Support of postcoordinated expressions

[sschaat]

Hi,
I am running Snowowl 8.7.1 in docker.

I am interested in the capabilites of classifying postcoordinated expressions (PCEs) with Snowowl. Would it be possible to POST a valueset to get its expansion containing all PCEs that are member of the implicite valueset (e.g. for viral lung infections):

{
  "resourceType": "ValueSet",
  "compose": {
    "include": [{
      "system": "http://snomed.info/sct",
      "concept": [ {"code": [PCE1]}, {"code": [PCE2]} ... ] // for all PCEs
      "valueSet": "http://snomed.info/sct?fhir_vs=ecl/<<128601007:246075003=<<49872002"
    }]
  }
}

However, following the doc (https://github.com/b2ihealthcare/snow-owl/blob/8.x/docs/api/fhir/valuesets.md), in Snowowl it seems that the $expand operation is not implemented with the "valueSet" param (as specified in http://hl7.org/fhir/valueset-operation-expand.html)?

Or is there any other possibility to classify PCEs in Snowowl, e.g. using $validate-code with an implicite valueset, something like:
{{baseUrl}}/ValueSet/$validate-code?system=http://snomed.info/sct&code=128601007:246075003=49872002&url=http://snomed.info/sct?fhir_vs=isa/840539006

Best, Samer

[cmark]

Hi @sschaat,

Postcoordinated expressions in Snow Owl are currently not supported. Intensional/Extensional Value Sets can be created from any supported Code System, but currently, there is no Postcoordination Repository available for Snow Owl, not to mention classification of them.

Do you have an example PCE that would be specified in the code property? We might have an alternative way of handling them depending on the look of those expressions.

Regarding FHIR Value Set and Concept Map support in the OSS version:
FHIR Value Set and Concept Map resources (and their corresponding operations like $expand, $translate, etc.) are available in the paid version of our Snow Owl Terminology Server. See more info here and get in touch here

I hope this helps.

Cheers,
Mark

[sschaat]

Hi Mark,

thanks for the fast reply. The resource is coded with some SNOMED-PCT like 128601007:246075003=84101006

In the end I want to request all conditions with viral lung infections.

Best,
Samer

[cmark]

Could you please check the following JSON response? (It is an implicit Value Set generated via an $expand request)

Request
GET http://localhost:8080/snowowl/fhir/ValueSet/$expand?url=http://snomed.info/sct/900000000000207008?fhir_vs=ecl/<<128601007:246075003=<<49872002&count=50

Response
{
  "resourceType": "ValueSet",
  "id": "1ed09589",
  "url": "http://snomed.info/sct/900000000000207008?fhir_vs=ecl/<<128601007:246075003=<<49872002",
  "name": "SNOMEDCT Concepts matching <<128601007:246075003=<<49872002",
  "status": "active",
  "description": "All SNOMED CT concepts that match the expression constraint <<128601007:246075003=<<49872002",
  "compose": {
    "include": [
      {
        "filter": [
          {
            "property": "constraint",
            "value": "<<128601007:246075003=<<49872002",
            "op": "="
          }
        ]
      }
    ]
  },
  "expansion": {
    "identifier": "1ed09589",
    "timestamp": "2022-12-19T14:20:01.854+00:00",
    "total": 42,
    "contains": [
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "10625271000119109",
        "display": "Bronchopneumonia caused by Human metapneumovirus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "10625551000119103",
        "display": "Bronchopneumonia caused by respiratory syncytial virus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "10625751000119106",
        "display": "Bronchopneumonia due to virus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "10629191000119100",
        "display": "Bronchiolitis caused by influenza virus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "1092361000119109",
        "display": "Rubella pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "1187256004",
        "display": "Viral pneumonia due to infectious mononucleosis caused by human herpesvirus 4 (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "120639003",
        "display": "Hantavirus pulmonary syndrome (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "12571000132104",
        "display": "Pneumonitis due to Herpes zoster (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "13089009",
        "display": "Adenoviral bronchiolitis (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "142931000119100",
        "display": "Pneumonia caused by H1N1 influenza (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "16311000119108",
        "display": "Pneumonia caused by influenza (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "195739001",
        "display": "Acute bronchiolitis caused by respiratory syncytial virus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "195881003",
        "display": "Pneumonia caused by respiratory syncytial virus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "195900001",
        "display": "Pneumonia due to measles (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "195911009",
        "display": "Chickenpox pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "233602006",
        "display": "Acute viral bronchiolitis (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "233603001",
        "display": "Acute bronchiolitis caused by adenovirus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "233624006",
        "display": "Herpes simplex pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "233625007",
        "display": "Giant cell pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "276692000",
        "display": "Congenital viral pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "31920006",
        "display": "Hemorrhagic varicella pneumonitis (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "41207000",
        "display": "Adenoviral pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "41269000",
        "display": "Influenzal bronchopneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "420544002",
        "display": "Bacterial pneumonia with acquired immunodeficiency syndrome (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "420787001",
        "display": "Pneumococcal pneumonia with acquired immunodeficiency syndrome (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "421047005",
        "display": "Candidiasis of lung with acquired immunodeficiency syndrome (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "421508002",
        "display": "Viral pneumonia with acquired immunodeficiency syndrome (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "441590008",
        "display": "Pneumonia caused by Severe acute respiratory syndrome coronavirus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "445096001",
        "display": "Pneumonia caused by Human metapneumovirus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "445102008",
        "display": "Inflammation of bronchiole caused by Human metapneumovirus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "47082005",
        "display": "Congenital rubella pneumonitis (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "57089007",
        "display": "Respiratory syncytial virus bronchiolitis (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "58890000",
        "display": "Adenoviral bronchopneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "64880000",
        "display": "Parainfluenza virus bronchopneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "64917006",
        "display": "Parainfluenza virus pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "713084008",
        "display": "Pneumonia caused by Human coronavirus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "713526000",
        "display": "Recurrent bacterial pneumonia co-occurrent with human immunodeficiency virus infection (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "713544008",
        "display": "Bacterial pneumonia co-occurrent with human immunodeficiency virus infection (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "75570004",
        "display": "Viral pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "7678002",
        "display": "Cytomegaloviral pneumonia (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "772839003",
        "display": "Pneumonia caused by Influenza A virus (disorder)"
      },
      {
        "system": "http://snomed.info/sct/900000000000207008",
        "code": "882784691000119100",
        "display": "Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (disorder)"
      }
    ],
    "after": "AoIyODgyNzg0NjkxMDAwMTE5MTAwMjg4Mjc4NDY5MTAwMDExOTEwMA=="
  }
}

If this looks like a response you'd like to get then this is possible in the paid version of our terminology server. If not, could you please elaborate on your use case a bit more?

Regards,
Mark

[sschaat]

Ehe response returns all precoordinated SNOMED codes.

To elaborate on the use case:

We want to query all viral lung infections of a patient at a resource server (RS)

1. Coded condition resources stored in a RS
2. Some of those are coded using postcoordinated expressions (PCE)
3. At query time we do not know how those resources are coded (and which PCE are used respectively)
4. Hence we need to classify, if a given PCE is a viral lung infection.

[cmark]

Thank you for the use case clarification! It is not scheduled yet, but it is very likely that postcoordination support will come sometime in 2023.

[cmark]

Just in case someone is interested in this, the support of this feature has been pushed to 2024.