Discovery health information model - Revision history

DavidStables: Replaced content with "Up to date information on the [https://wiki.endeavourhealth.org/index.php?title=Discovery_health_information_model information mode]l can be seen at"

2022-02-27T18:50:15Z

Replaced content with "Up to date information on the [https://wiki.endeavourhealth.org/index.php?title=Discovery_health_information_model information mode]l can be seen at"

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	~~This article describes the approach taken to producing information models, including ; what they are, what their purpose is, and what the technical components of the models are.~~		Up to date information on the [https://wiki.endeavourhealth.org/index.php?title=Discovery_health_information_model information mode]l can be seen at

	~~The article does not include the content of any particular model.~~

	~~== What is the Discovery health information model (IM)? ==~~
	~~The IM is a representation of the meaning and structure of data held in the electronic records of the health and social care sector, together with libraries of query, extract and mappings.~~

	It is an abstract logical model, not a physical structure or schema. As a logical model it models data that may be physically held any a variety of different types of data stores, including relational or graph data stores. Because the model is independent of the physical schemas, the model itself has to be interoperable and without any proprietary lock in.

	~~The IM is a broad model that integrates a set of different approaches to modelling using a common vocabulary. The components of the model are:~~

	# An ontology, which is a vocabulary and definitions of the concepts used in healthcare, or more simply put, a vocabulary of health. The ontology is made up of the world's leading ontology Snomed-CT, with a London extension and supplemented with additional concepts for data modelling.
	# A data model, which is a set of classes and properties, using the vocabulary, that represent the data and relationships as published by live systems that have published data, Note that this data model is NOT a standard model but a collated set of entities and relationships bound to the concepts based on real data, that are mapped to a single model.
	~~# A library of business specific concept and value sets, which are expression constraints on the ontology for the purpose of query~~
	~~# A catalogue of reference data such as geographical areas, organisations and people derived and updated from public resources.~~
	~~# A library of Queries for querying and extracting instance data from reference data or health records.~~
	~~# A set of maps creating mappings between published concepts and the core ontology as well as structural mappings between submitted data and the data model.~~
	~~# An open source set of utilities that can be used to browse, search, or maintain the model.~~
	~~# A modelling language using the World wide web semantic languages that can be used to exchange all elements of the model.~~

	~~The remainder of this article considers how models and ontologies can be constructed using this approach.~~

	~~== What is different? ==~~
	The main difference between the Discovery IM and other approaches is the harmonisation of the terms used in the conventional 'terminology' domain and the terms used in the conventional 'data model' domain. Both are considered part of the one ontology and the concepts often differ only in the approach to their definition..

	For example, an encounter may be defined as an "interaction between a patient (or on behalf of the patient) and a health professional or health provider". The definition of an encounter with Description logic as a subclass with some properties can be produced using the open world OWL2 grammar.

	~~However, an encounter can also be said~~ to ~~be a type of entry in a health record, as modelled in FHIR or openEHR. From this perspective an encounter will be defined as a logical 'schema' with a set of properties such as a~~ date ~~or encounter type.~~

	The two disciplines (Description logic and data model constraints) are different, but they are obviously related. The binding between a data model and the range of values that should be applied to a property blurs the boundary between one and the other. This boundary is artificial and historical and harmonising the two into a single holistic whole enables very flexible storage database designs.

	Because ontologies use inheritance and entailment as their main approach to definitions this also enables simple hierarchical approaches to data models. Instead of everyone having to make the same choice between having an encounter table or consultation table, or A&E attendance table, a system can be designed to suit, for example having a single high level table such as an event table, or a small number of core tables with extensions, or a complete library of tables, or no tables at all. A map between the information model and the chosen schema is all that is needed.<br />Benefits of harmonisation accrue in user interfaces. For example, is a user elects to search for a systolic blood pressure, if the application uses the information model it knows that a systolic blood pressure is held as a concept which is a value set of the concept property in an observation and can automatically produce the related properties such as data and value
	~~== Conceptualisation ==~~
	~~[[File:Graph.jpg\|thumb\|Types of data as a graph]]~~

	~~The data in a health record stored can be conceptualised as a set of relationships between one thing and many others.~~

	~~Some people call this a graph. Others call these objects , properties and values. From a grammatical language perspective they are subjects, predicates and objects.~~

	~~The example~~ on the ~~right is entirely arbitrary but illustrates a problem. What does "condition record" mean, or indeed what is a "condition"? Why is a patient linked to a person and what does "linked to" mean?~~

	The answer is that the "terms" or "concepts" used in a model should be derived from a vocabulary whose terms have meaning and are formally defined. Some terms have meaning in whatever context they are used whereas others have different meanings in different contexts. In defining terms, it is necessary to defined them precisely enough for a computer to interpret the meaning safely i.e. the context of an idea is part of the idea itself.

	The most difficult challenge is to agree the definition and meaning of the concepts in the context they are used. The agreement as to a particular model is less important. A definition defines a concept in relation to other concepts. Within a domain of interest such as healthcare, all concepts are indirectly related in some way to all other concepts in that domain.

	~~Luckily, standards have evolved to enable machine readable definitions.~~

	~~The crucial step in the discovery approach is to apply this principle to both the things that are being recorded (such as clinical concepts), as well as the structure of entries in records themselves.~~

	~~== Information model language ==~~

	~~''Main article''~~ [~~[Health Information modelling language - overview\|information modelling language]] describes the language in more detail.~~

	The semantic web approach is adopted. In this approach, data can be described via the use of a plain language grammar consisting of a subject, a predicate, and an object. A triple. The theory is that all health data can be described in this way (with predicates being extended to include functions).

	~~The consequence of this approach is that W3C web standards can be used such as the use of [[wikipedia~~:~~Resource_Description_Framework\|Resource Descriptor Framework o]]<nowiki/>r RDF. This sees the world as a set of triples (subject~~/ ~~predicate~~/ ~~object) with some things named and somethings anonymous~~. ~~Systems that adopt this approach can exchange data in a way that the semantics can be preserved~~. ~~Whilst RDF is an incredibly arcane language at a machine level, the things it can describe can be very intuitive when represented visually~~. ~~In other words the Information modelling approach involves an RDF Graph.~~

	However RDF has no inherent semantics or schematics. To bring those in the model uses the semantic web languages of RDFS, OWL2 DL and SHACL as its main languages with SPARQL as its query representation. It incorporates ontologies such as Snomed-CT and W3C-PROV.

	It is recognised that other languages are in common use. Consequently mappings are constructed to enable the model to be used. For example the Snomed-CT expression constraint language is a common way of defining concept sets. ECL is logically equivalent to a closed world query on an open world OWL ontology. The IM language uses the semantic language of SPARQL together with entailment to model ECL but ECL can be exported or used as input as an alternative.

	~~== Mapping from published data ==~~
	~~''main article'' [[Mapping and matching concepts\|mapping concepts and structures]]~~

	~~which describes the current mapping and approach to mappings of codes or text, in context from publisher systems.~~
	~~== Information manager=~~=

	~~''Main article'' [[Information model service\|~~information ~~model services.~~]~~]For an information model to be useable, it has to be accessible in some way either via user interfaces or by APIS.~~
	~~Thus the information model comes with a set of open source modules making up an application "Information manager" , which is a web based application designed to show the model.~~

	~~For a web application or set of APIs to~~ be ~~useful there has to be at least one service. There is a free to use [[information model service]], i.e. an operational service that provides access to one or more information models.~~

	~~The service provides a set of APIs as well as provide instances of the model for implementations to use directly should they wish to.~~

	~~All implementation code including the evolving service, APIs, language grammars and object models are also available on Github in the following repositories:~~

	~~https://github.com/endeavourhealth-discovery/IMAPI~~

	~~A viewer of the information model and an early version of the manager is~~ at:

	~~https://github.com/endeavourhealth-discovery/IMViewer~~

DavidStables: /* Mapping from published data */

2021-09-27T11:53:14Z

Mapping from published data

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	== Mapping from published data ==		== Mapping from published data ==
	''main article''		''main article'' [[Mapping and matching concepts\|mapping concepts and structures]]

	~~<br />~~		which describes the current mapping and approach to mappings of codes or text, in context from publisher systems.
	== Information manager==		== Information manager==

DavidStables: /* Information model language */

2021-09-27T11:32:06Z

Information model language

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	It is recognised that other languages are in common use. Consequently mappings are constructed to enable the model to be used. For example the Snomed-CT expression constraint language is a common way of defining concept sets. ECL is logically equivalent to a closed world query on an open world OWL ontology. The IM language uses the semantic language of SPARQL together with entailment to model ECL but ECL can be exported or used as input as an alternative.		It is recognised that other languages are in common use. Consequently mappings are constructed to enable the model to be used. For example the Snomed-CT expression constraint language is a common way of defining concept sets. ECL is logically equivalent to a closed world query on an open world OWL ontology. The IM language uses the semantic language of SPARQL together with entailment to model ECL but ECL can be exported or used as input as an alternative.

			== Mapping from published data ==
			''main article''

	<br />		<br />

DavidStables: /* Information manager */

2021-09-26T12:20:07Z

Information manager

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	== Information manager==		== Information manager==

			''Main article'' [[Information model service\|information model services.]]For an information model to be useable, it has to be accessible in some way either via user interfaces or by APIS.
	For an information model to be useable, it has to be accessible in some way either via user interfaces or by APIS.
	Thus the information model comes with a set of open source modules making up an application "Information manager" , which is a web based application designed to show the model.		Thus the information model comes with a set of open source modules making up an application "Information manager" , which is a web based application designed to show the model.

DavidStables: /* Information model language */

2021-09-26T08:55:50Z

Information model language

← Older revision		Revision as of 08:55, 26 September 2021
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	== Information model language ==		== Information model language ==

			''Main article'' [[Health Information modelling language - overview\|information modelling language]] describes the language in more detail.

	The semantic web approach is adopted. In this approach, data can be described via the use of a plain language grammar consisting of a subject, a predicate, and an object. A triple. The theory is that all health data can be described in this way (with predicates being extended to include functions).		The semantic web approach is adopted. In this approach, data can be described via the use of a plain language grammar consisting of a subject, a predicate, and an object. A triple. The theory is that all health data can be described in this way (with predicates being extended to include functions).
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	It is recognised that other languages are in common use. Consequently mappings are constructed to enable the model to be used. For example the Snomed-CT expression constraint language is a common way of defining concept sets. ECL is logically equivalent to a closed world query on an open world OWL ontology. The IM language uses the semantic language of SPARQL together with entailment to model ECL but ECL can be exported or used as input as an alternative.		It is recognised that other languages are in common use. Consequently mappings are constructed to enable the model to be used. For example the Snomed-CT expression constraint language is a common way of defining concept sets. ECL is logically equivalent to a closed world query on an open world OWL ontology. The IM language uses the semantic language of SPARQL together with entailment to model ECL but ECL can be exported or used as input as an alternative.

	~~Details of the [[Health Information modelling language - overview\|information modelling language]] are described in a separate article.~~		<br />
	== Information manager==		== Information manager==

DavidStables at 08:54, 26 September 2021

2021-09-26T08:54:32Z

DavidStables at 08:50, 26 September 2021

2021-09-26T08:50:00Z

Show changes

DavidStables: /* Sets and classes */

2021-07-07T10:38:18Z

Sets and classes

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	== Sets and classes ==		== Sets and classes ==
	See ''main article ~~xxxxxx~~ , which describes the types of sets and difference between sets and classes''		See ''main article [[sets and classes]] , which describes the types of sets and difference between sets and classes''

	== Data sets and schemas ==		== Data sets and schemas ==

DavidStables: /* Concepts, sets and codes */

2021-07-07T07:56:14Z

Concepts, sets and codes

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	The consequence of this approach is that W3C web standards can be used such as the use of [[wikipedia:Resource_Description_Framework\|Resource Descriptor Framework o]]<nowiki/>r RDF. This sees the world as a set of triples (subject/ predicate/ object) with some things named and somethings anonymous. Systems that adopt this approach can exchange data in a way that the semantics can be preserved. Whilst RDF is an incredibly arcane language at a machine level, the things it can describe can be very intuitive when represented visually.In other words the Information modelling approach involves an RDF Graph. However RDF has no inherent semantics or schematics. To bring those in the model uses RDFS, OWL2 DL and SHACL as its main languages. It incorporates ontologies such as Snomed-CT and W3C-PROV.		The consequence of this approach is that W3C web standards can be used such as the use of [[wikipedia:Resource_Description_Framework\|Resource Descriptor Framework o]]<nowiki/>r RDF. This sees the world as a set of triples (subject/ predicate/ object) with some things named and somethings anonymous. Systems that adopt this approach can exchange data in a way that the semantics can be preserved. Whilst RDF is an incredibly arcane language at a machine level, the things it can describe can be very intuitive when represented visually.In other words the Information modelling approach involves an RDF Graph. However RDF has no inherent semantics or schematics. To bring those in the model uses RDFS, OWL2 DL and SHACL as its main languages. It incorporates ontologies such as Snomed-CT and W3C-PROV.
	== Concepts~~, sets~~ and codes==		== Concepts and codes==
	See ''main article [[Term based vs code based concepts]]'' which considers the different philosophies and the relationships (mappings) between them.		See ''main article [[Term based vs code based concepts]]'' which considers the different philosophies and the relationships (mappings) between them.

			== Sets and classes ==
			See ''main article xxxxxx , which describes the types of sets and difference between sets and classes''

	== Data sets and schemas ==		== Data sets and schemas ==

DavidStables: /* Concepts, versus codes */

2021-07-07T07:53:50Z

Concepts, versus codes

← Older revision		Revision as of 07:53, 7 July 2021
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	The consequence of this approach is that W3C web standards can be used such as the use of [[wikipedia:Resource_Description_Framework\|Resource Descriptor Framework o]]<nowiki/>r RDF. This sees the world as a set of triples (subject/ predicate/ object) with some things named and somethings anonymous. Systems that adopt this approach can exchange data in a way that the semantics can be preserved. Whilst RDF is an incredibly arcane language at a machine level, the things it can describe can be very intuitive when represented visually.In other words the Information modelling approach involves an RDF Graph. However RDF has no inherent semantics or schematics. To bring those in the model uses RDFS, OWL2 DL and SHACL as its main languages. It incorporates ontologies such as Snomed-CT and W3C-PROV.		The consequence of this approach is that W3C web standards can be used such as the use of [[wikipedia:Resource_Description_Framework\|Resource Descriptor Framework o]]<nowiki/>r RDF. This sees the world as a set of triples (subject/ predicate/ object) with some things named and somethings anonymous. Systems that adopt this approach can exchange data in a way that the semantics can be preserved. Whilst RDF is an incredibly arcane language at a machine level, the things it can describe can be very intuitive when represented visually.In other words the Information modelling approach involves an RDF Graph. However RDF has no inherent semantics or schematics. To bring those in the model uses RDFS, OWL2 DL and SHACL as its main languages. It incorporates ontologies such as Snomed-CT and W3C-PROV.
	== Concepts, ~~versus~~ codes==		== Concepts, sets and codes==
	See ''main article [[Term based vs code based concepts]]'' which considers the different philosophies and the relationships (mappings) between them.		See ''main article [[Term based vs code based concepts]]'' which considers the different philosophies and the relationships (mappings) between them.

← Older revision		Revision as of 08:54, 26 September 2021
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	== What is the Discovery health information model (IM)? ==		== What is the Discovery health information model (IM)? ==
	It is a representation of the meaning and structure of data held in the electronic records of the health and social care sector, together with ~~a model~~ of query, extract and mappings.		The IM is a representation of the meaning and structure of data held in the electronic records of the health and social care sector, together with libraries of query, extract and mappings.

	It is an abstract logical model, not a physical structure or schema. As a logical model it models data that may be physically held any a variety of different types of data stores, including relational or graph data stores.		It is an abstract logical model, not a physical structure or schema. As a logical model it models data that may be physically held any a variety of different types of data stores, including relational or graph data stores. Because the model is independent of the physical schemas, the model itself has to be interoperable and without any proprietary lock in.

	It is a broad model that integrates a set of different approaches to modelling using a common vocabulary. The components of the model are:		The IM is a broad model that integrates a set of different approaches to modelling using a common vocabulary. The components of the model are:

	# An ontology, which is a vocabulary and definitions of the concepts used in healthcare, or more simply put, a vocabulary of health. ~~the~~ ontology is made up of the world's leading ontology Snomed-CT, with a London extension and supplemented with additional concepts for data modelling.		# An ontology, which is a vocabulary and definitions of the concepts used in healthcare, or more simply put, a vocabulary of health. The ontology is made up of the world's leading ontology Snomed-CT, with a London extension and supplemented with additional concepts for data modelling.
	# A data model, which is a set of classes and properties ~~made up of~~ the vocabulary, that represent ~~all of~~ the data relationships as published by live systems that have published data, Note that this data model is NOT a standard model but a collated set of entities and relationships bound to the concepts based on real data, mapped to a single model.		# A data model, which is a set of classes and properties, using the vocabulary, that represent the data and relationships as published by live systems that have published data, Note that this data model is NOT a standard model but a collated set of entities and relationships bound to the concepts based on real data, that are mapped to a single model.
	# A library of business specific sets, which are expression constraints on the ontology for the purpose of query		# A library of business specific concept and value sets, which are expression constraints on the ontology for the purpose of query
	# A catalogue of reference data such as geographical areas, organisations and people derived and updated from public resources.		# A catalogue of reference data such as geographical areas, organisations and people derived and updated from public resources.
	# A library of Queries for querying and extracting instance data from reference data or health records.		# A library of Queries for querying and extracting instance data from reference data or health records.
Line 52:		Line 52:
	The semantic web approach is adopted. In this approach, data can be described via the use of a plain language grammar consisting of a subject, a predicate, and an object. A triple. The theory is that all health data can be described in this way (with predicates being extended to include functions).		The semantic web approach is adopted. In this approach, data can be described via the use of a plain language grammar consisting of a subject, a predicate, and an object. A triple. The theory is that all health data can be described in this way (with predicates being extended to include functions).

	The consequence of this approach is that W3C web standards can be used such as the use of [[wikipedia:Resource_Description_Framework\|Resource Descriptor Framework o]]<nowiki/>r RDF. This sees the world as a set of triples (subject/ predicate/ object) with some things named and somethings anonymous. Systems that adopt this approach can exchange data in a way that the semantics can be preserved. Whilst RDF is an incredibly arcane language at a machine level, the things it can describe can be very intuitive when represented visually. In other words the Information modelling approach involves an RDF Graph.		The consequence of this approach is that W3C web standards can be used such as the use of [[wikipedia:Resource_Description_Framework\|Resource Descriptor Framework o]]<nowiki/>r RDF. This sees the world as a set of triples (subject/ predicate/ object) with some things named and somethings anonymous. Systems that adopt this approach can exchange data in a way that the semantics can be preserved. Whilst RDF is an incredibly arcane language at a machine level, the things it can describe can be very intuitive when represented visually. In other words the Information modelling approach involves an RDF Graph.

	However RDF has no inherent semantics or schematics. To bring those in the model uses the semantic web languages of RDFS, OWL2 DL and SHACL as its main languages with SPARQL as its query representation. It incorporates ontologies such as Snomed-CT and W3C-PROV.		However RDF has no inherent semantics or schematics. To bring those in the model uses the semantic web languages of RDFS, OWL2 DL and SHACL as its main languages with SPARQL as its query representation. It incorporates ontologies such as Snomed-CT and W3C-PROV.