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

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-<font color="#e74c3c">DRAFT - this article is in a very draft state and must not be relied upon as being up to date or an actual reflection of the world's true state.</font>
-The Information model service is a set of services that enables the Discovery common information model to be created, updated, distributed and accessed.
-The service includes a set of web applications and a set of APIs to an&nbsp;[[IM_Server|information model server]]&nbsp;and an'''&nbsp;'''[[IM_Distribution_service|information_model_distribution_service]]
-All components of the service are open source and available at the Discovery Endeavour githubs&nbsp;[https://github.com/endeavourhealth https://github.com/endeavourhealth]&nbsp;and&nbsp;[https://github.com/endeavourhealth-discovery https://github.com/endeavourhealth-discovery]
-The information model itself is internally defined via the [[Discovery_information_model_language|Discovery_information_model_language]] which is a group of standards based languages with some pragmatic additions that enable the service to operate.&nbsp; Externally, the Information model can be accessed via standards based APIs or by Discovery language based APIs that are supported by the Information model server.
-The following lists the functional groupings of the IM Service. Some of these use web applications , some use the information model server, and some use the information model distribution service components that maintain locally owned copies of the information model.
 __TOC__
-== Support for Value sets ==
+The ontology services can be categorised into two main forms
-The service supports the creation of, maintenance of, distribution of, and access to value set definitions and value sets.
-A value set definition&nbsp;is a collection of&nbsp;concept expressions&nbsp;that have been brought together for particular business purposes. They are different from standard concept definitions because the meaning of some members of a value set may not be subsumed by the implied meaning of the value set. Value set definitions are desribed in more detail in the [[Discovery_Information_model_language.|Discovery_Information_model_language.]]
+# 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
-=== Value set editor ===
+===Ontology and information model model application===
-The value set editor enables people to create and maintain value set definitions which can then be downloaded, accessed via an API or distributed via the information&nbsp;model distribution service.&nbsp;
+The live manager is accessible at https://im.endeavourhealth.net/#/
-=== Value set run time generator&nbsp; ===
+The development version is accessible at https://dev.endhealth.co.uk/#/ which is generally a month or two further forward
-The value set generator returns a list of concepts that are defined by a value set definition for use in queries,&nbsp;thus supporting advanced [[Subsumption_test|subsumption_testing]] against health care records.
+Default contents include
-The [[Value_set_generator_API|value set&nbsp;]][[Generator_AP|generator AP]][[Value_set_generator_API|I 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#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.
+* 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
-=== Value set distributor ===
+Information service APIs
-The value set distributor maintains tables of value sets for databases that use local instances of the Discovery information model.&nbsp;
+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.&nbsp;
-This is part of the [[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.
+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.
-&nbsp;
+=== 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.
-&nbsp;
+Details of the underlying models can be viewed on the extensive det of [[Information modelling|Information model]] pages