API for all Data

bifrost · April 16, 2021, 2:22pm

Hi there,

I am new to LOINC FHIR system. AS I am creating brand new structure in our system, I am looking for an API that would give me entire data set for the system. For Example, LoincCore table (available in csv file).

Thanks in Advance.

xaviergansel · April 23, 2021, 2:43am

hi all

<a class=“bbp-user-mention bbp-user-id-2” style=“box-sizing: border-box; margin: 0px; padding: 0px; border: none; outline: 0px; font-size: 14.82px; text-size-adjust: 100%; vertical-align: baseline; background-image: initial; background-position: 0px 0px; background-size: initial; background-repeat: initial; background-attachment: initial; background-origin: initial; background-clip: initial; color: #1b966b; text-decoration-line: none; box-shadow: none; transition: none 0s ease 0s; display: inline; font-weight: 600; text-shadow: none; font-family: Lato, Helvetica, Arial, Lucida, sans-serif;” href=“https://loinc.org/forums/users/timbriscoe/”>@TimBriscoe</a> I have a similar question as @bifrost above : I would like to access the value of properties “CHNG_TYPE” (Change type code) and “CHANGE_REASON_PUBLIC" (Detailed explanation about special changes to the term over time) as specified in the LOINC table (see users manual).

This would streamline code check after each loinc release, and make it easier than a one per one analysis or a fight with xls to work with the loinc.csv file

I am unable to find those properties in the fhir output. Could you assist me with that ?

best,

Xavier

xaviergansel · April 26, 2021, 2:26am

<p style=“box-sizing: border-box; margin: 13px 0px 0px; padding: 0px 0px 1em; border: 0px; outline: 0px; font-size: 14.82px; text-size-adjust: 100%; vertical-align: baseline; background-image: initial; background-position: initial; background-size: initial; background-repeat: initial; background-attachment: initial; background-origin: initial; background-clip: initial; line-height: 1.4em; font-family: Lato, Helvetica, Arial, Lucida, sans-serif;”>hi all,
Sorry for the troublesome copy / past ; here is a clean version of it
<p style=“box-sizing: border-box; margin: 13px 0px 0px; padding: 0px 0px 1em; border: 0px; outline: 0px; font-size: 14.82px; text-size-adjust: 100%; vertical-align: baseline; background-image: initial; background-position: initial; background-size: initial; background-repeat: initial; background-attachment: initial; background-origin: initial; background-clip: initial; line-height: 1.4em; font-family: Lato, Helvetica, Arial, Lucida, sans-serif;”>I have a similar question as @bifrost above : I would like to access the value of properties “CHNG_TYPE” (Change type code) and “CHANGE_REASON_PUBLIC” ”(Detailed explanation about special changes to the term over time) as specified in the LOINC table (see users manual).
<p style=“box-sizing: border-box; margin: 13px 0px 0px; padding: 0px 0px 1em; border: 0px; outline: 0px; font-size: 14.82px; text-size-adjust: 100%; vertical-align: baseline; background-image: initial; background-position: initial; background-size: initial; background-repeat: initial; background-attachment: initial; background-origin: initial; background-clip: initial; line-height: 1.4em; font-family: Lato, Helvetica, Arial, Lucida, sans-serif;”>This would streamline my LOINC mapping code check after each loinc release, and make it easier than a one per one analysis or a fight with xls to work with the loinc.csv file 
<p style=“box-sizing: border-box; margin: 13px 0px 0px; padding: 0px 0px 1em; border: 0px; outline: 0px; font-size: 14.82px; text-size-adjust: 100%; vertical-align: baseline; background-image: initial; background-position: initial; background-size: initial; background-repeat: initial; background-attachment: initial; background-origin: initial; background-clip: initial; line-height: 1.4em; font-family: Lato, Helvetica, Arial, Lucida, sans-serif;”>I am unable to find those properties in the FHIR output. Could you assist me with that ?
<p style=“box-sizing: border-box; margin: 13px 0px 0px; padding: 0px 0px 1em; border: 0px; outline: 0px; font-size: 14.82px; text-size-adjust: 100%; vertical-align: baseline; background-image: initial; background-position: initial; background-size: initial; background-repeat: initial; background-attachment: initial; background-origin: initial; background-clip: initial; line-height: 1.4em; font-family: Lato, Helvetica, Arial, Lucida, sans-serif;”>best,
<p style=“box-sizing: border-box; margin: 13px 0px 0px; padding: 0px 0px 1em; border: 0px; outline: 0px; font-size: 14.82px; text-size-adjust: 100%; vertical-align: baseline; background-image: initial; background-position: initial; background-size: initial; background-repeat: initial; background-attachment: initial; background-origin: initial; background-clip: initial; line-height: 1.4em; font-family: Lato, Helvetica, Arial, Lucida, sans-serif;”>Xavier
<p style=“box-sizing: border-box; margin: 13px 0px 0px; padding: 0px 0px 1em; border: 0px; outline: 0px; font-size: 14.82px; text-size-adjust: 100%; vertical-align: baseline; background-image: initial; background-position: initial; background-size: initial; background-repeat: initial; background-attachment: initial; background-origin: initial; background-clip: initial; line-height: 1.4em; font-family: Lato, Helvetica, Arial, Lucida, sans-serif;”>

pdbanning · April 27, 2021, 9:14am

Hello Xavier and BiFrost Team,

The question of specific content columns has been taken to Regenstrief staff for consideration. Will keep you posted.

Pam

petitr · June 8, 2021, 3:39am

Hello,

In order to avoid manual step on our side, we try to access the loinc resource thanks to FHIR.
We have quite good success in this task : we try calls on
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=71775-1
https://fhir.loinc.org/CodeSystem/$lookup?system=http://unitsofmeasure.org&code=mmol/ml
and we plan to use
https://fhir.loinc.org/ConceptMap/?url=http://loinc.org/cm/loinc-parts-to-ncbi-taxonomy
https://fhir.loinc.org/ValueSet/deprecated-loinc-terms/

We are still in the learning stage and we face 2 issues
we are able to to retrieve VersionFirstReleased=2.40 VersionLastChanged=2.64 associated to the loinc code 71775-1
but not the version of the loinc itself 2.69

we try to seek in the following resource without success
https://fhir.loinc.org/metadata
https://fhir.loinc.org/CodeSystem/?url=http://loinc.org

Another topic is the ability to retrieve information not yet released
it is possible with the human website but not with the resource
https://loinc.org/96754-7/
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=96754-7

Thank you for any advise

system · June 9, 2021, 5:57am

This would streamline my LOINC mapping code check after each loinc release, and make it easier than a one per one analysis or a fight with xls to work with the loinc.csv file

timbriscoe · July 20, 2021, 2:08pm

Hello Xavier and Raphael,

My apologies for the time between messages. I hope to address some of your requests and concerns regarding LOINC’s Terminology Service (TS) using FHIR. Please keep in mind that this API carries a Beta maturity status. The FHIR standard continues to evolve and functionality of this service may change.

Development of CodeSystem and ValueSet versioning has been delayed a few times but should be on track now for release in late August or early September. This should provide the explicit LOINC version number you are needing. Below is a snippet of JSON provided on our development server where this versioning is partially in place. This is the response to a CodeSystem lookup operation request for LOINC 4544-3. Notice how version 2.70 is referenced as a parameter.

{
  "resourceType": "Parameters",
  "parameter": [ {
    "name": "name",
    "valueString": "LOINC"
  }, {
    "name": "version",
    "valueString": "2.70"
  }, {
    "name": "display",
    "valueString": "Hematocrit [Volume Fraction] of Blood by Automated count"
  }, {
    "name": "abstract",
    "valueBoolean": false
  }, {
    "name": "property",
    "part": [ {
      "name": "code",
      "valueCode": "CLASS"
    }, {
      "name": "value",
      "valueCoding": {
        "system": "http://loinc.org",
        "code": "LP7803-2",
        "display": "HEM/BC"
      }
    } ]

[TRUNCATED]

Once available publicly, we will do our best to load previous versions of the LOINC CodeSystem and make them available via this API. I believe we should be able to provide the past 2 or 3 releases as you have requested.

Providing pre-release LOINC terms, even those given a Special Use status for emergent conditions, remains a concern for us. We have consulted with several FHIR experts and received differing opinions. Our forthcoming work to enable versioning will provide us some additional functionality but we remain concerned about making available pre-release terms—codes that are likely to change and may not even be officially released—via this programmatic means.

In regard to providing the full license via this API, can you please reiterate your use case? I am not sure I understand what you are trying to accomplish. Is it to capture the necessary text required by the license or is it to create a delta between license versions? It may be that this API is not the best tool to fill your need. Incidentally, we will be changing the copyright line provided by this FHIR server. Our next release will use a style similar to the following. It may not be noteworthy to you but it is important for us to make this change.

  <code>&quot;copyright&quot;: &quot;This material contains content from LOINC (http://loinc.org). LOINC is copyright ©1995-2021, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.&quot;,</code>

The goal of our TS is provide a reliable means of making LOINC content available programmatically while leveraging the common H7 FHIR standard. We want to make it as useful as possible to users’ needs. Please know that we are also bound by available resources.

I hope we can continue this conversation as we advance our work.

Best regards,
Tim

xaviergansel · November 4, 2021, 3:37am

Hi Tim,

Do you have any input on the above mentioned FHIR terminology server release ?

I failed to identify the current LOINC version in it.

I’ll mail you directly to give you a more detailed overview of our use case of your API

best,

Xavier

timbriscoe · November 4, 2021, 3:24pm

Hi Xavier,

We are still working on the finishing touches with our software vendor to provide parallel versioning of resources. The process has taken far longer than we all had planned. We are confident we will have upgraded resources in place prior to 2021’s conclusion. You can expect a full announcement to the community when all is unveiled.

Best,
Tim

xaviergansel · November 5, 2021, 4:17am

Hi Tim,
Thanks for the update.
Xavier