Page tree
Skip to end of metadata
Go to start of metadata







© 2019 International Health Terminology Standards Development Organisation.  All rights reserved.  SNOMED CT® was originally created by the College of American Pathologists.

This document forms part of the International Edition Complete OWL file DEMONSTRATION release of SNOMED CT® distributed by International Health Terminology Standards Development Organisation, trading as SNOMED International, and is subject to the SNOMED CT® Affiliate License, details of which may be found at  https://www.snomed.org/snomed-ct/get-snomed.

No part of this document may be reproduced or transmitted in any form or by any means, or stored in any kind of retrieval system, except by an Affiliate of SNOMED International in accordance with the SNOMED CT® Affiliate License. Any modification of this document (including without limitation the removal or modification of this notice) is prohibited without the express written permission of SNOMED International.

Any copy of this document that is not obtained directly from SNOMED International [or a Member of SNOMED International] is not controlled by SNOMED International, and may have been modified and may be out of date. Any recipient of this document who has received it by other means is encouraged to obtain a copy directly from SNOMED International [or a Member of SNOMED International. Details of the Members of SNOMED International may be found at http://www.snomed.org/members/].



Date

20190201

Document Version

1.0

Release Status

DEMO RELEASE



Page At A Glance

Introduction

The SNOMED CT terminology provides a common language that enables a consistent way of indexing, storing, retrieving, and aggregating clinical data across specialties and sites of care. The International Health Terminology Standards Development Organisation (IHTSDO®) maintains the SNOMED CT technical design, the content architecture, the SNOMED CT content (including the concepts table, the descriptions table, the relationships table, a history table and ICD mappings), and related technical documentation. 

This DEMONSTRATION release package is distributed for evaluation purposes only.  It must not be used in production clinical systems or in clinical settings, or distributed to Affiliate Licensees or any third parties.   

Audience for this document

This document should be read by all those who will be reviewing or submitting questions or comments related to the Demonstration Release, including participation in any follow up meetings. 

Scope and Purpose

The complete OWL axiom reference set has been developed to replace the stated relationship file following the first release of a partial OWL axiom reference set in the July 2018 International Edition. In this demonstration release, the OWL axiom reference set represents all stated relationships including all new description logic features, such as general concept inclusion (GCI) axioms and additional axioms. The purpose is to provide an early view to help our community to evaluate their tooling, systems and release process.  Please note that the content modeling is still a work-in-progress and these examples are being provided for demonstration purposes only and are not necessarily reflective of content that will be in the July 2019 Releases.

Release content

Content detail

Therapeutic role modeling

  • As previously communicated, therapeutic roles associated with concepts in the 763158003 |Medicinal product (product)| will be modeled using additional axioms beginning in the 2019-January Release. 
  • For examples of therapeutic role remodeling using the new attribute 766939001 |Plays role (attribute)|, see descendants of:
    • 763087004 |Medicinal product categorized by therapeutic role (product)|
    • 386757008 |Medicinal product acting as antiglaucoma agent (product)|
    • 96326006 |Medicinal product acting as ceruminolytic agent (product)|
    • 61621000 |Medicinal product acting as laxative (product)|
  • Medicinal product containing only and Medicinal product form containing only concepts have been added; concepts are sufficiently defined and modeled to proximal primitive

Remodeling of hypersensitive conditions

The new concept model for hypersensitive conditions has been approved for implementation. Hypersensitivity condition is a direct descendant of clinical finding. Allergic and Nonallergic hypersensitivity (pseudoallergic) condition both of which are primitive each have three main sub-hierarchies representing diseases (mostly abnormal structures), processes (allergic and nonallergic hypersensitivity (pseudoallergic) reactions) and findings of propensities to developing allergic and nonallergic hypersensitivity (pseudoallergic) reactions (dispositions).

Hypersensitive condition and allergic condition are modelled by four general concept inclusion axioms. The relationships in the GCIs are sufficient conditions and are excluded from the inferred relationships. The concept model for allergic disposition and allergy concepts with semantic tag (finding) have been updated in the demonstration release. These concepts would not be classified under the allergic condition (finding) without the GCIs. 

Detailed documentation regarding changes to the Substance and Drug hierarchies that are in scope to be reviewed for this Demonstration release are located on the project Confluence sites:

Please note that comments and questions submitted related to content not specifically identified as in scope for this Demonstration release will be rejected.

Effective date

The Demonstration release will be made available for your review with an effectiveTime of 20190131.

Technical Notes

RF2 package format

The RF2 package convention dictates that it contains all relevant files, regardless of whether or not there is content to be included in each particular release.  Therefore, the package contains a mixture of files which contain both header rows and content data, and also files that are intentionally left blank (including only a header record).  The reason that these files are not removed from the package is to draw a clear distinction between:

  1. ...files that have been deprecated (and therefore removed from the package completely), due to the content no longer being relevant to RF2 in this or future releases, and 
  2. ...files that just happen to contain no data in this particular release (and are therefore included in the package but left blank, with only a header record), but are still relevant to RF2, and could therefore potentially contain data in future releases.

This allows users to easily distinguish between files that have purposefully been removed or not, as otherwise if files in option 2 above were left out of the package it could be interpreted as an error, rather than an intentional lack of content in that release.

Release of OWL reference sets

As an essential part of SNOMED CT Logic Profile Enhancements, the OWL refsets have been developed to represent logic definitions following the international standard of OWL 2 Web Ontology Language. In the International Edition releases for July 2018 and January 2019, the scope for the content in the OWL axiom refset is limited to property chains, transitive properties, reflexive properties, the general concept inclusion (GCI) axioms and additional axioms that are implemented to support the Drug/Anatomy content projects. 

In this Demonstration release, the complete OWL Expression refset has been developed. In addition to those axioms in the partial OWL axiom refset, all active relationships in the stated relationship file have been transformed into the OWL axiom refset. Therefore, the OWL axiom refset represents all logical definitions for the entire SNOMED CT International Edition. The OWLAxiom refset and OWLOntology refset files are merged into a single file called OWLExpression Refset in the January 2019 releases.

The OWLExpression refset is placed under the Terminology folder in the release file package.

  • xsct2_sRefset_OWLExpressionSnapshot_INT_20190131.txt

The complete OWLExpression refset will be mandatory from the July 2019 release.

Stated relationship file

The stated relationship file will be inactivated after the January 2019 release. As noted in the July 2018 release, the stated relationship file is no longer the complete representation of all logical definitions. The partial OWL axiom refset must be used for description logic classification.

In this Demonstration release package then, all entries are inactivated in the stated relationship file.  All changes to the stated relationships in the January 2019 cycle are excluded. Similarly, in the July 2019 release, all changes to the stated relationships in the July 2019 cycle will not be included. The purpose is to avoid duplications with the complete OWLExpression refset. We encourage users to utilise this Demonstration release for evaluating their tooling, systems and release process, but not to use it in any Production or clinical systems.

Following feedback from the community, the stated relationship file will still be available in the upcoming release packages (rather than being deprecated entirely) and the partial OWL axiom refset will include all description logic features that cannot be represented in the stated relationship file.

Inferred relationship file

The inferred relationship file will maintain the same format and structure, and it is no longer an equivalent to the stated form (containing all necessary and sufficient conditions). It is a collection of all the necessary conditions and represents a subset of the full semantics.

The rules for generating the relationship file are included in the document SNOMED CT OWL Guide. The examples in the document can be used as testing cases for the tooling and systems to produce consistent inferred relationships.

Improvement for the representation of role groups

It is important to clearly indicate if an attribute is grouped or not because role group has impact to semantics and classification results. The majority of the Modeling Advisory Group members recommended explicit representation for role groups. There will be two key improvements for the representation in the July 2019 International Edition release. The changes are previewed in this Demonstration release package:

Firstly, role groups are explicitly stated and represented by the concept 609096000|Role group (attribute)| as an object property in the OWL axiom refset.

Secondly, for inferred relationship file, role group 0 will be only applied to attributes that are not logically grouped, e.g. not a value of 609096000|Role group (attribute)| in an OWL axiom, or grouped = 0 in the MRCM. This addresses the potential confusion whether an attribute is grouped or not in the role group 0. 

The improvements will provide consistent representation for role groups in the OWL axioms, inferred relationship file, and diagramming of concept model. 

Known Issue

There is one concept that is missing two inferred relationship records - this is due to an edge case scenario that the classifier has yet to correctly deal with:

id    effectiveTime    active    moduleId    sourceId    destinationId    relationshipGroup    typeId    characteristicTypeId    modifierId

        1        79410001    255399007    1    246454002    900000000000011006    900000000000451002
        1        79410001    78076003    1    363698007    900000000000011006    900000000000451002

This will be resolved with a code fix to the external classifier service in time for the start of the Release cycle for the July 2019 International Edition, and will therefore not be a problem in any Production content.  It should be expected as a Known Issue as part of the January 2019 Demonstration release.


A set of documentation has been developed to support the Logic Profile Enhancements. Please see the detail in the following links.

Documentations

SNOMED CT OWL Guide

SNOMED CT Logic Profile Specification

SNOMED CT Logic Profile Enhancements


Approvals


Final Version

Date

Approver

Comments

1.0

 

Yongsheng GaoApproved
1.0

 

Kai KewleyApproved





Download .pdf here:








Draft Amendment History


Version

Date

Editor

Comments

0.1

20190107

Andrew AtkinsonInitial draft
0.220190131Yongsheng GaoUpdates
0.320190131Andrew AtkinsonMinor refinements + added known issue



  • No labels