Regarding ref set - Githubissues

ghost commented 5 years ago

Hello team,

This is more of a please help rather than an issue but i didn’t know any other place to post it. I’m trying to use a new simpler refset that was released by India. Using the snomed CT api, I’m able to search the entire snomed CT DB whichcurrently resides in mongo. Can someone please guide me how to only search within the refset?

Thanks! Vybhav

kaicode commented 5 years ago

Hi @tacack There is a refsetFilter param available in the description search API: https://snomedctsnapshotapi.docs.apiary.io/#reference/concepts/search/search-descriptions That should do it.

ghost commented 5 years ago

Thanks @kaicode

I'm trying to search within the Indian Neurosurgeory refset that was published. When I try using the refsetID seen in the picture below in the "### refsetFilter" value in the API call, I don't get any responses.

I'm sure I'm doing something wrong. Sorry if I'm off-topic, but I'm stuck and any help is appreciated.

Regards, Vybhav

kaicode commented 5 years ago

Hi @tacack I'm assuming you have loaded the content from India into your own sct-snapshot-rest-api installation.

You are correct to take the 1231000189105 number from the refsetId column of the reference set RF2 file.

Here are some things to try:

You can check that the content has loaded using the members endpoint: https://snomedctsnapshotapi.docs.apiary.io/#reference/concepts/children/retrieve-reference-set-members. If you set the sctid to 1231000189105 you should get a list of concepts from that reference set. Here is an example in the public browser using the 450970008 |General Practice / Family Practice reference set (foundation metadata concept)|: https://browser.ihtsdotools.org/api/v1/snomed/en-edition/v20180731/concepts/450970008/members?limit=100
You could check your URL format matches this example of using filtering in the public browser using the same GPFP reference set: https://browser.ihtsdotools.org/api/v1/snomed/en-edition/v20180731/descriptions?query=pregnant&refsetFilter=450970008 There are only 7 results when the refsetFilter is used and 79 without so this example appears to be working.

ghost commented 5 years ago

Thanks for your response @kaicode .

Regarding the content, I've loaded the International edition of SNOMED CT.

I tried the first URL that you mentioned and when I add the SCT ID as 1231000189105, I don't see any results.

The second URL is precisely the format i'm using for my autocomplete search and it fails to return any results when I include 1231000189105 as the refsetFilter.

Regards, Vybhav

kaicode commented 5 years ago

Hi @tacack, the 1231000189105 reference set is not included in the International Edition of SNOMED CT. This is why you can not find any content relating to that reference set. You will need to load a SNOMED extension or edition containing that reference set in order to use that content. I hope that helps.

ghost commented 5 years ago

Hello,

I checked the release notes of the Refsets and I saw this ->

This release includes 30 refsets covering common diseases under National Public Health Programs and Medical Specialty / Department-wise refsets.

This package depends on the SNOMED CT July 2017 International Edition, and should be used and analyzed accordingly.

Please refer to the Release Note downloadable from this MLDS release package. The release note is also available at NRCeS website (https://www.nrces.in)

When it says it depends on the July 2017 international edition, is it safe to assume that the 2018 Jan 1st international edition will also have the changes?

Thanks! Vybhav

kaicode commented 5 years ago

If a SNOMED package depends on a specific version of another package it is not safe to assume that a later version will contain all the same content. SNOMED CT concepts can be made inactive when they are no longer wanted in an edition so later releases may not contain all the same active concepts. It sounds like you will need to load the July 2017 International Edition at the same time as the India Reference Sets extension in order to use this content in the sct-snapshot-rest-api.

I assume that is possible with the rf2-to-json-conversion project.

The other option for loading, managing and querying this content is to use a Terminology Server like Snowstorm for your SNOMED content API.

This would give you the following advantages:

Ability to load content into the API using RF2 zip files directly (automatic RF2 to JSON conversion)
Store many releases and extensions of of SNOMED CT using Terminology Server branches (like a version control system)
Ability to load reference set packages after loading the International Edition on a child branch
Combine description search with Expression Constraint Language search to constrain by reference set, SNOMED hierarchy, part of the body or any other SNOMED attribute.

Snowstorm is a free Open Source Terminology Server written for SNOMED CT by Snomed International - https://github.com/IHTSDO/snowstorm

ghost commented 5 years ago

I'm going to check out Snowstorm. Thank you for all your help @kaicode . I'll try Snowstorm, downgrade to the July 2017 version and give it a shot.

Again, appreciate all your help!

kaicode commented 5 years ago

👍 Don't hesitate to ask questions Snowstorm issues/questions section 😸

IHTSDO / sct-snapshot-rest-api

Regarding ref set #39