FHIR Chat · VSAC · IG creation

Stream: IG creation

Topic: VSAC

Grahame Grieve (Aug 25 2020 at 06:02):

@Sean McIlvenna we have a VSAC package now. To use it, you need something like this in your IG dependencies:

dependsOn
     uri = http://fhir.org/packages/us.nlm.vsac
     packageId = us.nlm.vsac
     version =  0.1.0

Value set canonical URIs are http://vsac.nlm.nih.gov/fhir/ValueSet/{oid}

Eric Haas (Aug 25 2020 at 17:12):

does that mean we can now offload the terminology to vsac?

Grahame Grieve (Aug 25 2020 at 21:08):

if the value set exists in vsac, you should just reference it there, yes. Except that you should check carefully, since (a) the import from vsac has issues and (b) the vsac value set in FHIR isn't actually 'published' anywhere. But you can see the source here: https://github.com/FHIR/packages/tree/master/packages/us.nlm.vsac/package

Gay Dolin (Aug 27 2020 at 13:04):

Yippee! @Jerry Goodnough

James Shalaby (Aug 27 2020 at 13:20):

That's very helpful. How does it deal with intensional value sets that have been published? Is that supported?

Gay Dolin (Aug 27 2020 at 13:51):

I hope it retrieves the expansion (latest). If one prefers an earlier expansion in their IG -- not sure how that is handled @Robert McClure

Chris Moesel (Aug 27 2020 at 16:26):

@Grahame Grieve -- the FHIR API provided by VSAC returns value sets with the following canonicals: http://cts.nlm.nih.gov/fhir/ValueSet/{oid}. Why does the VSAC package redefine the canonical?

Grahame Grieve (Aug 27 2020 at 21:31):

Follow up on #terminology

Grahame Grieve (Aug 27 2020 at 22:20):

@James Shalaby what's an example of a VSAC intensional value set?

Chris Moesel (Aug 28 2020 at 12:47):

Alcohol Abuse Disorder SCT (2.16.840.1.113762.1.4.1222.22) is defined intensionally. I expect that @James Shalaby asked that question because the FHIR API provided by NLM currently does not support intensional value sets; if you try to get an intensional value set over the NLM FHIR API, you get a not-found error. It is a known limitation.

James Shalaby (Aug 28 2020 at 21:17):

That's correct @Chris Moesel

Grahame Grieve (Aug 28 2020 at 22:08):

well, the answer is, that's not a value set that VSAC includes in any of the downloads, so it's not one that I processed

Chris Moesel (Aug 31 2020 at 13:27):

Oh. You're using VSAC downloads? What downloads are you using? Are you using the ones listed at https://vsac.nlm.nih.gov/download (which redirects to https://vsac.nlm.nih.gov/download/ecqm)? Or different ones?

Sean McIlvenna (Aug 31 2020 at 16:02):

@Grahame Grieve how do updates to VSAC get incorporated into your vsac package?

Sean McIlvenna (Aug 31 2020 at 16:03):

Is it a manual process? (i.e. you rebuild the fhir vsac package upon request)
or is it an automated/scheduled process? (the fhir package for vsac is rebuilt every XX days, or weeks, or months)

Grahame Grieve (Aug 31 2020 at 19:34):

I found 4 downloads, I think, on the VSAC site. All of them. And I don't know how to automate that, so it's manually by request right now

Chris Moesel (Aug 31 2020 at 19:51):

Ah, OK. I'm guessing that those don't represent the complete set -- and are probably primarily focused on value sets used in eCQMs. How many value sets do you have? If I use the "Search" feature and don't filter on anything, it reports 9,108 value sets. I can download them all from the search results using the "Export Search Results" button.
image.png

Grahame Grieve (Aug 31 2020 at 20:03):

I didn't find that. I'll do it that way when I get a chance

Grahame Grieve (Sep 04 2020 at 05:36):

@Chris Moesel that only downloads the list, not the actual value sets

Grahame Grieve (Sep 04 2020 at 07:34):

still, I can use that list to tell me what value sets I can fetch from the VSAC API. About 3% of the value sets can't be fetched:

Grahame Grieve (Sep 04 2020 at 07:35):

1.3.6.1.4.1.6997.4.1.2.271.13.38398.1.11.1.999.722
1.3.6.1.4.1.6997.4.1.2.271.13.38398.1.11.1.999.723
2.16.840.1.113762.1.4.1010.5
2.16.840.1.113762.1.4.1010.7
2.16.840.1.113762.1.4.1010.9
2.16.840.1.113762.1.4.1018.98
2.16.840.1.113762.1.4.1021.40
2.16.840.1.113762.1.4.1021.41
2.16.840.1.113762.1.4.1029.61
2.16.840.1.113762.1.4.1029.62
2.16.840.1.113762.1.4.1032.151
2.16.840.1.113762.1.4.1032.77
2.16.840.1.113762.1.4.1034.100
2.16.840.1.113762.1.4.1034.151
2.16.840.1.113762.1.4.1034.152
2.16.840.1.113762.1.4.1034.153
2.16.840.1.113762.1.4.1034.4
2.16.840.1.113762.1.4.1034.89
2.16.840.1.113762.1.4.1034.99
2.16.840.1.113762.1.4.1047.115
2.16.840.1.113762.1.4.1047.277
2.16.840.1.113762.1.4.1095.10
2.16.840.1.113762.1.4.1095.14
2.16.840.1.113762.1.4.1095.2
2.16.840.1.113762.1.4.1099.10
2.16.840.1.113762.1.4.1099.12
2.16.840.1.113762.1.4.1099.33
2.16.840.1.113762.1.4.1111.84
2.16.840.1.113762.1.4.1111.86
2.16.840.1.113762.1.4.1116.312
2.16.840.1.113762.1.4.1146.1008
2.16.840.1.113762.1.4.1146.1063
2.16.840.1.113762.1.4.1146.1064
2.16.840.1.113762.1.4.1146.1065
2.16.840.1.113762.1.4.1146.1066
2.16.840.1.113762.1.4.1146.1067
2.16.840.1.113762.1.4.1146.1070
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2.16.840.1.113762.1.4.1146.1109
2.16.840.1.113762.1.4.1146.1110
2.16.840.1.113762.1.4.1146.1123
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2.16.840.1.113762.1.4.1146.1155
2.16.840.1.113762.1.4.1146.1203
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2.16.840.1.113762.1.4.1146.304
2.16.840.1.113762.1.4.1146.704
2.16.840.1.113762.1.4.1166.61
2.16.840.1.113762.1.4.1179.1
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2.16.840.1.113762.1.4.1179.5
2.16.840.1.113762.1.4.1180.15
2.16.840.1.113762.1.4.1180.16
2.16.840.1.113762.1.4.1182.127
2.16.840.1.113762.1.4.1182.310
2.16.840.1.113762.1.4.1190.6
2.16.840.1.113762.1.4.1195.332
2.16.840.1.113762.1.4.1196.158
2.16.840.1.113762.1.4.1196.87
2.16.840.1.113762.1.4.1219.1
2.16.840.1.113762.1.4.1219.2
2.16.840.1.113762.1.4.1219.4
2.16.840.1.113762.1.4.1221.100
2.16.840.1.113762.1.4.1221.101
2.16.840.1.113762.1.4.1221.102
2.16.840.1.113762.1.4.1221.103
2.16.840.1.113762.1.4.1221.17
2.16.840.1.113762.1.4.1221.19
2.16.840.1.113762.1.4.1221.20
2.16.840.1.113762.1.4.1221.21
2.16.840.1.113762.1.4.1221.22
2.16.840.1.113762.1.4.1221.24
2.16.840.1.113762.1.4.1221.25
2.16.840.1.113762.1.4.1221.26
2.16.840.1.113762.1.4.1221.29
2.16.840.1.113762.1.4.1221.3
2.16.840.1.113762.1.4.1221.31
2.16.840.1.113762.1.4.1221.33
2.16.840.1.113762.1.4.1221.34
2.16.840.1.113762.1.4.1221.36
2.16.840.1.113762.1.4.1221.37
2.16.840.1.113762.1.4.1221.39
2.16.840.1.113762.1.4.1221.4
2.16.840.1.113762.1.4.1221.40
2.16.840.1.113762.1.4.1221.41
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2.16.840.1.113762.1.4.1221.46
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2.16.840.1.113762.1.4.1221.49
2.16.840.1.113762.1.4.1221.5
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2.16.840.1.113762.1.4.1221.51
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2.16.840.1.113762.1.4.1221.56
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2.16.840.1.113762.1.4.1221.62
2.16.840.1.113762.1.4.1221.63
2.16.840.1.113762.1.4.1221.64
2.16.840.1.113762.1.4.1221.65
2.16.840.1.113762.1.4.1221.68
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2.16.840.1.113762.1.4.1221.71
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2.16.840.1.113762.1.4.1221.73
2.16.840.1.113762.1.4.1221.75
2.16.840.1.113762.1.4.1221.88
2.16.840.1.113762.1.4.1221.90
2.16.840.1.113762.1.4.1221.99
2.16.840.1.113762.1.4.1222.1
2.16.840.1.113762.1.4.1222.100
2.16.840.1.113762.1.4.1222.101
2.16.840.1.113762.1.4.1222.104
2.16.840.1.113762.1.4.1222.105
2.16.840.1.113762.1.4.1222.106
2.16.840.1.113762.1.4.1222.107
2.16.840.1.113762.1.4.1222.108
2.16.840.1.113762.1.4.1222.11
2.16.840.1.113762.1.4.1222.111
2.16.840.1.113762.1.4.1222.113
2.16.840.1.113762.1.4.1222.114
2.16.840.1.113762.1.4.1222.116
2.16.840.1.113762.1.4.1222.117
2.16.840.1.113762.1.4.1222.118
2.16.840.1.113762.1.4.1222.119
2.16.840.1.113762.1.4.1222.12
2.16.840.1.113762.1.4.1222.120
2.16.840.1.113762.1.4.1222.121
2.16.840.1.113762.1.4.1222.122
2.16.840.1.113762.1.4.1222.123
2.16.840.1.113762.1.4.1222.124
2.16.840.1.113762.1.4.1222.125
2.16.840.1.113762.1.4.1222.126
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2.16.840.1.113762.1.4.1222.129
2.16.840.1.113762.1.4.1222.13
2.16.840.1.113762.1.4.1222.130
2.16.840.1.113762.1.4.1222.131
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2.16.840.1.113762.1.4.1222.2
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2.16.840.1.113762.1.4.1222.31
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2.16.840.1.113762.1.4.1222.34
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2.16.840.1.113762.1.4.1222.39
2.16.840.1.113762.1.4.1222.4
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2.16.840.1.113762.1.4.1222.45
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2.16.840.1.113762.1.4.1222.48
2.16.840.1.113762.1.4.1222.49
2.16.840.1.113762.1.4.1222.5
2.16.840.1.113762.1.4.1222.51
2.16.840.1.113762.1.4.1222.52
2.16.840.1.113762.1.4.1222.58
2.16.840.1.113762.1.4.1222.59
2.16.840.1.113762.1.4.1222.62
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2.16.840.1.113762.1.4.1222.65
2.16.840.1.113762.1.4.1222.68
2.16.840.1.113762.1.4.1222.69
2.16.840.1.113762.1.4.1222.7
2.16.840.1.113762.1.4.1222.71
2.16.840.1.113762.1.4.1222.72
2.16.840.1.113762.1.4.1222.74
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2.16.840.1.113762.1.4.1222.77
2.16.840.1.113762.1.4.1222.78
2.16.840.1.113762.1.4.1222.79
2.16.840.1.113762.1.4.1222.8
2.16.840.1.113762.1.4.1222.80
2.16.840.1.113762.1.4.1222.82
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2.16.840.1.113762.1.4.1222.86
2.16.840.1.113762.1.4.1222.87
2.16.840.1.113762.1.4.1222.88
2.16.840.1.113762.1.4.1222.89
2.16.840.1.113762.1.4.1222.9
2.16.840.1.113762.1.4.1222.91
2.16.840.1.113762.1.4.1222.92
2.16.840.1.113762.1.4.1222.94
2.16.840.1.113762.1.4.1222.95
2.16.840.1.113762.1.4.1222.98
2.16.840.1.113762.1.4.1222.99
2.16.840.1.113883.1.11.10416
2.16.840.1.113883.1.11.12212
2.16.840.1.113883.1.11.14914
2.16.840.1.113883.1.11.20.2.3
2.16.840.1.113883.1.11.20.2.4
2.16.840.1.113883.1.11.20.22
2.16.840.1.113883.1.11.20275
2.16.840.1.113883.10.20.22.5.300
2.16.840.1.113883.11.20.1.1
2.16.840.1.113883.11.20.4.1
2.16.840.1.113883.11.20.6.1
2.16.840.1.113883.11.20.8.1
2.16.840.1.113883.11.20.9.31
2.16.840.1.113883.11.20.9.34
2.16.840.1.113883.11.20.9.46
2.16.840.1.113883.11.20.9.52
2.16.840.1.113883.11.20.9.56
2.16.840.1.113883.11.20.9.87
2.16.840.1.113883.11.20.9.88
2.16.840.1.113883.11.20.9.90
2.16.840.1.113883.11.20.9.91
2.16.840.1.113883.3.1260.1.1978
2.16.840.1.113883.3.3157.1843
2.16.840.1.113883.3.464.1003.113.11.1068
2.16.840.1.113883.3.464.1003.195.11.1011
2.16.840.1.113883.3.464.1003.195.12.1009
2.16.840.1.113883.3.464.1003.196.11.1448
2.16.840.1.113883.3.464.1003.196.11.1502
2.16.840.1.113883.3.464.1003.196.12.1404
2.16.840.1.113883.3.526.2.264
2.16.840.1.113883.3.526.3.367
2.16.840.1.113883.3.666.5.1250
2.16.840.1.113883.3.666.5.1566
2.16.840.1.113883.3.666.5.1679
2.16.840.1.113883.3.666.5.1680
2.16.840.1.113883.3.666.5.1681
2.16.840.1.113883.3.666.5.2316
2.16.840.1.113883.3.88.12.3221.7.4
2.16.840.1.113883.3.88.12.3221.8.9
2.16.840.1.113883.3.88.12.80.16
2.16.840.1.113883.3.88.12.80.17
2.16.840.1.113883.3.88.12.80.18
2.16.840.1.113883.3.88.12.80.28
2.16.840.1.113883.3.88.12.80.32
2.16.840.1.114222.4.11.1066
2.16.840.1.114222.4.11.877

Chris Moesel (Sep 08 2020 at 13:04):

@Grahame Grieve -- sorry for the mixup. You're right -- I forgot that search mechanism only gives you the basic details, but I'm glad it's still useful. As for the the value sets that you can't download, I expect those are all intensional value sets -- which the VSAC FHIR API does not currently support. You can get them via the SVS2 API, but I'm guessing you're not too interested in that.

Grahame Grieve (Sep 08 2020 at 13:35):

It's not really a question of interest - I only have a limited amount of time. I don't mind if someone chooses to extend my framework to get them too - and I suppose eventually it will be necessary

Chris Moesel (Sep 08 2020 at 13:43):

Yeah, that's what I mean by "not too interested" -- poor choice of words, but I really just meant that you likely don't have time for it. NLM wants to support intensional value sets in the FHIR API -- so I guess we'll see if/when that happens.

Robert McClure (Sep 09 2020 at 21:39):

So I've been on the beach and not opening zulip, and am on the plane home so hamstrung. @Grahame Grieve I think we should chat about the vsac pkg so we're on the same page as to what you have included. VSAC has lots of nuances, even beyond the obvious issues with intensionals not supported by the FHIR API. For example, you have to use VSAC expansion profiles to get the expected expansion when a retired code is included in the definition. Does your pkg include expansions at all?

I'm also a bit confused when you say you found "4 downloads" I'm wondering if you mean the four tabs on the download tab
Screen-Shot-2020-09-09-at-5.36.39-PM.png
Because that seems unlikely to get you a majority of available published value sets.

Grahame Grieve (Sep 09 2020 at 22:24):

yes that was, and that was what I originally used, and yes, it wasn't a majority. The distribution now includes 8894 value sets. You can peruse the source at your leisure here: https://github.com/FHIR/packages/tree/master/packages/us.nlm.vsac/package. All criticisms are welcome, but probably most of them I'll just pass back to you ;-)

Last updated: Apr 12 2022 at 19:14 UTC

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