the fibula (outer ankle bone), and the talus (which is the bone that connects your leg to your foot). [https://www.hss.edu/condition-list_ankle-fractures.asp]",
"classType": "Definition",
"sourceOriginated": true
},
{
"rootSource": "MSHNOR",
"value": "Brudd i ankelbeina.",
"classType": "Definition",
"sourceOriginated": true
},
{
"rootSource": "MSHPOR",
"value": "Fraturas de quaisquer ossos do TORNOZELO.",
"classType": "Definition",
"sourceOriginated": true
},
{
"rootSource": "MSHSPA",
"value": "Fracturas de cualquiera de los huesos del TOBILLO.",
"classType": "Definition",
"sourceOriginated": true
}
]
} |
For LONIC, the first 2 steps work, but there is no definition... Step 1 for a LONIC code looks the same in terms of a response. For the 2nd response, the LONIC res looks like this. {
"pageSize": 25,
"pageNumber": 1,
"pageCount": 1,
"result": {
"ui": "C4739649",
"name": "Fracture Risk Assessment:-:Pt:^Patient:-:FRAX",
"dateAdded": "05-06-2019",
"majorRevisionDate": "01-03-2019",
"classType": "Concept",
"suppressible": false,
"status": "R",
"semanticTypes": [
{
"name": "Clinical Attribute",
"uri": "https://uts-ws.nlm.nih.gov/rest/semantic-network/2022AB/TUI/T201"
}
],
"atoms": "https://uts-ws.nlm.nih.gov/rest/content/2022AB/CUI/C4739649/atoms",
"definitions": "NONE",
"relations": "NONE",
"defaultPreferredAtom": "https://uts-ws.nlm.nih.gov/rest/content/2022AB/CUI/C4739649/atoms/preferred",
"atomCount": 4,
"cvMemberCount": 0,
"attributeCount": 0,
"relationCount": 0
}
} |
Hey @j-dogcoder So it sounds like you were able to find the "Description" for SNOMED codes but not LOINC? Hm. Is there another way that we can pull the LOINC descriptions? maybe using a medical wiki database query? |
Hrm.... none of the suggested links seem to have anything. I will keep looking. The SNOMED description seems to be patent friendly enough |
Are you looking for a dataset you can store? Or will API queries be sufficient? Being able to store the data will allow Fasten to be closer to offline able |
@j-dogcoder fixed some of the links above. Basically wikidata is a wiki-like database, with easy access to data in json format.
Agreed, ideally we'd be able to generate a dataset of patient-friendly descriptions for each code, and have that available in the Fasten database, without requiring API access. Since you found SNOMED patient-friendly descriptions already, should we start with them? |
I also posted on LOINC's contact-us page, asking them the same question as my FHIR Tulip post |
Hell, it might be interesting to use ChatGPT to create summaries of each code as well -- if we had a good way to verify that the results weren't complete lies 😨 |
That could be interesting, but without a way to verify that, we should steer clear for now. |
I agree that ideally we would have it in the DB... I will write a script to extract it all... do you just want it as json? or... how are we getting this into the db? |
@AnalogJ What kind of db do we use? |
I was browsing https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html |
@AnalogJ what one looks better for our usecase? |
Or is there something else on that page that looks better? |
would you like be to import it into the db?? or just upload the file for you to use? |
sorry for the delay getting back to you @j-dogcoder
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on the other hand, the Definitions file - |
I can't seem to find that file in the download, and I don't seem to see definitions in the other one. The definitions I found were in the API... maybe I need to write some script to query the API for every single code? |
@AnalogJ what are your thoughts on this? |
Ugh... when searching with exact, it doesn’t work at all... (doesn’t provide any results) 😠 😠 😠 |
Just some notes for future me: Here are some medical databases that can be used to find patient-friendly articles by LOINC code:
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👍🏻 |
@AnalogJ Should have this done on the repo by the 2nd week in April |
I think this is what we're going to want to use: Search By Codes* https://medlineplus.gov/about/developers/webservices/ examples:
*Search By Text https://medlineplus.gov/about/developers/webservices/ It's not perfect, but it supports SNOMED, LOINC and ICD-9/10 codes. |
I'm going to try to play around with it today. Our fallback might be the wikidata database or Unified Medical Language System (UMLS) api. |
👍🏻 |
Hey @AnalogJ, looking at your changes... For best offline usability, perhaps these things can be stored in the lighthouse db? I am planning on updating the script in Vital-Link/patient-friendly-codes, which exports it all to JSON, and periodically updates it if anything changes (will do something similar with Issue #95 (NPI numbers) after I get this finished up. In the long term, I will probably expose the codes over an API as well... Fasten is welcome to use one or both of those when it's complete, so only one of us has to maintain it if that makes sense. |
Ah! Keep putting things in the wrong repo! |
Hey @j-dogcoder
Yep, this data needs to be available offline. I think the best place to do this caching is in the Fasten db (locally).
I think the next step should be to work on NPI numbers, finding a way to look them up/map them to each Organization. I've been noodling around with a couple of ideas for how we can build something to allow the community to contribute. I'll update #95 |
Glad this got completed! Left you a comment on the NPI numbers issue. Will continue to keep this open in Vital-Link/patient-friendly-codes#2 for anyone interested. |
Creating this issue to stash some resources we have found to find "patient-friendly" descriptions of LOINC/SNOMED/etc codes.
I will post resources here shortly.
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