Pattern: Representing Controlled Vocabularies for EMA SPOR Referentials - REVIEW

Introduction

Many of the regulatory data sets for substances and medicinal products include controlled vocabularies. The vocabularies published by the European Medicines Agency (EMA), via the Substances, Products, Organisations, and Referentials (SPOR) Registry are extensive and required for many regulatory submissions. The SPOR controlled vocabularies have a specific structure and follow a pattern that extends the basic controlled vocabulary pattern defined for the IDMP-O ontologies.

The extended SPOR pattern and a mapping from the SPOR schemas to IDMP-O is provided below. Note that while these details do not pertain to any specific use case / set of competency questions for IDMP-O to date, they are required for reporting purposes in the EU and are integrated with a number of our examples to show how to use the IDMP-O ontologies to represent and make use of these controlled vocabularies.

Related EMA SPOR Referentials Documentation

For reference the SPOR API Specification EMA/241514/2016: pages 68-  (SPOR-API-Specification.pdf) specifies what lists, terms and translations are composed of.

Lists are specified in Section 7.1:

7.1. List

List is a collection of related terms, e.g. countries list, units of measure list. List has additional properties like description, list owner and other. RMS manages multiple lists.

List schema definitions are in the attached XML Schema.

List properties can be represented as:

Collection of summary list information	Global element: <list-of-list>
Detailed information on a single list	Global element: <list-details>

Summary list information has the following properties (non-exhaustive, see schema for details):

Property	Card.	Type	Description
<list-id>	[1]	Complex	List identifier and link to list detailed information Format:   nnnnnnnnnnnn Example: 100000155052
<list-name>	[1]	String	Name of the list
<list-short-name>	[0..1]	String	Short name of the list
<list-status>	[1]	Enumeration	Status of the list
<terms-link>	[1]	Complex	List to a complete collection of terms for a given list
<terms-summaries-link>	[1]	Complex	List to a collection of terms summaries for a given list
<visibility>	[1]	Enumeration	Data visibility classification of the list
<domains>	[0..1]	Collection	Domains for which the list is defined
<list-operational-attributes>	[1]	Complex	Operational and lifecycle attributes of the list
<list-documents>	[0..1]	Complex	Collection of documents associated with the list
<list-description>	[0..1]	String	Description of the list
<owner>	[0..1]	String	The entity owning the vocabulary and its values
<version-provided-by-owner>	[0..1]	String	The version under the owner published a given list

Detailed list information extends the above by (non-exhaustive, see schema for details):

Property	Card.	Type	Description
<oid>	[0..1]	anyURI	Globally unique object identifier defined for the list
<list-level-definition>	[0..1]	Complex	Definitions of named list levels for a given list. Note: individual terms will be assigned to lists levels using list-level assignment element in controlled-term
<extended-relationship-definitions>	[0..1]	Complex	Collection of definitions of relationships to other lists
<extended-attributes-definitions>	[0..1]	Complex	Collection of extended attribute definitions defined for a given list

Terms are specified in section 7.2

7.2. Term

Term is a word or phrase used to describe a thing or to express a concept. All RMS terms have a name
in English and possible translations of this name to other languages. Related terms are grouped into
lists.
Term schema definitions are in the attached XML Schema.
This schema is authoritative source of information on resource properties for this API. 

Termproperties can be represented as:

Collection of summary terms information from a single list. Contains additional information on	Global element: <controlled-terms-list-summary>
Collection of controlled terms details from a single list	Global element:  <controlled-terms-list>
Collection of controlled term details or summaries from multiple lists	Global element: <controlled-terms-collection>
Details of an individual controlled term	Global element: <term-details>

Summary term information has the following properties (non-exhaustive, see schema for details): 

Property	Card.	Type	Description
<term-id>	[1]	Complex	Agreed European Identifier, this will be a unique sequential number for each term. Format: nnnnnnnnnnnn Example: 100000155052
<term-names>	[1]	Collection	Term names in different languages. Max. one name per language.
<short-names>	[0..1]	Collection	Short term names in different languages. Max. one name per language.
<status>	[1]	Enumeration	The status of the term
<children-link>	[0..1]	Complex	Link to a collection of direct children of this term.

Detailed term information extends the above by (non-exhaustive, see schema for details):

Property	Card.	Type	Description
<operational-attributes>	[1]	Complex	Operational and life cycle attributes
<visibility>	[1]	Enumeration	Data visibility classification of the list
<domains>	[0..1]	Collection	Domains for which the term is defined (e.g. human, veterinary)
<other-names>	[0..1]	Collection	Other term names in different languages. Multiple names allowed per language
<term-descriptions>	[0..1]	Collection	Term description in different languages. Max. one description per language
<term-comments>	[0..1]	String	Comments to the term
<current-term-ids>	[0..1]	Collection	References to current terms replacing a term with the status NULLIFIED or NON_CURRENT. The implementing system is responsible to update its local records in order to start using the current terms instead of the deactivated one.
<parents>	[0..1]	Collection	References to the parents of this controlled term in the hierarchical structure
<children>	[0..1]	Collection	References to the children of this controlled term in the hierarchical structure
<term-paths>	[0..1]	Collection	Paths from this term to a root of its hierarchical structure. For some lists multiple paths are possible.
<related-terms>	[0..*]	Collection	Other terms related to this term as defined in the extended relationships of the list definition.
<extended-attributes>	[0..1]	Collection	Extended attributes of this term as defined in the list definition.
<mappings>	[0..1]	Collection	Mappings of this controlled term to codes and identifiers in systems other than RMS.
<term-applicability>	[0..*]	Complex	Applicability of this term to some specific context, e.g. applicable to a particular country or applicable to a particular IT system.
<list-level-assignment>	[0..1]	Complex	Information to which named list level a given term is assigned. Note: definition of named list levels defined for a list are in list-level-definition element of the list-information.
<symbols>	[0..1]	Collection	Term symbols
<unit-of-measure-conversions>	[0..1]	Collection	Conversion formulas between different units of measure. Applicable only for units of measure (UoM)
<user-preferences>	[0..1]	Complex	User specific preferences for this term (e.g. tag assignments or user preferred name).
<terms-link>	[0..1]	Complex	Reference to the collection of term details in a given list
<terms-summaries-link>	[0..1]	Complex	Reference to the collection of term summaries in a given list
<list-reference>	[0..1]	Complex	Reference to the list details
<versions>	[0..*]	Complex	Contains a collection of historical representations of the term. A historical representation is created whenever a term is modified, where the historical representation represents the state of the organisation prior to the modification. Note, the collection includes all historical representations (previous versions) and the current representation (current version).

Mapping of properties in the IDMP-O SubstancesProductsOrganisationsReferentionals ontology to the SPOR XML schema (SPOR-all-V2.0.xsd) for terms

Languages for names are modeled in the XML schema using lang attributes of datatype xsd:language. The ontology uses the mvf:hasLanguage predicate to assign the language. So the xsd:language code must be mapped to the language instance.

Prefixes/Namespace declarations

SPOR domains must be mapped via the href attribute of the embedded link element. This contains the SPOR IRI of the domain term.

Mapping of  idmp-spor:SPORRecordStatus  with  spor:rmsStatusValues.

Only the status values that are listed in the SPOR RMS list https://spor.ema.europa.eu/v1/lists/200000005003 are available in the IDMP SPOR ontology

Mapping of  idmp-spor:SPOR-DataClassification  with  spor:rmsVisibilityValues.

All the status values that are listed in the SPOR RMS list  https://spor.ema.europa.eu/v1/lists/200000004983 are available in the IDMP SPOR ontology