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Support for implicit value sets #2092

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JohnTimm opened this issue Mar 15, 2021 · 1 comment
Closed

Support for implicit value sets #2092

JohnTimm opened this issue Mar 15, 2021 · 1 comment
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@JohnTimm
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Add support for implicit value sets per:
https://www.hl7.org/fhir/snomedct.html#implicit

JohnTimm added a commit that referenced this issue Mar 15, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
JohnTimm added a commit that referenced this issue Mar 16, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
JohnTimm added a commit that referenced this issue Mar 16, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
JohnTimm added a commit that referenced this issue Mar 16, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
@JohnTimm JohnTimm self-assigned this Mar 17, 2021
@JohnTimm JohnTimm added this to the Sprint 2021-04 milestone Mar 17, 2021
JohnTimm added a commit that referenced this issue Mar 27, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
JohnTimm added a commit that referenced this issue Mar 27, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
JohnTimm added a commit that referenced this issue Mar 27, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
JohnTimm added a commit that referenced this issue Mar 27, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
JohnTimm added a commit that referenced this issue Mar 29, 2021
Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>
JohnTimm added a commit that referenced this issue Mar 29, 2021
Issue #2092, Issue #1733, Issue #1980 - miscellaneous updates
@lmsurpre
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After loading SnomedCT_USEditionRF2_PRODUCTION_20210301T120000Z to a local berkely db (with lucene index) I was able to expand numerous implicit value sets. For example:
https://localhost:9443/fhir-server/api/v4/ValueSet/$expand?url=http://snomed.info/sct?fhir_vs=isa/73211009

Properly returns:

{
    "resourceType": "ValueSet",
    "text": {
        "status": "generated",
        "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">All SNOMED CT concepts subsumed by 73211009</div>"
    },
    "url": "http://snomed.info/sct?fhir_vs=isa/73211009",
    "name": "SNOMED CT Concept 73211009 and descendants",
    "status": "active",
    "description": "All SNOMED CT concepts for 73211009",
    "copyright": "This value set includes content from SNOMED CT, which is copyright © 2002+ International Health Terminology Standards Development Organisation (SNOMED International), and distributed by agreement between SNOMED International and HL7. Implementer use of SNOMED CT is not covered by this agreement",
    "compose": {
        "include": [
            {
                "system": "http://snomed.info/sct",
                "filter": [
                    {
                        "property": "concept",
                        "op": "is-a",
                        "value": "73211009"
                    }
                ]
            }
        ]
    },
    "expansion": {
        "timestamp": "2021-03-31T12:16:10.542Z",
        "total": 120,
        "contains": [
            {
                "system": "http://snomed.info/sct",
                "code": "73211009",
                "display": "Diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "8801005",
                "display": "Secondary diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "44054006",
                "display": "Type 2 diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "199223000",
                "display": "Diabetes mellitus during pregnancy, childbirth and the puerperium"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609569007",
                "display": "Diabetes mellitus due to genetic defect in insulin action"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609568004",
                "display": "Diabetes mellitus due to genetic defect in beta cell function"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "722206009",
                "display": "Pancreatic hypoplasia, diabetes mellitus, congenital heart disease syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "890171006",
                "display": "Ketosis-prone diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "105401000119101",
                "display": "Diabetes mellitus due to pancreatic injury"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "530558861000132104",
                "display": "Atypical diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "733072002",
                "display": "Stimmler syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "46635009",
                "display": "Type 1 diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "123763000",
                "display": "Houssay's syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "111552007",
                "display": "Diabetes mellitus without complication"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "703136005",
                "display": "Diabetes mellitus in remission"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "716362006",
                "display": "Gingival disease co-occurrent with diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "5368009",
                "display": "Drug-induced diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "5969009",
                "display": "Diabetes mellitus associated with genetic syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "51002006",
                "display": "Diabetes mellitus associated with pancreatic disease"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "75524006",
                "display": "Malnutrition related diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "276560009",
                "display": "Diabetes mellitus in neonate small for gestational age"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "408539000",
                "display": "Insulin autoimmune syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "445260006",
                "display": "Posttransplant diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "737212004",
                "display": "Diabetes mellitus caused by chemical"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "42954008",
                "display": "Diabetes mellitus associated with receptor abnormality"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "59079001",
                "display": "Diabetes mellitus associated with hormonal aetiology"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237601000",
                "display": "Secondary endocrine diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "190389009",
                "display": "Type 2 diabetes mellitus with ulcer"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "81531005",
                "display": "Type 2 diabetes mellitus in obese"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237599002",
                "display": "Insulin treated type 2 diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237627000",
                "display": "Pregnancy and type 2 diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "313436004",
                "display": "Type 2 diabetes mellitus without complication"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "368101000119109",
                "display": "Diabetes mellitus type 2 with periodontal disease"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "199230006",
                "display": "Pre-existing type 2 diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "703138006",
                "display": "Type II diabetes mellitus in remission"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "359642000",
                "display": "Type 2 diabetes mellitus in nonobese"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "11687002",
                "display": "Gestational diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "199225007",
                "display": "Diabetes mellitus during pregnancy - baby delivered"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "199227004",
                "display": "Diabetes mellitus during pregnancy - baby not yet delivered"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "199226008",
                "display": "Diabetes mellitus in the puerperium - baby delivered during current episode of care"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609566000",
                "display": "Pregnancy and type 1 diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609563008",
                "display": "Pre-existing diabetes mellitus in pregnancy"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "76751001",
                "display": "Diabetes mellitus in mother complicating pregnancy, childbirth AND/OR puerperium"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "199228009",
                "display": "Diabetes mellitus in the puerperium - baby delivered during previous episode of care"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "24203005",
                "display": "Extreme insulin resistance with acanthosis nigricans, hirsutism AND abnormal insulin receptors"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "111307005",
                "display": "Leprechaunism syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "127012008",
                "display": "Lipoatrophic diabetes"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237652003",
                "display": "Insulin resistance - type B"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237651005",
                "display": "Insulin resistance - type A"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "33559001",
                "display": "Rabson-Mendenhall syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "49817004",
                "display": "Neonatal diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609561005",
                "display": "Maturity-onset diabetes of the young"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "23045005",
                "display": "Insulin dependent diabetes mellitus type 1A"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "313435000",
                "display": "Type 1 diabetes mellitus without complication"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "190368000",
                "display": "Type 1 diabetes mellitus with ulcer"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "199229001",
                "display": "Pre-existing type 1 diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "703137001",
                "display": "Type I diabetes mellitus in remission"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "368521000119107",
                "display": "Disorder of nerve co-occurrent and due to type 1 diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "722454003",
                "display": "Intellectual disability, craniofacial dysmorphism, hypogonadism, diabetes mellitus syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "28032008",
                "display": "Insulin dependent diabetes mellitus type 1B"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "190372001",
                "display": "Type 1 diabetes mellitus maturity onset"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "426875007",
                "display": "Latent autoimmune diabetes mellitus in adult"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "31321000119102",
                "display": "Diabetes mellitus type 1 without retinopathy"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "709147009",
                "display": "Gingivitis co-occurrent with diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "190447002",
                "display": "Steroid-induced diabetes"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "408540003",
                "display": "Diabetes mellitus induced by non-steroid drugs"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "367391000119102",
                "display": "Diabetes mellitus caused by drug without complication"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "70694009",
                "display": "Diabetes mellitus AND insipidus with optic atrophy AND deafness"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237613005",
                "display": "Hyperproinsulinemia"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237619009",
                "display": "Diabetes-deafness syndrome maternally transmitted"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237612000",
                "display": "Photomyoclonus, diabetes mellitus, deafness, nephropathy and cerebral dysfunction"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "816067005",
                "display": "Woodhouse Sakati syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "427089005",
                "display": "Diabetes mellitus due to cystic fibrosis"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "782755007",
                "display": "Primary microcephaly, mild intellectual disability, young-onset diabetes syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "783722008",
                "display": "Myopathy and diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237617006",
                "display": "Megaloblastic anaemia, thiamine-responsive, with diabetes mellitus and sensorineural deafness"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "734022008",
                "display": "Wolfram-like syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "426705001",
                "display": "Diabetes mellitus associated with cystic fibrosis"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "720519003",
                "display": "Atherosclerosis, deafness, diabetes, epilepsy, nephropathy syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "2751001",
                "display": "Fibrocalculous pancreatic diabetes"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "91352004",
                "display": "Diabetes mellitus due to structurally abnormal insulin"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "190410002",
                "display": "Malnutrition-related diabetes mellitus with peripheral circulatory complications"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "190412005",
                "display": "Malnutrition-related diabetes mellitus without complications"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "190407009",
                "display": "Malnutrition-related diabetes mellitus with renal complications"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "199231005",
                "display": "Pre-existing malnutrition-related diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "57886004",
                "display": "Protein-deficient diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237600004",
                "display": "Malnutrition-related diabetes mellitus - fibrocalculous"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "75682002",
                "display": "Diabetes mellitus due to insulin receptor antibodies"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609567009",
                "display": "Pre-existing type 2 diabetes mellitus in pregnancy"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "1481000119100",
                "display": "Diabetes mellitus type 2 without retinopathy"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "75022004",
                "display": "Gestational diabetes mellitus, class A>1<"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "40801000119106",
                "display": "Gestational diabetes mellitus complicating pregnancy"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "46894009",
                "display": "Gestational diabetes mellitus, class A>2<"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "40791000119105",
                "display": "Postpartum gestational diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "10753491000119101",
                "display": "Gestational diabetes mellitus in childbirth"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609564002",
                "display": "Pre-existing type 1 diabetes mellitus in pregnancy"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "4783006",
                "display": "Maternal diabetes mellitus with hypoglycaemia affecting foetus OR newborn"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "10754881000119104",
                "display": "Diabetes mellitus in mother complicating childbirth"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237603002",
                "display": "Transient neonatal diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609565001",
                "display": "Permanent neonatal diabetes mellitus"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "721088003",
                "display": "DEND syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "237604008",
                "display": "Maturity onset diabetes of the young, type 2"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609572000",
                "display": "Maturity-onset diabetes of the young, type 5"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609570008",
                "display": "Maturity-onset diabetes of the young, type 3"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609576002",
                "display": "Maturity-onset diabetes of the young, type 9"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609577006",
                "display": "Maturity-onset diabetes of the young, type 10"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609575003",
                "display": "Maturity-onset diabetes of the young, type 8"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609562003",
                "display": "Maturity onset diabetes of the young, type 1"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609571007",
                "display": "Maturity-onset diabetes of the young, type 4"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609573005",
                "display": "Maturity-onset diabetes of the young, type 6"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609574004",
                "display": "Maturity-onset diabetes of the young, type 7"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609578001",
                "display": "Maturity-onset diabetes of the young, type 11"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "190416008",
                "display": "Steroid-induced diabetes mellitus without complication"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "413183008",
                "display": "Diabetes mellitus induced by non-steroid drugs without complication"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "106281000119103",
                "display": "Pre-existing diabetes mellitus in mother complicating childbirth"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609580007",
                "display": "Diabetes mellitus, transient neonatal 2"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609579009",
                "display": "Diabetes mellitus, transient neonatal 1"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "609581006",
                "display": "Diabetes mellitus, transient neonatal 3"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "724067006",
                "display": "Permanent neonatal diabetes mellitus with cerebellar agenesis syndrome"
            },
            {
                "system": "http://snomed.info/sct",
                "code": "782825008",
                "display": "Primary microcephaly, epilepsy, permanent neonatal diabetes syndrome"
            }
        ]
    }
}

About 400ms on the first call.
About 100ms on subsequent calls.
Then response times in the 20-40ms range on repeated calls.

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