FHIR API

Ontoserver supports the algorithmic concept maps listed below. These all extract the display text from a supplied Coding and CodeableConcept items (no code or system required) and attempt to find the best match in the target ValueSet.

Additionally, these strategies understand a special CodeSystem with URI http://ontoserver.csiro.au/fhir/CodeSystem/codesystem-terms which represents the code system of all strings (without leading/trailing whitespace). Hence, simple (cacheable) GET request style invocation is possible. For example, to automap “heart attack” to codes in SNOMED CT:

GET /ConceptMap/$translate
    ?url=http://ontoserver.csiro.au/fhir/ConceptMap/automapstrategy- default
    &system=http://ontoserver.csiro.au/fhir/CodeSystem/codesystem-terms
    &code=heart%20attack
    &target=http://snomed.info/sct?fhir_vs

• http://ontoserver.csiro.au/fhir/ConceptMap/automapstrategy-default Ontoserver’s default automapping strategy. It does not require all words to match, and also attempts simple spelling correction. It is designed for reasonably well-formed textual input, and is not suitable for arbitrary free text.
• http://ontoserver.csiro.au/fhir/ConceptMap/automapstrategy-strict A matching strategy much closer to that used by Ontoserver for the filter parameter to $expand. It is designed for reasonably well-formed textual input, and is not suitable for arbitrary free text.
• http://ontoserver.csiro.au/fhir/ConceptMap/automapstrategy-MML A re-implementation approximation of the MetaMapLite strategy. It is designed for reasonably well-formed textual input, and is somewhat suitable for short spans of arbitrary free text.
• http://ontoserver.csiro.au/fhir/ConceptMap/automapstrategy-seq(;name)+ This is a sequenced-strategy. The semi-colon separated sequence of names may include any of automapstrategy-default, automapstrategy-strict, and automapstrategy-MML. Each strategy will be attempted in turn until a match is found. Once a strategy has syccessfully found a match, the evaluation terminates (i.e., short-circuit evaluation).

   For example, http://ontoserver.csiro.au/fhir/ConceptMap/automapstrategy-seq;automapstrategy-default;automapstrategy-MML

The logs that Ontoserver produces allow an Ontoserver operator to track the searches, lookups, translations, etc, that are conducted. However, it does not allow the operator to track the selection of a code.

To facilitate this, Ontoserver provides an endpoint for the creation of FHIR AuditEvent resources, by posting them as JSON/XML resources to /fhir/AuditEvent. These are not persisted, but are logged in order to allow capture and analysis.

An example of an AuditEvent (in JSON) follows. This event indicates the selection of a code (in this case the SNOMED code for ‘Elbow Region Structure’, following a search (i.e. ValueSet $expand with a filter) of the SNOMED Body Structure implicit ValueSet. More detail about AuditEvent can be found in its definition in the FHIR® Specification

{
  "resourceType": "AuditEvent",
  "type": {
    "system": "http://ontoserver.csiro.au/CodeSystem/ontoserver-reporting",
    "code": "code-selected",
    "display": "Code Selected"
  },
  "action": "E",
  "recorded": "2017-06-02T22:04:27+11:00",
  "outcome": "0",
  "agent": [{
    "requestor": false
  }],
  "source": {
    "site": "IT Department",
    "observer": {
      "display": "John's Laptop"
    }
  },
  "entity": [{
    "what": {
      "identifier": {
        "system": "http://snomed.info/sct",
        "value": "127949000"
      }
    },
    "name": "selected code",
    "detail": [{
      "type": "valueSetExpansionUrl",
      "valueString": "http://snomed.info/sct?fhir_vs=refset/32570061000036105"
    },
    {
      "type": "valueSetExpansionFilter",
      "valueString": "elbow"
    },
    {
      "type": "indexInSearchResult",
      "valueString": "2"
    }]
  }]
}

The Extension URL http://ontoserver.csiro.au/profiles/boost can be added to the ValueSet.compose.include element to adjust the ranking up (value > 1.0) or down (value < 1.0) of codes when performing an $expand with filter.

The following example demonstrates usage:

{
  "resourceType" : "ValueSet",
  "url" : "http://csiro.au/example/ValueSet/boost1",
  "compose" : {
    "include" : [ {
      "system" : "http://snomed.info/sct",
      "filter" : [ {
        "property" : "concept",
        "op" : "is-a",
        "value" : "30560011000036108"
      } ],
      // This extension reduces the significance of codes matching this filter
      "extension" : [ {
        "url" : "http://ontoserver.csiro.au/profiles/boost",
        "valueDecimal" : 0.01
      } ]
    }, {
      "system" : "http://snomed.info/sct",
      "filter" : [ {
        "property" : "concept",
        "op" : "is-a",
        "value" : "30404011000036106"
      } ],
      "extension" : [ {
        // This extension increases the significance of codes matching this filter
        "url" : "http://ontoserver.csiro.au/profiles/boost",
        "valueDecimal" : 10.01
      } ]
    }, {
      "valueSet": [
        "http://snomed.info/sct?fhir_vs=refset/30513011000036104"
      ],
      "extension" : [ {
        // This extension increases the significance of codes in the imported ValueSet
        "url" : "http://ontoserver.csiro.au/profiles/boost",
        "valueDecimal" : 5.0
      } ]
    } ]
  }
}

Once you have chosen or defined the code systems and value sets, you can:

• Determine the binding strength
• Set up the code system and value set maintenance and update processes
  • Concepts can become deprecated over time – you need to watch and plan for this!
  • You may be able to use ConceptMaps to find the concepts that have changed

Once you have chosen or defined the code systems and value sets, you can:

• use $validate-code to check whether the codes are valid in your context, and whether the display text is correct (Clinical systems often allow users to change the display term)
• use $translate to map local or non-standard coded data to the standard code systems/value sets for analysis

• You can use $lookup to retrieve the properties and display them in a table (or other useful format)
• You can navigate the hierarchy between concepts using the ‘child’ and ‘parent’ properties or by $subsumes (or $closure)