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We highly recommend going through this page to understand different features available with SNOMED Integration before proceeding for the setup |
This page contains the steps to setup SNOMED enabled integration of Bahmni with SNOMED Terminology Server over FHIR in local machine
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| 1 | ts.fhir.valueset.urltemplate | Valueset URL template for FHIR terminology server | ValueSet/$expand?url={0}&filter={1}&count={2}&displayLanguage={3}&includeDesignations={4} |
| 2 | ts.fhir.diagnosissearch.valueseturl | Valueset URL for Diagnosis Search on terminology server | http://snomed.info/sct?fhir_vs=ecl/<404684003 i.e includes subset of Clinical finding (finding) |
| 3 | ts.fhir.conceptDetailsUrl | URL template pattern for fetching concept details from terminology server | http://snomed.info/sct?fhir_vs=ecl/%7B0%7D{0} |
| 4 | ts.fhir.diagnosiscount.valueseturl | Valueset URL for Diagnosis Count on terminology server | http://snomed.info/sct?fhir_vs=ecl/<< |
| 5 | ts.fhir.diagnosiscount.valueset.urltemplate | Valueset URL template for Diagnosis Count Reports | ValueSet/$expand?url={0}{1}&displayLanguage={2}&count={3,number,#}&offset={4,number,#} |
| 6 | ts.fhir.observation.valueset.urltemplate | Valueset URL template for Observation on terminology server | ValueSet/$expand?url={0}&displayLanguage={1}&_format={2}&filter={3}&count={4} |
| 7 | ts.fhir.procedure.valueset.urltemplate | URL template pattern for fetching valueset for procedure details from terminology server | http://bahmni.org/fhir/ValueSet/ |
| 8 | cdss.fhir.baseurl | Base URL for CDSS service | http://cdss:8080/cds-services |
| 9 | fhir.export.anonymise.config.path | Path of the config file that controls the anonymisation mechanism during bulk-export of patient data | /openmrs/data/fhir-export-anonymise-config.json see this page for more details |
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As an example, the SNOMED CoVID form shipped out-of-the-box in config needs three custom ValueSets to be manually created. http://bahmni.org/fhir/ValueSet/bahmni-valueset-covid,http://bahmni.org/fhir/ValueSet/bahmni-valueset-hospitalisation,http://bahmni.org/fhir/ValueSet/bahmni-valueset-symptoms. A POST request needs to be made to https://<SNOWSTORM_URL>/fhir/ValueSet with the Payload below to create the ValueSets. Also CURL commands are added which can be used to create the ValuseSets by running them directly inside the snowstorm-lite container.
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| title | bahmni-valueset-covid |
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| Code Block |
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| {
"resourceType": "ValueSet",
"url": "http://bahmni.org/fhir/ValueSet/bahmni-valueset-covid",
"version": "0.1",
"name": "bahmni-valueset-covid",
"description": "Bahmni Valueset for CoVID",
"status": "draft",
"experimental": true,
"compose": {
"include": [
{
"system": "http://snomed.info/sct",
"concept": [
{
"code": "1240581000000104"
},
{
"code": "1240591000000102"
}
]
}
]
}
} |
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| title | bahmni-valueset-hospitalisation |
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| Code Block |
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CURL Command that can be executed inside snoswtorm-lite container. Remember to replace password in the --user argument.
| Code Block |
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| curl --location 'http://localhost:8080/fhir/ValueSet' --user admin:Admin123 -X POST --header 'Content-Type: application/json' --data '{
"resourceType": "ValueSet",
"url": "http://bahmni.org/fhir/ValueSet/bahmni-valueset-hospitalisation",
"version": "0.1",
"name": "bahmni-valueset-hospitalisation",
"description": "Bahmni Valueset for Hospitalisation",
"status": "draft",
"experimental": true,
"compose": {-covid",
"version": "0.1",
"name": "bahmni-valueset-covid",
"description": "Bahmni Valueset for CoVID",
"status": "draft",
"experimental": true,
"compose": {
"include": [
{
"system": "http://snomed.info/sct",
"concept": [
{
"code": "1240581000000104"
},
{
"code": "1240591000000102"
}
]
}
]
}
}' |
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| title | bahmni-valueset-hospitalisation |
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|
| Code Block |
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{
"resourceType": "ValueSet",
"url": "http://bahmni.org/fhir/ValueSet/bahmni-valueset-hospitalisation",
"version": "0.1",
"name": "bahmni-valueset-hospitalisation",
"description": "Bahmni Valueset for Hospitalisation",
"status": "draft",
"experimental": true,
"compose": {
"include": [
{
"system": "http://snomed.info/sct",
"concept": [
{
"code": "707852009"
},
{
"code": "707851002"
}
]
}
]
}
} |
CURL Command that can be executed inside snoswtorm-lite container. Remember to replace password in the --user argument. | Code Block |
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| curl --location 'http://localhost:8080/fhir/ValueSet' --user admin:Admin123 -X POST --header 'Content-Type: application/json' --data '{
"resourceType": "ValueSet",
"url": "http://bahmni.org/fhir/ValueSet/bahmni-valueset-hospitalisation",
"version": "0.1",
"name": "bahmni-valueset-hospitalisation",
"description": "Bahmni Valueset for Hospitalisation",
"status": "draft",
"experimental": true,
"compose": {
"include": [
{
"system": "http://snomed.info/sct",
"concept": [
{
"code": "707852009"
},
{
"code": "707851002"
}
]
}
]
}
}' |
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| title | bahmni-valueset-symptoms |
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|
| Code Block |
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| {
"resourceType": "ValueSet",
"url": "http://bahmni.org/fhir/ValueSet/bahmni-valueset-symptoms",
"version": "0.1",
"name": "bahmni-valueset-symptoms",
"description": "Bahmni Valueset for Covid Symptoms",
"status": "draft",
"experimental": true,
"compose": {
"include": [
{
"system": "http://snomed.info/sct",
"concept": [
{
"code": "84387000"
},
{
"code": "82272006"
},
{
"code": "38666106"
},
{
"code": "79890006"
},
{
"code": "44169009"
},
{
"code": "36955009"
},
{
"code": "162397003"
},
{
"code": "29857009"
},
{
"code": "21522001"
},
{
"code": "131148009"
},
"include": [ {
{ "system": code"http://snomed.info/sct",: "49727002"
"concept": [ },
{
"code": "70785200984229001"
},
{
"code": "70785100225064002"
}
]
}
}
]
}
} |
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| title | bahmni-valueset-symptoms |
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|
CURL Command that can be executed inside snoswtorm-lite container. Remember to replace password in the --user argument. | Code Block |
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| curl --location 'http://localhost:8080/fhir/ValueSet' --user admin:Admin123 -X POST --header 'Content-Type: application/json' --data '{
"resourceType": "ValueSet",
"url": "http://bahmni.org/fhir/ValueSet/bahmni-valueset-symptoms",
"version": "0.1",
"name": "bahmni-valueset-symptoms",
"description": "Bahmni Valueset for Covid Symptoms",
"status": "draft",
"experimental": true,
"compose": {
"include": [
{
"system": "http://snomed.info/sct",
"concept": [
{
"code": "84387000"
},
{
"code": "82272006"
},
{
"code": "38666106"
},
{
"code": "79890006"
},
{
"code": "44169009"
},
{
"code": "36955009"
},
{
"code": "162397003"
},
{
"code": "29857009"
},
{
"code": "21522001"
},
{
"code": "131148009"
},
{
"code": "49727002"
},
{
"code": "84229001"
},
{
"code": "25064002"
}
]
}
]
}
}' |
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Known Issues with SNOMED CLINIC CONFIGURATION
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