Improved Ontology Search #11
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|
The first 3-ish ideas for json objects to store in elastic (which would have to be generated by the ontology generator or by another tool in cooperation with the ontology generator for that matter) are as follows. Please consider this as some sort of "mix and match" - I didn't want to include each and every permutation of the options. The "contextualized-termcode-hash" in each of those examples would be removed from the json and used as id in elastic search (or maybe it can also stay in the json, but I don't see any benefit from it) Option 1This is pretty verbose and contains the full information needed to a) display and b) load any relatives. Availability is a numeric value (either absolute or relative?) - not sure if this is a) possible b) allowed c) desired {
"name": "Diabetes Mellitus",
"contextualized-termcode-hash": "203e04cd-4f0a-321b-b1ad-9ec6d211e0a8",
"availability": "96",
"domain": "Diagnosis",
"terminology": "icd-10",
"termcode": "E10-E14",
"kds-module": "Condition",
"translations" : [
{
"lang": "de",
"value": "Diabetes Mellitus"
},
{
"lang": "en-UK",
"value": "Diabetes Mellitus"
}
],
"parents" : [
{
"name": "Endokrine, Ernährungs- und Stoffwechselerkrankungen",
"contextualized-termcode-hash": "c55d0d62-6c47-30b0-94b2-afa383ce35f7"
}
],
"children": [
{
"name": "Diabetes Mellitus, Typ 1",
"contextualized-termcode-hash": "b303cc1c-0776-3d78-9f18-98847173a73d"
},
{
"name": "Diabetes Mellitus, Typ 2",
"contextualized-termcode-hash": "29451c0c-e26d-3d43-9b74-6e43230ac9f5"
}
]
}Option 2This limits the information about the relatives to their ids. It also groups the terminology parts to an object (good ideas for a name are welcome). The translations part is also a bit condensed, but contain the information about which of those are verified. Availability is restricted to a boolean {
"name": "Diabetes Mellitus",
"contextualized-termcode-hash": "203e04cd-4f0a-321b-b1ad-9ec6d211e0a8",
"availability": true,
"to-be-named": {
"domain": "Diagnosis",
"terminology": "icd-10",
"termcode": "E10-E14",
"kds-module": "Condition"
},
"translations" : [
{
"de": "Diabetes Mellitus",
"verified": false
},
{
"en-UK": "Diabetes Mellitus",
"verified": true
}
],
"parents" : [
"c55d0d62-6c47-30b0-94b2-afa383ce35f7"
],
"children": [
"b303cc1c-0776-3d78-9f18-98847173a73d",
"29451c0c-e26d-3d43-9b74-6e43230ac9f5"
]
}
Option 3This removes all information about relatives. This information would have to be gathered from the backend and injected before sending back to the gui (or who/whatever uses the rest api). The language contains information about a preferred translation (not really sure if this should be in elastic search). The "name" part is lacking, because it can be retrieved from the translations array and it would be up to the gui which one to display (based on browser language or user setting?) {
"contextualized-termcode-hash": "203e04cd-4f0a-321b-b1ad-9ec6d211e0a8",
"availability": true,
"to-be-named": {
"domain": "Diagnosis",
"terminology": "icd-10",
"termcode": "E10-E14",
"kds-module": "Condition"
},
"translations" : [
{
"lang": "de",
"value": "Diabetes Mellitus",
"verified": true,
"preferred": true
},
{
"lang": "en-UK",
"value": "Diabetes Mellitus",
"verified": false
}
]
}
|
|
As a proposal for the API, ideally just paste the following to https://editor-next.swagger.io . This also is one example, which would be mutable, depending on what we choose to store in elastic. There is once more a placeholder for parameters we might want to add, like limiting to a certain amount of results, or giving an offset to enable pagination, or maybe a minimum required score for a result to be included. It would also be an option to use a json request body for the query instead of query parameters. Click to expand OpenAPI codeopenapi: 3.0.3
info:
title: MII Feasibility Backend REST API - Terminology Search Draft
description: todo
contact:
email: noreply@todo.de
license:
name: Apache 2.0
url: http://www.apache.org/licenses/LICENSE-2.0.html
version: 0.0.1
externalDocs:
description: Check out the github repository
url: https://github.com/medizininformatik-initiative/feasibility-backend
servers:
- url: https://to.be.defined
variables:
basePath:
default: /
tags:
- name: terminology
description: operations on the terminology
paths:
/terminology/search:
get:
tags:
- terminology
summary: "Parametrized search in the configured elastic search service."
operationId: "search"
parameters:
- name: query
in: query
description: The term to search for
schema:
type: "string"
example: Diabetes Mellitus
- name: placeholder
in: query
description: Maybe include limit/offset/min-score?
schema:
type: "string"
example: example
- name: domain
in: query
description: Limit the search to a given domain (or domains?)
schema:
type: "string"
example: Diagnosis
- name: terminology
in: query
description: Limit the search to a given terminology (or terminologies?)
schema:
type: "string"
example: ICD10
- name: kds
in: query
description: Limit the search to a given KDS module (or modules?)
schema:
type: "string"
example: Condition
- name: availability
in: query
description: Limit the search to available items? (Maybe better invert this one to make this the default?)
schema:
type: boolean
example: true
responses:
200:
description: Ok, return the list of results (maybe limited/offset - to be decided) for the search
content:
application/json:
schema:
type: "array"
items:
$ref: "#/components/schemas/ElasticSearchResult"
components:
schemas:
ElasticSearchResult:
type: object
properties:
totalHits:
type: integer
example: 42
results:
type: array
items:
$ref: "#/components/schemas/ElasticSearchResultEntry"
ElasticSearchResultEntry:
type: object
properties:
name:
type: string
example: Diabetes Mellitus
contextualizedTermcodeHash:
type: string
format: uuid
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
availability:
description: Not sure if we want this as numeric value, percentage or just boolean?
type: integer
minimum: 0
maximum: 100
example: 94
domain:
type: string
example: Diagnosis
terminology:
type: string
example: icd-10
termcode:
type: string
example: E10-E14
kdsModule:
type: string
example: Condition
translations:
type: array
items:
$ref: "#/components/schemas/ElasticSearchTranslationEntry"
parents:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
children:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
ElasticSearchTranslationEntry:
type: object
properties:
lang:
type: string
example: en
value:
type: string
example: Diabetes Mellitus
ElasticSearchRelationEntry:
type: object
properties:
name:
type: string
example: Endokrine, Ernährungs- und Stoffwechselerkrankungen
contextualizedTermcodeHash:
type: string
example: c55d0d62-6c47-30b0-94b2-afa383ce35f7 |
|
Following a discussion between @juliangruendner @Shayan1375 @thkoehler11 and myself from today (2024-05-15), the following has been decided: ElasticsearchData StoragePlease note that the object below is NOT necessarily what will be returned to the frontend. For that part, look below in the OpenAPI code. Objects will be stored in elastic search as suggested in option 1 above, with the minor change that domain will be renamed to context, resulting in: Click to expand JSON{
"name": "Diabetes Mellitus",
"contextualized-termcode-hash": "203e04cd-4f0a-321b-b1ad-9ec6d211e0a8",
"availability": "96",
"context": "Diagnosis",
"terminology": "icd-10",
"termcode": "E10-E14",
"kds-module": "Condition",
"translations" : [
{
"lang": "de",
"value": "Diabetes Mellitus"
},
{
"lang": "en-UK",
"value": "Diabetes Mellitus"
}
],
"parents" : [
{
"name": "Endokrine, Ernährungs- und Stoffwechselerkrankungen",
"contextualized-termcode-hash": "c55d0d62-6c47-30b0-94b2-afa383ce35f7"
}
],
"children": [
{
"name": "Diabetes Mellitus, Typ 1",
"contextualized-termcode-hash": "b303cc1c-0776-3d78-9f18-98847173a73d"
},
{
"name": "Diabetes Mellitus, Typ 2",
"contextualized-termcode-hash": "29451c0c-e26d-3d43-9b74-6e43230ac9f5"
}
],
"relatedTerms": [
{
"name": "foo",
"contextualized-termcode-hash": "81e98694-bb61-4e1f-844e-399806b67b08"
},
{
"name": "bar",
"contextualized-termcode-hash": "644de523-636a-4afe-9ade-997db8487f81"
}
]
}For now, availability will be stored as an absolute numeric value. There is some optimism that this will be allowed to display, since it will have no site-correlation as it is only an aggregated number over all sites (however, there is always a chance that it will have to be removed later) Search behaviourFor now, a search query will only check the fields termcode and name. In further iterations, the translations might be included (maybe prioritized by accept-language priority?) API frontend <-> backendThe API will be modified from the former suggestion, following a refined proposal for the frontend. TL;DR:
Possible additions to do later:
OpenAPI With the aforementioned changes...just copy the following to https://editor-next.swagger.io/ Click to expand OpenAPI codeopenapi: 3.0.3
info:
title: MII Feasibility Backend REST API - Terminology Search Draft
description: todo
contact:
email: noreply@todo.de
license:
name: Apache 2.0
url: http://www.apache.org/licenses/LICENSE-2.0.html
version: 0.0.1
externalDocs:
description: Check out the github repository
url: https://github.com/medizininformatik-initiative/feasibility-backend
servers:
- url: https://to.be.defined
variables:
basePath:
default: /
tags:
- name: terminology
description: operations on the terminology
paths:
/terminology/search/filter:
get:
tags:
- terminology
summary: "Get the list of available filters"
operationId: "getFilters"
responses:
200:
description: Ok, return the list of available filters
content:
application/json:
schema:
type: "array"
items:
$ref: "#/components/schemas/Filter"
/terminology/search:
get:
tags:
- terminology
summary: "Parametrized search in the configured elastic search service."
operationId: "search"
parameters:
- name: searchterm
in: query
description: The term to search for
schema:
type: "string"
example: Diabetes Mellitus
- name: context
in: query
description: Limit the search to a given context (or contexts?)
schema:
type: "string"
example: Diagnosis
- name: terminology
in: query
description: Limit the search to a given terminology (or terminologies?)
schema:
type: "string"
example: ICD10
- name: kds
in: query
description: Limit the search to a given KDS module (or modules?)
schema:
type: "string"
example: Condition
- name: availability
in: query
description: Limit the search to available items? (Maybe better invert this one to make this the default?)
schema:
type: boolean
example: true
- name: limit
in: query
description: How many results shall be returned
schema:
type: integer
example: 10
- name: offset
in: query
description: What should be the index of the first item to be displayed
schema:
type: integer
example: 100
responses:
200:
description: Ok, return the list of results (maybe limited/offset - to be decided) for the search
content:
application/json:
schema:
$ref: "#/components/schemas/ElasticSearchResult"
/terminology/search/{id}:
get:
tags:
- terminology
summary: "Get the detailed entry for a criterion, containing children and translations"
operationId: "getEntryById"
parameters:
- name: id
in: path
description: The id (contextualized termcode hash) of the entry that shall be retrieved
required: true
schema:
type: string
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
responses:
200:
description: Entry found
content:
application/json:
schema:
$ref: '#/components/schemas/ElasticSearchResultEntryWithRelations'
401:
description: Unauthorized - please login first
403:
description: Forbidden - insufficient access rights
404:
description: Entry not found
components:
schemas:
ElasticSearchResult:
type: object
properties:
totalHits:
type: integer
example: 42
results:
type: array
items:
$ref: "#/components/schemas/ElasticSearchResultEntry"
ElasticSearchResultEntryWithRelations:
type: object
properties:
name:
type: string
example: Diabetes Mellitus
contextualizedTermcodeHash:
type: string
format: uuid
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
availability:
description: Not sure if we want this as numeric value, percentage or just boolean?
type: integer
minimum: 0
maximum: 100
example: 94
context:
type: string
example: Diagnosis
terminology:
type: string
example: icd-10
termcode:
type: string
example: E10-E14
kdsModule:
type: string
example: Condition
translations:
type: array
items:
$ref: "#/components/schemas/ElasticSearchTranslationEntry"
parents:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
children:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
relatedTerms:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
ElasticSearchResultEntry:
type: object
properties:
name:
type: string
example: Diabetes Mellitus
contextualizedTermcodeHash:
type: string
format: uuid
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
availability:
description: Not sure if we want this as numeric value, percentage or just boolean?
type: integer
minimum: 0
example: 119578
context:
type: string
example: Diagnosis
terminology:
type: string
example: icd-10
termcode:
type: string
example: E10-E14
kdsModule:
type: string
example: Condition
ElasticSearchTranslationEntry:
type: object
properties:
lang:
type: string
example: en
value:
type: string
example: Diabetes Mellitus
ElasticSearchRelationEntry:
type: object
properties:
name:
type: string
example: Endokrine, Ernährungs- und Stoffwechselerkrankungen
contextualizedTermcodeHash:
type: string
example: c55d0d62-6c47-30b0-94b2-afa383ce35f7
Filter:
type: object
properties:
name:
type: string
example: Terminology
values:
type: array
items:
$ref: "#/components/schemas/FilterValue"
example:
- ICD10
- SNOMED
- LOINC
FilterValue:
type: string
example: "icd10" |
|
Following another discussion on 2024-05-29, we decided to combine some of the former endpoints in order to reduce the amount of calls. The legacy calls to the backend to get entries from the ui tree files will be removed. The ui profiles will be included in the regular call to retrieve an entry. This means an additional call to the database when retrieving an entry, but is more efficient than having two seperate rest calls for that. Click to expand JSON{
"name": "Diabetes Mellitus",
"contextualized-termcode-hash": "203e04cd-4f0a-321b-b1ad-9ec6d211e0a8",
"availability": 96,
"terminology": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"termCode": "E10-E14",
"kds-module": "Condition",
"selectable": true,
"context": {
"code": "Diagnose",
"display": "Diagnose",
"system": "fdpg.mii.cds",
"version": "1.0.0"
},
"termCodes": [
{
"code": "E10-E14",
"display": "Diabetes mellitus",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023"
}
],
"translations" : [
{
"lang": "de",
"value": "Diabetes Mellitus"
},
{
"lang": "en-UK",
"value": "Diabetes Mellitus"
}
],
"parents" : [
{
"name": "Endokrine, Ernährungs- und Stoffwechselerkrankungen",
"contextualized-termcode-hash": "c55d0d62-6c47-30b0-94b2-afa383ce35f7"
}
],
"children": [
{
"name": "Diabetes Mellitus, Typ 1",
"contextualized-termcode-hash": "b303cc1c-0776-3d78-9f18-98847173a73d"
},
{
"name": "Diabetes Mellitus, Typ 2",
"contextualized-termcode-hash": "29451c0c-e26d-3d43-9b74-6e43230ac9f5"
}
],
"relatedTerms": [
{
"name": "foo",
"contextualized-termcode-hash": "81e98694-bb61-4e1f-844e-399806b67b08"
},
{
"name": "bar",
"contextualized-termcode-hash": "644de523-636a-4afe-9ade-997db8487f81"
}
]
}Click to expand OpenAPIopenapi: 3.0.3
info:
title: MII Feasibility Backend REST API - Terminology Search Draft
description: todo
contact:
email: noreply@todo.de
license:
name: Apache 2.0
url: http://www.apache.org/licenses/LICENSE-2.0.html
version: 0.0.1
externalDocs:
description: Check out the github repository
url: https://github.com/medizininformatik-initiative/feasibility-backend
servers:
- url: https://to.be.defined
variables:
basePath:
default: /
tags:
- name: terminology
description: operations on the terminology
paths:
/terminology/search/filter:
get:
tags:
- terminology
summary: "Get the list of available filters"
operationId: "getFilters"
responses:
200:
description: Ok, return the list of available filters
content:
application/json:
schema:
type: "array"
items:
$ref: "#/components/schemas/Filter"
/terminology/search:
get:
tags:
- terminology
summary: "Parametrized search in the configured elastic search service."
operationId: "search"
parameters:
- name: searchterm
in: query
description: The term to search for
schema:
type: "string"
example: Diabetes Mellitus
- name: context
in: query
description: Limit the search to a given context (or contexts?)
schema:
type: "string"
example: Diagnosis
- name: terminology
in: query
description: Limit the search to a given terminology (or terminologies?)
schema:
type: "string"
example: ICD10
- name: kds
in: query
description: Limit the search to a given KDS module (or modules?)
schema:
type: "string"
example: Condition
- name: availability
in: query
description: Limit the search to available items? (Maybe better invert this one to make this the default?)
schema:
type: boolean
example: true
- name: pageSize
in: query
description: How many results shall be returned per page
schema:
type: integer
example: 10
- name: page
in: query
description: Which page shall be returned
schema:
type: integer
example: 42
responses:
200:
description: Ok, return the list of results (maybe limited/offset - to be decided) for the search
content:
application/json:
schema:
type: "array"
items:
$ref: "#/components/schemas/ElasticSearchResult"
/terminology/entry/{id}:
get:
tags:
- terminology
summary: "Get the detailed entry for a criterion, containing children and translations"
operationId: "getEntryById"
parameters:
- name: id
in: path
description: The id (contextualized termcode hash) of the entry that shall be retrieved
required: true
schema:
type: string
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
responses:
200:
description: Entry found
content:
application/json:
schema:
$ref: '#/components/schemas/ElasticSearchResultEntry'
401:
description: Unauthorized - please login first
403:
description: Forbidden - insufficient access rights
404:
description: Entry not found
/terminology/entry/{id}?detail=true:
get:
tags:
- terminology
summary: "Get the detailed entry for a criterion, containing children and translations"
description: "This should be in the getEntryById call, but for better distinction between the return values it is listed seperately here"
operationId: "getEntryByIdWithDetail"
parameters:
- name: id
in: path
description: The id (contextualized termcode hash) of the entry that shall be retrieved
required: true
schema:
type: string
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
responses:
200:
description: Entry found
content:
application/json:
schema:
$ref: '#/components/schemas/ElasticSearchResultEntryWithRelations'
401:
description: Unauthorized - please login first
403:
description: Forbidden - insufficient access rights
404:
description: Entry not found
components:
schemas:
ElasticSearchResult:
type: object
properties:
totalHits:
type: integer
example: 42
results:
type: array
items:
$ref: "#/components/schemas/ElasticSearchResultEntry"
ElasticSearchResultEntryWithRelations:
type: object
properties:
name:
type: string
example: Diabetes Mellitus
id:
type: string
format: uuid
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
availability:
description: Not sure if we want this as numeric value, percentage or just boolean?
type: integer
minimum: 0
maximum: 100
example: 94
terminology:
type: string
example: icd-10
termcode:
type: string
example: E10-E14
kdsModule:
type: string
example: Condition
selectable:
type: boolean
example: false
context:
$ref: "#/components/schemas/TermCode"
termCodes:
type: array
items:
$ref: "#components/schemas/TermCode"
translations:
type: array
items:
$ref: "#/components/schemas/ElasticSearchTranslationEntry"
parents:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
children:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
relatedTerms:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
uiprofile:
$ref: "#/components/schemas/UiProfileEntry"
ElasticSearchResultEntry:
type: object
properties:
name:
type: string
example: Diabetes Mellitus
id:
type: string
format: uuid
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
availability:
description: Not sure if we want this as numeric value, percentage or just boolean?
type: integer
minimum: 0
example: 119578
context:
type: string
example: Diagnosis
terminology:
type: string
example: icd-10
termcode:
type: string
example: E10-E14
kdsModule:
type: string
example: Condition
selectable:
type: boolean
example: true
ElasticSearchTranslationEntry:
type: object
properties:
lang:
type: string
example: en
value:
type: string
example: Diabetes Mellitus
ElasticSearchRelationEntry:
type: object
properties:
name:
type: string
example: Endokrine, Ernährungs- und Stoffwechselerkrankungen
contextualizedTermcodeHash:
type: string
example: c55d0d62-6c47-30b0-94b2-afa383ce35f7
Filter:
type: object
properties:
name:
type: string
example: Terminology
values:
type: array
items:
$ref: "#/components/schemas/FilterValue"
example:
- ICD10
- SNOMED
- LOINC
FilterValue:
type: string
example: "icd10"
TermCode:
type: object
properties:
code:
type: string
example: "E14.0"
system:
type: string
example: "http://fhir.de/CodeSystem/bfarm/icd-10-gm"
version:
type: string
example: "2023"
display:
type: string
example: "Diabetes mellitus"
UiProfileEntry:
type: object
properties:
attributeDefinitions:
type: array
items:
$ref: "#/components/schemas/AttributeDefinition"
name:
type: string
example: "Diagnose"
timeRestrictionAllowed:
type: boolean
example: false
valueDefinition:
type: string
Unit:
type: object
properties:
code:
type: string
display:
type: string
AttributeDefinition:
type: object
properties:
allowedUnits:
type: array
items:
$ref: "#/components/schemas/Unit"
attributeCode:
$ref: "#/components/schemas/TermCode"
max:
type: number
example: null
min:
type: number
example: null
optional:
type: boolean
example: true
precision:
type: number
example: 1
referenceCriteriaSet:
type: string
example: "http://fdpg.mii.cds/CriteriaSet/Diagnose/icd-10-gm"
selectableConcepts:
type: array
items:
$ref: "#/components/schemas/TermCode"
type:
type: string
example: "reference" |
Additional Changes: New GET Endpoint for UI ProfilesAfter further discussion, we have decided to make additional changes. We will introduce a new GET endpoint: Details:
Example Response: Click to expand JSON{
[
{
"id": "afd0b036-625a-3aa8-b639-9dc8c8fff0ff",
"uiProfile": {
"attributeDefinitions": [
{
"allowedUnits": [
{
"code": "string",
"display": "string"
}
],
"attributeCode": {
"code": "E14.0",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Diabetes mellitus"
},
"max": null,
"min": null,
"optional": true,
"precision": 1,
"referenceCriteriaSet": "http://fdpg.mii.cds/CriteriaSet/Diagnose/icd-10-gm",
"selectableConcepts": [
{
"code": "E14.0",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Diabetes mellitus"
}
],
"type": "reference"
}
],
"name": "Diagnose",
"timeRestrictionAllowed": false,
"valueDefinition": "string"
}
},
{
"id": "9c45c2f1-1761-3daa-ad31-1ff8703ae846",
"uiProfile": {
"attributeDefinitions": [
{
"allowedUnits": [
{
"code": "string",
"display": "string"
}
],
"attributeCode": {
"code": "E14.0",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Diabetes mellitus"
},
"max": null,
"min": null,
"optional": true,
"precision": 1,
"referenceCriteriaSet": "http://fdpg.mii.cds/CriteriaSet/Diagnose/icd-10-gm",
"selectableConcepts": [
{
"code": "E14.0",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Diabetes mellitus"
}
],
"type": "reference"
}
],
"name": "Diagnose",
"timeRestrictionAllowed": false,
"valueDefinition": "string"
}
}
]
}This change means that when retrieving data from Click to expand JSON{
"id": "5dfe270a-d520-1de8-24eb-19452f270561",
"name": "Angeborene Torsion des Ovars",
"availability": 2915,
"terminology": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"termCode": "Q50.2",
"kdsModule": null,
"translations": [],
"parents": [
{
"name": "Angeborene Fehlbildungen der Ovarien, der Tubae uterinae und der Ligg. lata uteri",
"id": "8b4035b0-a6d1-dadf-a423-d4af8383ae0b"
}
],
"children": [],
"relatedTerms": [],
} |
|
The response containing the list of ui profiles will be the array itself, not a json object containing the array as in the JSON posted above. Click to expand JSON[
{
"id": "afd0b036-625a-3aa8-b639-9dc8c8fff0ff",
"uiProfile": {
"attributeDefinitions": [
{
"allowedUnits": [
{
"code": "string",
"display": "string"
}
],
"attributeCode": {
"code": "E14.0",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Diabetes mellitus"
},
"max": null,
"min": null,
"optional": true,
"precision": 1,
"referenceCriteriaSet": "http://fdpg.mii.cds/CriteriaSet/Diagnose/icd-10-gm",
"selectableConcepts": [
{
"code": "E14.0",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Diabetes mellitus"
}
],
"type": "reference"
}
],
"name": "Diagnose",
"timeRestrictionAllowed": false,
"valueDefinition": "string"
}
},
{
"id": "9c45c2f1-1761-3daa-ad31-1ff8703ae846",
"uiProfile": {
"attributeDefinitions": [
{
"allowedUnits": [
{
"code": "string",
"display": "string"
}
],
"attributeCode": {
"code": "E14.0",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Diabetes mellitus"
},
"max": null,
"min": null,
"optional": true,
"precision": 1,
"referenceCriteriaSet": "http://fdpg.mii.cds/CriteriaSet/Diagnose/icd-10-gm",
"selectableConcepts": [
{
"code": "E14.0",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Diabetes mellitus"
}
],
"type": "reference"
}
],
"name": "Diagnose",
"timeRestrictionAllowed": false,
"valueDefinition": "string"
}
}
]Also, the response to the entry with details will still contain the context and termcodes as objects like decided earlier. Only the uiprofile will be removed, resulting in the following: Click to expand JSON{
"id": "5dfe270a-d520-1de8-24eb-19452f270561",
"name": "Angeborene Torsion des Ovars",
"availability": 2915,
"terminology": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"termCode": "Q50.2",
"kdsModule": null,
"translations": [],
"parents": [
{
"name": "Angeborene Fehlbildungen der Ovarien, der Tubae uterinae und der Ligg. lata uteri",
"id": "8b4035b0-a6d1-dadf-a423-d4af8383ae0b"
}
],
"children": [],
"relatedTerms": [],
"context": {
"code": "Diagnose",
"system": "fdpg.mii.cds",
"version": "1.0.0",
"display": "Diagnose"
},
"termCodes": [
{
"code": "Q50.2",
"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
"version": "2023",
"display": "Angeborene Torsion des Ovars"
}
]
}(Also, terminology will no longer be a URL in the future, but this is not relevant for this discussion.) |
|
We've made updates to the endpoints and responses in the Swagger documentation to better align them with their names and expected responses. We have introduced a new GET endpoint Additionally, we have established the endpoint The endpoint Click to expand OpenAPIopenapi: 3.0.3
info:
title: MII Feasibility Backend REST API - Terminology Search Draft
description: todo
contact:
email: noreply@todo.de
license:
name: Apache 2.0
url: http://www.apache.org/licenses/LICENSE-2.0.html
version: 0.0.1
externalDocs:
description: Check out the github repository
url: https://github.com/medizininformatik-initiative/feasibility-backend
servers:
- url: https://to.be.defined
variables:
basePath:
default: /
tags:
- name: terminology
description: operations on the terminology
paths:
/terminology/search/filter:
get:
tags:
- terminology
summary: "Get the list of available filters"
operationId: "getFilters"
responses:
200:
description: Ok, return the list of available filters
content:
application/json:
schema:
type: "array"
items:
$ref: "#/components/schemas/Filter"
/terminology/entry/search:
get:
tags:
- terminology
summary: "Parametrized search in the configured elastic search service."
operationId: "search"
parameters:
- name: searchterm
in: query
description: The term to search for
schema:
type: "string"
example: Diabetes Mellitus
- name: context
in: query
description: Limit the search to a given context (or contexts?)
schema:
type: "string"
example: Diagnosis
- name: terminology
in: query
description: Limit the search to a given terminology (or terminologies?)
schema:
type: "string"
example: ICD10
- name: kds
in: query
description: Limit the search to a given KDS module (or modules?)
schema:
type: "string"
example: Condition
- name: availability
in: query
description: Limit the search to available items? (Maybe better invert this one to make this the default?)
schema:
type: boolean
example: true
- name: pageSize
in: query
description: How many results shall be returned per page
schema:
type: integer
example: 10
- name: page
in: query
description: Which page shall be returned
schema:
type: integer
example: 42
responses:
200:
description: Ok, return the list of results (maybe limited/offset - to be decided) for the search
content:
application/json:
schema:
$ref: "#/components/schemas/ElasticSearchResult"
/terminology/entry/{id}/relations:
get:
tags:
- terminology
summary: "Get the detailed entry for a criterion, containing children and translations"
operationId: "getEntryById"
parameters:
- name: id
in: path
description: The id (contextualized termcode hash) of the entry that shall be retrieved
required: true
schema:
type: string
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
responses:
200:
description: Entry found
content:
application/json:
schema:
$ref: '#/components/schemas/ElasticSearchResultEntryWithRelations'
401:
description: Unauthorized - please login first
403:
description: Forbidden - insufficient access rights
404:
description: Entry not found
/terminology/entry/{id}:
get:
tags:
- terminology
summary: "Get the detailed entry for a criterion, containing children and translations"
description: "This should be in the getEntryById call, but for better distinction between the return values it is listed seperately here"
operationId: "getEntriesById"
parameters:
- name: id
in: path
description: The ids (contextualized termcode hash) of the entries that shall be retrieved
required: true
schema:
type: string
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
responses:
200:
description: Entry found
content:
application/json:
schema:
$ref: '#/components/schemas/ElasticSearchResultEntry'
401:
description: Unauthorized - please login first
403:
description: Forbidden - insufficient access rights
404:
description: Entry not found
/terminology/criteria-profile-data:
get:
tags:
- terminology
summary: "Get the profile data for criteria, containing uiProfile context and termCodes"
description: "This should return all the information needed to build criteria in the frontend."
operationId: "getEntriesByIdsWithDetail"
parameters:
- name: ids
in: query
style: form
explode: false
description: "A comma-separated list of IDs (contextualized termcode hashes) of the entries that shall be retrieved."
required: true
schema:
type: string
example: "203e04cd-4f0a-321b-b1ad-9ec6d211e0a8,203e04cd-4f0a-321b-b1ad-9ec6d211e0a9"
responses:
200:
description: "Entries found. May contain empty entries if some were not found."
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/CriteriaProfileData'
401:
description: "Unauthorized - please login first."
403:
description: "Forbidden - insufficient access rights."
components:
schemas:
ElasticSearchResult:
type: object
properties:
totalHits:
type: integer
example: 42
results:
type: array
items:
$ref: "#/components/schemas/ElasticSearchResultEntry"
ElasticSearchResultEntryWithRelations:
type: object
properties:
translations:
type: array
items:
$ref: "#/components/schemas/ElasticSearchTranslationEntry"
parents:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
children:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
relatedTerms:
type: array
items:
$ref: "#/components/schemas/ElasticSearchRelationEntry"
ElasticSearchResultEntry:
type: object
properties:
name:
type: string
example: Diabetes Mellitus
id:
type: string
format: uuid
example: 203e04cd-4f0a-321b-b1ad-9ec6d211e0a8
availability:
description: Not sure if we want this as numeric value, percentage or just boolean?
type: integer
minimum: 0
example: 119578
context:
type: string
example: Diagnosis
terminology:
type: string
example: icd-10
termcode:
type: string
example: E10-E14
kdsModule:
type: string
example: Condition
selectable:
type: boolean
example: true
ElasticSearchTranslationEntry:
type: object
properties:
lang:
type: string
example: en
value:
type: string
example: Diabetes Mellitus
ElasticSearchRelationEntry:
type: object
properties:
name:
type: string
example: Endokrine, Ernährungs- und Stoffwechselerkrankungen
contextualizedTermcodeHash:
type: string
example: c55d0d62-6c47-30b0-94b2-afa383ce35f7
CriteriaProfileData:
type: object
properties:
id:
type: string
format: uuid
uiprofile:
type: array
items:
$ref: "#/components/schemas/UiProfileEntry"
termCodes:
type: array
items:
$ref: "#/components/schemas/TermCode"
context:
$ref: "#/components/schemas/TermCode"
Filter:
type: object
properties:
name:
type: string
example: Terminology
values:
type: array
items:
$ref: "#/components/schemas/FilterValue"
example:
- ICD10
- SNOMED
- LOINC
FilterValue:
type: string
example: "icd10"
TermCode:
type: object
properties:
code:
type: string
example: "E14.0"
system:
type: string
example: "http://fhir.de/CodeSystem/bfarm/icd-10-gm"
version:
type: string
example: "2023"
display:
type: string
example: "Diabetes mellitus"
UiProfileEntry:
type: object
properties:
attributeDefinitions:
type: array
items:
$ref: "#/components/schemas/AttributeDefinition"
name:
type: string
example: "Diagnose"
timeRestrictionAllowed:
type: boolean
example: false
valueDefinition:
type: string
Unit:
type: object
properties:
code:
type: string
display:
type: string
AttributeDefinition:
type: object
properties:
allowedUnits:
type: array
items:
$ref: "#/components/schemas/Unit"
attributeCode:
$ref: "#/components/schemas/TermCode"
max:
type: number
example: null
min:
type: number
example: null
optional:
type: boolean
example: true
precision:
type: number
example: 1
referenceCriteriaSet:
type: string
example: "http://fdpg.mii.cds/CriteriaSet/Diagnose/icd-10-gm"
selectableConcepts:
type: array
items:
$ref: "#/components/schemas/TermCode"
type:
type: string
example: "reference" |
|
We discussed the new endpoints for searching in profiles. The first draft is below. Please comment @juliangruendner @Shayan1375 @thkoehler11 Click to expand OpenAPI fragmentopenapi: 3.0.3
info:
title: MII Feasibility Backend REST API - Terminology Search Draft
description: todo
contact:
email: noreply@todo.de
license:
name: Apache 2.0
url: http://www.apache.org/licenses/LICENSE-2.0.html
version: 0.0.1
externalDocs:
description: Check out the github repository
url: https://github.com/medizininformatik-initiative/feasibility-backend
servers:
- url: https://to.be.defined
variables:
basePath:
default: /
tags:
- name: tdb
description: to be decided
paths:
/terminology/healthrecord/tree:
get:
tags:
- tbd
responses:
200:
description: "Tree found and loaded. Will be delivered."
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/HealthRecordTree'
401:
description: "Unauthorized - please login first."
403:
description: "Forbidden - insufficient access rights."
/terminology/healthrecord/profile:
get:
tags:
- tbd
parameters:
- name: ids
in: query
style: form
explode: false
description: "A comma-separated list of IDs of the profiles that shall be retrieved."
required: true
schema:
type: string
example: "203e04cd-4f0a-321b-b1ad-9ec6d211e0a8,203e04cd-4f0a-321b-b1ad-9ec6d211e0a9"
responses:
200:
description: "HealthRecord Profiles found - may contain empty entries"
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/HealthRecordProfileData'
401:
description: "Unauthorized - please login first."
403:
description: "Forbidden - insufficient access rights."
/terminology/url-mapping:
get:
tags:
- tbd
responses:
200:
description: ok
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/UrlMapping'
components:
schemas:
UrlMapping:
type: object
properties:
url:
type: string
format: url
example: http://hl7.org/fhir/sid/icd-o-3
display:
type: string
example: icd-o3
HealthRecordProfileData:
type: object
properties:
id:
type: string
format: uuid
profiles:
type: array
items:
$ref: '#/components/schemas/HealthRecordProfileEntry'
HealthRecordProfileEntry:
type: object
properties:
entry:
description: this is to be decided by julian
type: string
format: json
HealthRecordTree:
type: object
properties:
entry:
description: full json tree containing all profiles for now. might change if lazy loading or server-side filtering is required
type: string
format: json |
This was referenced Jul 12, 2024
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Overview
Searching through the ontology shall become more convenient. This requires changes to the frontend and the backend as well. The frontend part (except the API to it) is not the scope of this issue, however, the input of the frontend team is much appreciated (as well as from others).
For the backend, the plan is to add an instance of elastic search that will be populated with data generated by the fhir ontology generator and queried by the backend application.
This issue is meant to collect and discuss ideas first.
Current State
The documents below are the place to track changes for this. If it is not reflected here - it is not happening ;) (for now)
Click to expand OpenAPI (copy to https://editor-next.swagger.io/ for your convenience)
Click to expand Elastic Search index for ontology
{ "settings": { "analysis": { "tokenizer": { "edge_ngram_tokenizer": { "type": "edge_ngram", "min_gram": 1, "max_gram": 20, "token_chars": [ "letter", "digit" ] } }, "analyzer": { "edge_ngram_analyzer": { "type": "custom", "tokenizer": "edge_ngram_tokenizer", "filter": [ "lowercase" ] }, "lowercase_analyzer": { "type": "custom", "tokenizer": "standard", "filter": [ "lowercase" ] } } } }, "mappings": { "properties": { "availability": { "type": "long", "index": false }, "children": { "properties": { "contextualized_termcode_hash": { "type": "text", "index": false }, "name": { "type": "text", "index": false } } }, "context": { "properties": { "code": { "type": "keyword" }, "display": { "type": "keyword" }, "system": { "type": "keyword" }, "version": { "type": "keyword" } } }, "criteria_sets": { "type": "keyword" }, "kds_module": { "type": "keyword" }, "name": { "type": "text", "analyzer": "edge_ngram_analyzer", "search_analyzer": "lowercase_analyzer" }, "parents": { "properties": { "contextualized_termcode_hash": { "type": "text", "index": false }, "name": { "type": "text", "index": false } } }, "related_terms": { "properties": { "contextualized_termcode_hash": { "type": "text", "index": false }, "name": { "type": "text", "index": false } } }, "selectable": { "type": "boolean" }, "termcode": { "type": "text", "analyzer": "edge_ngram_analyzer", "search_analyzer": "lowercase_analyzer" }, "termcodes": { "properties": { "code": { "type": "text", "index": false }, "display": { "type": "text", "index": false }, "system": { "type": "text", "index": false }, "version": { "type": "text", "index": false } } }, "terminology": { "type": "keyword" }, "translations": { "properties": { "lang": { "type": "text", "index": false }, "value": { "type": "text", "index": false } } } } } }Click to expand Elastic Search index for codeable concepts
{ "settings": { "analysis": { "tokenizer": { "edge_ngram_tokenizer": { "type": "edge_ngram", "min_gram": 1, "max_gram": 20, "token_chars": [ "letter", "digit" ] } }, "analyzer": { "edge_ngram_analyzer": { "type": "custom", "tokenizer": "edge_ngram_tokenizer", "filter": [ "lowercase" ] }, "lowercase_analyzer": { "type": "custom", "tokenizer": "standard", "filter": [ "lowercase" ] } } } }, "mappings": { "properties": { "termcode": { "properties": { "code": { "type": "text", "analyzer": "edge_ngram_analyzer", "search_analyzer": "lowercase_analyzer" }, "display": { "type": "text", "analyzer": "edge_ngram_analyzer", "search_analyzer": "lowercase_analyzer" }, "system": { "type": "text", "index": false }, "version": { "type": "long", "index": false } } }, "value_sets": { "type": "keyword" } } } }The text was updated successfully, but these errors were encountered: