Ontology services: Difference between revisions

Latest revision as of 17:24, 7 December 2023

The ontology services can be categorised into two main forms

An Application that enables people to view and maintain ontologies, value sets, information models and query definitions
A set of (REST) APIs so that the resources can be extracted and used by other systems i.e. integrated into other systems.

All are built using open source code available in a set of repositories at https://github.com/endeavourhealth-discovery

Ontology and information model model application

The live manager is accessible at https://im.endeavourhealth.net/#/

The development version is accessible at https://dev.endhealth.co.uk/#/ which is generally a month or two further forward

Default contents include

The major health ontologies such as Snomed-CT (UK version and London extensions), considered as "core ontology"
The standard code based taxonomies such as OPCS-4 and ICD10 and the maps between them and the core ontology
The local code schemes such as EMIS, TPP and some Hospital trusts, and legacy code taxonomies such as Read 2 and CTV3 and the maps between them and the core ontology
A proven real world common data model based on FHIR like types (extended to real data) , modelled as an RDF graph, with maps to the model from source data formats used in primary, community, acute and urgent care providers that used the London One London Level 2 Discovery data service.
Libraries of live in use value sets bound to the fields within the model
Library of value sets used in queries including the core Snomed-CT UK reference sets and sets used in queries including QOF concept sets.
Example Libraries of feature and query definitions used as actual operational queries for data on health records.

Application functionality to enable creation and maintenance of Libraries for organisational specific ontologies, value sets, data models and queries

Information service APIs

As well as the information model manager and various modules, the service provides a suite of APIs to support the use of data held within the information model libraries.

Web APIs

The ability to obtain resources such as Value sets using FHIR APIs

Distribution services

As well as accessible by APIs and applications, the information model services provide distribution facilities for content of the IM for use in subscriber data bases or subscriber applications. All content of the information model can be distributed both in bulk and delta form

Set distributor

The concept and value set distributor maintains tables of value sets for databases that use local instances of the Discovery information model.

This is part of the information model distribution service that runs on an application server, and is designed to detect changes to the content of the information model and regenerate the value sets from the value set definitions. The value sets are regenerated whenever a value set definition changes or whenever there is an update to the concepts within the information model.

Underpinning modelling architectures

All of the services are based on RDF graphs with classes defined in SHACL shapes from which code classes are generated and made available as Java or Typescript.

Details of the underlying models can be viewed on the extensive det of Information model pages

@@ Line 5: / Line 5: @@
 # An Application that enables people to view and maintain ontologies, value sets, information models and query definitions
 # A set of (REST) APIs so that the resources can be extracted and used by other systems i.e. integrated into other systems.
+All are built using open source code available in a set of repositories at https://github.com/endeavourhealth-discovery
-===Information model viewer and manager===
+===Ontology and information model model application===
-The model manager has two forms
+The live manager is accessible at https://im.endeavourhealth.net/#/
-=== IM Directory and viewer ===
+The development version is accessible at https://dev.endhealth.co.uk/#/ which is generally a month or two further forward
-A viewer form. The development version of the information model viewer is at [https://im.endeavourhealth.net/ IM Viewer] This has free access and can be used to browser various artefacts
-Artefacts include
+Default contents include
 * The major health ontologies such as Snomed-CT (UK version and London extensions), considered as "core ontology"
 * The standard code based taxonomies such as OPCS-4 and ICD10 and the maps between them and the core ontology
-* The local code schemes such as EMIS, TPP and Hosptital trusts, and legacy code  taxonomies such as Read 2 and CTV3 and the maps between them and the core ontology
+* The local code schemes such as EMIS, TPP and some Hospital trusts, and legacy code  taxonomies such as Read 2 and CTV3 and the maps between them and the core ontology
-* The common data model, a schema independent set of entity types and properties created as a single model holding the real data as mapped from source healthcare providers.
+* A proven real world common data model based on FHIR like types (extended to real data) , modelled as an RDF graph, with maps to the model from source data formats used in primary, community, acute and urgent care providers that used the London One London Level 2 Discovery data service.
-*Maps between source health data and the common data model, applying context to source data.
+* Libraries of live in use value sets bound to the fields within the model
-* Library of value sets bound to the fields within the model
+* Library of value sets used in queries including the core Snomed-CT UK reference sets and sets used in queries including QOF concept sets.
-* Library of concepts sets used in queries including QOF concept sets, Snomed reference sets, local query libraries from CEG/QMUL.
+* Example Libraries  of feature and query definitions used as actual operational queries for data on health records.
-* Library of query definitions used as actual operational queries for data on health records.
+Application functionality to enable creation and maintenance of Libraries for organisational specific ontologies, value sets, data models and queries
-=== IM Manager ===
+Information service APIs
-An application for maintaining the content of the information model including the generation of sets, query definitions, new concepts
-* (FHIA manager form. This enables the authoring of new concepts, concept sets, value sets, transformation maps, data model shapes and query definitions. The information model manager (IM manager) is a multi modular web application designed to provide a view of the and to support the<nowiki/> authoring of the content of the model.<br />
-==Information service APIs==
 As well as the information model manager and various modules, the service provides a suite of APIs to support the use of data held within the information model libraries.
-===Get expanded concept set&nbsp; (FHIR)===
+===Web APIs===
-The value set generator returns a list of concepts that are defined by a set definition for use in queries,&nbsp;thus supporting advanced [https://wiki.discoverydataservice.org/Subsumption_test subsumption_testing] against health care records.
+The ability to obtain resources such as Value sets using FHIR APIs
-Am expanded set can also contain details of mappings between core ontological concepts and legacy code systems where mappings are automated. Expansions also take account of concept replacements or substitutions thus enabling historical data to be retrieved.
-The [https://wiki.discoverydataservice.org/Value_set_generator_API set&nbsp;generator API] accepts the IRI of a&nbsp;value set either in full, or relative to a baseline IRI e.g.. [http://discoverydataservice/InformationModel#VSET_Covid1 http://DiscoveryDataService/InformationModel#CSET_Covid1]&nbsp;or simple VSET_Covid1, and returns a list of concepts to be used in the query. The API supports both core concepts and original codes that have been mapped to the core concepts, depending on whether the database uses Discovery concepts or actual original codes
-===Get Map APIs===
-The information model server provides a number of APIs and utilities that support the mapping of original fields and values into the common information model.
-The [https://wiki.discoverydataservice.org/Data_map_API data mapping APIs] article describes the use of the mapping server's mapping APIs to support inbound and outbound data transformation processes that involve a map between two data models. The [https://wiki.discoverydataservice.org/Map_maker_manager map maker manager] article describes the way that the map maker manager operates when authoring maps
-For example there are a set of [https://wiki.discoverydataservice.org/Mapping_hint_algorithms Mapping hint algorithms] that are machine assisted approaches to improving the speed and accuracy of mapping.
-===Get address and Get UPRN API===
-As well as providing an application the service supports the [https://wiki.discoverydataservice.org/UPRN_address_matching_API UPRN REST API], which  enables a system to make a call to the UPRN address matching service with an address, and receive a response with the matched address and UPRN
 ==Distribution services==
 As well as accessible by APIs and applications, the information model services provide distribution facilities for content of the IM for use in subscriber data bases or subscriber applications. All content of the information model can be distributed both in bulk and delta form
@@ Line 52: / Line 36: @@
 This is part of the [https://wiki.discoverydataservice.org/IM_Distribution_service information model distribution service] that runs on an application server,&nbsp;&nbsp;and is designed to detect changes to the content of the information model and regenerate the value sets from the value set definitions. The value sets are regenerated whenever a value set definition changes or whenever there is an update to the concepts within the information model.
-<br />
+=== Underpinning modelling architectures ===
+All of the services are based on RDF graphs with classes defined in SHACL shapes from which code classes are generated and made available as Java or Typescript.
+Details of the underlying models can be viewed on the extensive det of [[Information modelling|Information model]] pages