1. Introduction

1.1.  Background

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.

SNOMED International maintains the SNOMED CT technical design, the content architecture, the SNOMED CT content (includes the concepts table, the descriptions table, the relationships table, a history table, and ICD mappings), and related technical documentation.

1.2. Purpose

This document provides a summarized description of the content changes included in the January 2019 release of SNOMED Clinical Terms^® (SCT) International Release.

It also includes technical notes detailing the known issues which have been identified and agreed to be released. These are content or technical issues where the root cause is understood, and the fix has been discussed and agreed, but has yet to be implemented.

The SNOMED International Release Notes are available alongside the January 2019 International Edition release.

1.3. Scope

This document is written for the purpose described above and is not intended to provide details of the technical specifications for SNOMED CT or encompass every change made during the release.

1.4. Audience

The audience includes National Release Centers, WHO-FIC release centers, vendors of electronic health records, terminology developers and managers who wish to have an understanding of changes that have been incorporated into the January 2019 International Edition release.

2. Content Development Activity

2.1. Summary

Continuous quality improvement and enhancement of existing content is an ongoing process by SNOMED International for every release. The January 2019 International Release has seen a continuation of the work driven by contributions from: Kaiser Permanente Convergent Medical Terminology (CMT), Global Medical Device Nomenclature Agency (GMDNA), Orphanet and other domain specific collaborations as well as requests received via the Content Request System (CRS). Additionally quality improvement activities are in progress for new and enhanced content through project driven initiatives which are also summarized below.  Also included as work items for every release are various updates to SNOMED CT derived maps such as ICD-10 and ICD-O and details are also included in these release notes.  Information about editorial decisions may be found in the SNOMED CT Editorial Guide, mapping guidance for ICD-10 can be found at this link https://confluence.ihtsdotools.org/display/DOCICD10.

2.2. Content Quality Improvement

2.2.1. Anatomy 

New anatomy concepts: 442

Content quality improvements:

• • Descriptions of 44 concepts updated to conform to the editorial guidance for the naming convention for laterality. 
  • The attribute 123005000 |Part of (attribute)| has been inactivated and a new attribute |Proper part of| has been added in the January 2019 release. All part of relationships are inactivated and the different part of relationships will be implemented after the revision of hierarchical relationships for anatomy content. 
  • Revision of hierarchical relationships for anatomy content: the project plan is to review the hierarchical relationships for anatomy content in the production against the inferred relationships from the new anatomy model. The new anatomy concept model has implemented the Description Logic features, e.g. reflective and transitive property, general concept axioms, for consistent logical modeling and inferences. 
    Content review and revision are divided by body systems. There is a total of 12,458 hierarchical relationships in anatomy for review. The revision will improve classification in other hierarchies such as disorders, procedures, observables and situations. In this release, over 4,100 relationships in the musculoskeletal system in body structure and over 6,000 relationships in other hierarchies were reviewed. There are about 2,000 changes to hierarchical relationships in anatomy and concept model for disorders and procedures. Further details can be found at https://confluence.ihtsdotools.org/display/IAP/Progress+of+IS+A+revision 
    Please note, you may have to register for a Confluence user account in order to access the relevant links above.
  • Revision of nail structures - all 'nail structure' concepts are replaced by nail unit structures to avoid misinterpretation of nail plate structures. |Nail plate structure| is a skin appendage. |Nail unit structure| includes |Nail plate structure| and skin around and under the nail plate. The concept |Nail structure| and its subconcepts were inactivated. Over 60 new nail unit concepts were added. Changes were made to stated relationships for over 300 concepts with impact to inferred relationships for about 500 concepts.

2.2.2. Clinical finding

New concepts for clinical findings and disorders: 2114

Quality Initiative

The Quality Initiative (QI) project is the implementation of the Quality Strategy. After a successful pilot project for the July 2018 release the next stage has been implemented for the January 2019 release. 

Quality improvement tasks were deployed to improve internal structural consistency and ensure compliance with editorial policy related to the stated modeling of content. Additionally, correction or addition of defining relationships was carried out to accurately reflect current clinical knowledge and ensure the semantic reliability of descriptions associated with a concept.

The following subhierarchies of the Clinical Finding hierarchy were remodelled to the proximal primitive parent resulting in changes to inferred relationships.

• • • Fracture 
    • Bacterial infectious disease
    • Disease caused by parasite
    • Sexually transmitted disease
    • Chronic inflammatory disease
    • Aneurysm
    • Arthritis
    • Open wound
    • Closed wound
    • Bite wound
    • Congenital malformation
    • Protozoan infection
    • Closed wound
    • Viral disease
    • Hernia of abdominal cavity - Structural improvement of subtypes of the concept 52515009 |Hernia of abdominal cavity (disorder)|. Further work will be undertaken in a subsequent release on the combined disorders where gangrene and/or obstruction is present due to a hernia as well as incisional hernias.
      
    • Burn - Inactivation of burn concepts containing "with loss of body part" and "without loss of body part" approximately 161 concepts.
    • Abrasion - As a result of changes made during the QI project, there are now 2 concepts which have the same preferred term. 
      781488002 |Abrasion of foot (finding)
      211402004 |Abrasion of foot (disorder)
      782201009 |Abrasion (finding)|
      399963005 |Abrasion (disorder)|
      These concepts will be addressed as part the QI project for the July 2019 release.

Total count of changes for the QI project:

• • • Stated: A total of 12595 concepts had changes made to the Stated relationships in their models.
    • Inferred: This resulted in 20012 concepts affected by inferred changes.
    • Subsequent review of the Fracture hierarchy of 151 concepts identified no impact upon the previously published maps to ICD-10.
    • Subsequent review of the Burn hierarchy of 375 concepts identified no impact upon the previously published maps to ICD-10.
      
      

Changes to Allergy Content

Approximately 2,000 concepts relating to hypersensitivity conditions have been remodeled to conform with new editorial guidance (excluding hypersensitivity reaction):

• • • Hypersensitivity/Allergy/Non-allergic hypersensitivity condition classes defined using General Concept Inclusion (GCI) axioms in order to encompass disorders, dispositions and processes (reactions).
    • Propensity to adverse reaction and Allergic disposition moved from disorders to findings. The concepts were remodeled using the proximal primitive parents with a role group consisting of 719722006 |Has realization (attribute)| with value of allergic process or its subtype. The new convention for descriptions are Hypersensitivity/Allergy/Non-allergic hypersensitivity to X (finding).
    • New Allergic disorder (disorder) hierarchy representing abnormal structures. The allergic disorders are modeled by associated inflammation morphology + allergic process or subtype + finding site X e.g. Allergic rhinitis).
    • The contact hypersensitivity conditions have been remodeled using the new concepts for Immunoglobin E-mediated allergic contact hypersensitivity process (qualifier value) and Non-immunoglobin E-mediated allergic contact hypersensitivity process (qualifier value).
    • New Intolerance to substance (finding) hierarchy created under Propensity to adverse reaction (finding) as a sibling of Hypersensitivity disposition (finding).
    • 414029004 |Disorder of immune function (disorder)| is remodeled and defined by using a pathological process of 769247005 |Abnormal immune process (qualifier value). As a result, it subsumes allergic disorders and allergic reactions.
    • Pseudoallergy condition and Pseudoallergy disposition renamed to Non-allergic hypersensitivity condition (finding) and Non-allergic hypersensitivity disposition (finding) and they have been remodeled following the new concept model.
    • Inactivation of “Allergy to X" concepts where X is a modification of a base substance and replacement with Allergy to the base substance.

As the result of Allergy project requirements, the following top level groupers/Allergen classes in substance hierarchy were inactivated and their children assigned to appropriate structural and/or functional parents :

• • • 414052000 | Drug allergen by structure |
    • 414057006 | Drug pseudoallergen|
    • 414053005 | Drug allergen or pseudoallergen|
    • 414058001 | Drug pseudoallergen by function|

Note: Other top level groupers (as specified in project Allergies-19) will be inactivated in the future releases.

Any maps from SNOMED CT to ICD-10 impacted by this Quality Initiative have been reviewed and updated.

Work commenced on the following Content Projects:

• • • IHTSDO- 393 Diabetes Complications: The Diabetes Project Group has begun its work on reviewing the current SNOMED CT Diabetes Mellitus disorder concepts. The group is small but is truly international and each member is currently seeking to engage with diabetes specialists within their geographical zone in order to ensure international interoperability within this domain.
      
    • IHTSDO-41 Modeling of 'X' in remission - Approximately 170 disorder in remission concepts can now be found in the hierarchy 765205004 | Disorder in remission (disorder) | as well as the hierarchy relating to the underlying disorder.

Other content quality improvements:

• • • 371598009 |Heberden's node (finding)| changed to disorder. 201827009 |Heberden's nodes with arthropathy (disorder)| inactivated. 80400009 |External hyperostosis (morphologic abnormality)| moved from under 13814009 |Hypertrophy of bone (morphologic abnormality)| to 4147007 |Mass (morphologic abnormality)| and Heberden node (disorder) remodeled. The result is that Heberden node (disorder) is no longer a subtype of 298745009 |Hypertrophy of upper limb (finding)| but is now a subtype of 416189003 |Exostosis (disorder)|.
    • Intrinsic vs. Extrinsic Asthma - changes made: 
      • 424643009 |Immunoglobulin E-mediated allergic asthma (disorder)| removed synonym "Extrinsic asthma" as semantically non-equivalent and "refers to" 389145006 |Allergic asthma (disorder)|. 
      • 389145006 |Allergic asthma (disorder)| - added preferred term. 
      • "Extrinsic asthma" removed synonyms "Allergic atopic asthma" and "Atopic asthma" and "refers to" 424643009 |Immunoglobulin E-mediated allergic asthma (disorder)|. 
      • 424643009 |Immunoglobulin E-mediated allergic asthma (disorder)| added synonyms "Allergic atopic asthma" and "Atopic asthma".
    • Acquired disorder - Approximately 124 concepts were edited to continue with the work to remove the precoordinated morphology and replace with a single morphology and the occurrence "767023003|Period of life beginning after birth and ending before death (qualifier value)" in the relationship group. 
    • Remodeling of Joint instability - approximately 156 concepts remodeled using approach: FSN: |Instability of X (finding)|, Is a: 404684003|Clinical finding (finding), finding site: X body structure, relationship group: Interprets: 299444001 |Stability of X (observable entity)|/ Has interpretation: 263654008|Abnormal (qualifier value).
    • Additions and improvements in areas of suspected/risk of bullying, abuse, and abandonment in clinical finding hierarchy.
    • Inactivation of 112625008|Cutaneous eruption (morphologic abnormality) in favor of using 1806006|Eruption (morphologic abnormality)| relationship grouped with a finding site, approximately 51 concepts remodeled.
    • Remodeling of joint temperature-related concepts: adding parents, interprets values and sufficiently defining where appropriate.
      
      

2.2.3. Convergent Medical Terminologies (CMT)

New CMT concepts: 1365

The majority of these newly authored concepts are in scope for mapping to ICD-10 and from the following domains:

• • • • CMT Ear, Nose and Throat
      • CMT Genitourinary
      • CMT Infectious Disease
      • CMT Injuries
      • CMT Ophthalmology
      • CMT Skin
      • CMT Musculoskeletal

2.2.4. Procedure Hierarchy

New concepts for procedure hierarchy: 393

Diagnostic imaging - 121 requests were received for new imaging procedure concepts with various imaging modalities.

• • • • Computed tomography 26 new concepts.
      • Magnetic Resonance Imaging 26 new concepts.
      • X-ray 1 new concept.
      • Fluoroscopy 39 new concepts. 
      • Ultrasound 29 new concepts.

Repair of hernia - 102 new concepts

• • • Laparoscopic repair of hernia 54 new concepts.

  • • • Repair of hernia 48 new concepts.

Other content quality improvements:

• • • Improved representation of 305349003 |Admission to department (procedure)| in the area of pediatric specialty and dental clinics by adding additional parents where possible.
    • Relationships were added to, or changed in the procedure (and physical object) hierarchies in the area of spectacles, optical vision aids, telescopes in order to sufficiently define or correct the classification of these concepts.
    • Improved representation of 438579008|Focused ultrasound ablation (procedure)| and descendants.

2.2.5. Collaboration/Harmonization Projects

2.2.5.1. Orphanet

As a result of collaboration with Orphanet (http://www.orpha.net/consor/cgi-bin/index.php) 460 new SNOMED CT concepts have been created to represent rare diseases in the disorder hierarchy. All of these concepts have been mapped to ICD-10.

2.2.5.2. Global Medical Device Nomenclature Agency (GMDNA)

55 new SNOMED CT concepts created and mapped in the Physical object hierarchy to support the GMDN collaboration agreement.

2.2.6. Event

New concepts added: 27

Work continued on the following Content Projects:

• • • • IHTSDO-1071 - Continued inactivation of transport accidents; movement of all vehicle accidents to children of Transport accidents; Fully-defining some when possible and adding additional parents if appropriate.

2.2.7. Record Artifact

New concepts added: 61

54 new concepts added for care plan.

2.2.8. Organism

New organism concepts added: 326

Content quality improvements:

• • • • 268 New concepts (Including 117 Shiga toxin producing E coli concepts) and 12 changes to the existing concepts' descriptions.
      • Inactivation of 21 ambiguous concepts across multiple hierarchies which had included an animal species when referring to an Influenza virus (e.g., Myocarditis caused by avian influenza (disorder), Influenzavirus type A, avian, H5N1 strain (organism)). 6 new concepts were created in this process.
      • Correction of Influenza virus descriptions: Around 350 corrections/changes were made to Influenza virus descriptions over multiple hierarchies (majority in substance hierarchy but also including disorder, procedure and organism hierarchies). Most of the changes consisted of inactivation of the erroneous description and replacement with a new correct description. In addition, two new concepts were added in the organism hierarchy.
      • Application of consistent case sensitivity to organism descriptions containing "Taxon Rank": Change of the case sensitivity setting for 10282 descriptions (over 4964 concepts).
      • Concepts with descriptions that include the word 'unclassified' were inactivated (7 concepts).
      • Duplicate descriptions were identified and corrected for 11 Concepts.
      • Spelling errors were corrected for 29 concepts.
      • Historical associations were corrected for 32 concepts.

2.2.9. Pharmaceutical / biologic product

The following changes will be included in the 2019-January International Release.

2.2.10.  Veterinary Extension

10 concepts were moved to the Veterinary Extension. 

2.4.1.  ICD-10 map

The SNOMED CT to the International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (© World Health organisation 1994) 2016 Version map (SNOMED CT to ICD-10 Map) is included in the SNOMED CT International release as a Baseline. The SNOMED CT to ICD-10 Map was created to support the epidemiological, statistical and administrative reporting needs of SNOMED International member countries and WHO Collaborating Centres.

The SNOMED CT to ICD-10 Map is released in Release Format 2 (RF2) only. It is located in the file der2_iisssccRefset_ExtendedMapFull_INT_20190131.txt, which is in the Map folder under Refset, in each of the three RF2 Release Type folders. 

The SNOMED CT to ICD-10 Map is released as Refset 447562003 |ICD-10 complex map reference set (foundation metadata concept)|.

2.4.1.1. Content development activity summary

The map is a directed set of relationships from SNOMED CT source concepts to ICD-10 target classification codes.  The SNOMED CT source domains for the MAP are limited to subtypes of 404684003 |clinical finding|, 272379006 |event| and 243796009 |situation with explicit context|.  The target classification codes are ICD-10 2016 release. As part of the ongoing quality improvement of the published maps  SNOMED CT concepts mapped to code range Q90 - Q99 Chromosomal abnormalities, not elsewhere classified  have been reviewed and the previously assigned map advice POSSIBLE REQUIREMENT FOR AN EXTERNAL CAUSE CODE has been removed for consistency purposes.

2.4.1.2. Mapped content for January 2019

The map provided for the January 2019  release has been updated, and now represents a complete map from SNOMED CT International release to ICD-10 2016 version.

• • 2321 new concepts added

We would welcome feedback on any issues that users of the map may detect when using the map. Issues should be submitted via mapping@snomed.org

2.4.1.3. Technical Guide Exemplars

The Technical Guide Exemplars document has now been moved from the International Edition release package to a Confluence page.  This page can be found as part of the ICD-10 Mapping Technical Guide (see Appendix B), which is hosted here:  http://snomed.org/icd10map

2.4.2. ICD-O Map

       There are 5 updates for the ICD-O Morphological abnormality map in January 2019 release. 

2.4.3. SNOMED CT to OWL conversion and classification

The repository containing the toolkit enabling simple SNOMED CT to OWL conversion and classification can be found here, including documentation on its use:

https://github.com/IHTSDO/snomed-owl-toolkit

Please contact SNOMED International at support@snomed.org if you would like to provide any feedback on ways to extend and improve the new toolkit.

3. Technical notes

3.1. Known Issues

Known Issues are content or technical issues where the root cause is understood, and the resolution has been discussed and agreed but has yet to be implemented.  This can be due to a number of reasons, from lack of capacity within the current editing cycle, to the risk of impact to the stability of SNOMED CT if the fix were to be deployed at that stage in the Product lifecycle.  For this International edition, the following Known Issues were identified, and agreed to be resolved in the next editing cycle:

 

3.2. Resolved Issues

Resolved issues are Known Issues which were not fixed as part of the previous release lifecycle, but which have now been resolved in this latest release of the International Edition.  They can also be issues found during the Alpha and Beta testing of the current release, which were resolved before the final deployment of the associated Member release.  Finally they can be issues which were reported or found during the testing phase, but which have been closed without any action taken. The Resolved Issues for this release of the International edition were:

 

3.3. Technical updates

3.3.1. RF2 package format

For future reference, 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.

3.3.2. Combination of two new refsets - OWLAxiom and OWLOntology

Please see section "2.3.1 Logic Profile Enhancements" above for full details of the reason behind the introduction of these new refsets.  After the September 2018 Demonstration release, it was agreed to combine these two files into one "OWL Expression" file, which now contains both OWL Axiom + OWL Ontology refsets in the same file, in each section of the International Release package (Full, Snapshot and Delta):

• sct2_sRefset_OWLExpressionFull_INT_20190131.txt
• sct2_sRefset_OWLExpressionSnapshot_INT_20190131.txt
• sct2_sRefset_OWLExpressionDelta_INT_20190131.txt
  

The decision was taken to place the files in the "Terminology" folder in the release package (as opposed to the "Refset" folder), because these files are designed to eventually replace the Stated relationship files (in July 2019), and therefore contain core content which needs to be included in the Terminology folder.

3.3.3. Optional "on demand" package in addition to the January 2019 International edition

As part of the transition plan from Stated Relationships to OWL files, we are publishing an ancillary package alongside the January 2019 International Edition:

• This package contains a complete set of OWL records (including all Axioms - sufficient, transitivity etc) set to January 2019 effectiveTimes, as if this was the complete OWL file that we will introduce in July 2019.  This package also contains all stated relationships from the previous release (July 2018 International Edition) marked as inactive.  
• This acts as a second Demonstration release (similar to the September 2018 package), allowing everyone to thoroughly trial how the July 2019 Int Edition will work for them in practice.  It therefore retains the same nomenclature and formatting as the Sept 2018 Demo release, with everything x prefixed and labelled to warn against use in Production clinical systems.
• This package will be published in MLDS alongside the final Production release of the January 2019 International Edition, and will therefore be available to everyone who has access to the International Edition:

  • ************************************************************ [LOCATION] ************************************************************ 

3.3.4. Replacement of OWL conversion script with a link to the open source directory

In January 2017 the original OWL conversion script (a.k.a. the "Spackman OWL script") was removed from the International Edition package, and has since been published as a separate artefact alongside each Release. 

Because this script does not recognize the two new OWL refsets (see section 3.3.2 of these Release Notes), the Terminology Release Advisory Group has determined that the script should no longer be distributed.

Going forward, Release Notes will now include a link to the new open source OWL conversion toolkit that can be found in the following repository (including documentation on its use):

https://github.com/IHTSDO/snomed-owl-toolkit

Please contact SNOMED International at support@snomed.org if you would like to provide any feedback on ways to extend and improve the new toolkit.

3.3.5. Deprecation of the Technical Guide Exemplars document from the International Edition release package

The Terminology Release Advisory Group has confirmed that there should be no impact from removing this almost entirely static document from the International Edition release package, and hosting it instead in a Confluence Page. From the July 2018 International release then, we have deprecated this file (doc_Icd10MapTechnicalGuideExemplars_[date].xlsx) from the Release package, and instead provide a link in the Release Notes to the new Confluence Page.  Please see section 2.4.1.3 above for the relevant link.

3.3.6. Early visibility of impending change in the July 2019 International edition

Please see the following page for details of all upcoming changes planned for July 2019 and beyond:  

https://confluence.ihtsdotools.org/display/RMT/Early+Visibility+July+2019+Release+-+Planned+changes+to+upcoming+SNOMED+International+Release+packages

3.3.7. IMPORTANT CHANGES in the July 2019 International Edition

Replacement of the Stated Relationship files with the new OWL Axiom refset files

In the July 2019 release:

• The International Edition package will include both inactive Stated Relationships plus a complete OWL file (combined) from July 2019 effectiveTime onwards (ie) with NO history of OWL records that weren’t included in the January 2019 International Edition package itself (as opposed to the optional package).
• We will also publish a separate optional package containing an OWL (combined) Delta file, identifying which of the concepts have had modelling changes in relation to the optional package detailed in  section 3.3.3 of the Release notes above ("Optional "on demand" package in addition to the January 2019 International edition").
• No support for Stated Relationships will be provided from this point onwards, however we will continue to include the inactivated Stated Relationships in future International Edition packages, until it is decided that this is no longer required.
• Anyone who isn’t yet ready to move forward with OWL will therefore remain on the January 2019 International Edition until they are ready to update to OWL with the July 2019 version onwards.

The inferred relationship file will maintain the same format and structure, though it will no longer contain all necessary and sufficient conditions. The inferred relationship file is represented in Necessary Normal Form for distribution of relationships. It is a collection of all the necessary conditions and represents a subset of the full semantics from the 2018 July release and onwards. Most users will benefit from the improvements in the inferred relationships without requiring changes to their existing systems.

A set of documentations has been developed to support the Logic Profile Enhancements. 

• SNOMED DL Profile Enhancements - https://docs.google.com/document/d/1tqNEA6S4fEF4fgj15OPabYA2E0VTz8epxvRRwczKizQ/edit?usp=sharing
• SNOMED CT Logic Profile Specification - http://snomed.org/lps
• SNOMED CT OWL Guide (OWL Refsets specification) - http://snomed.org/owl
• Necessary Normal Form for Inferred Relationships - https://docs.google.com/document/d/1dt0r0aetwpwmHOfiT9wt0EVukVLRvVjXYUn_vq-QhIM/edit?usp=sharing
• Snomed OWL Toolkit - https://github.com/IHTSDO/snomed-owl-toolkit
• Classifying SNOMED CT using the Snomed OWL Toolkit - https://youtu.be/-91egY9mJqA
• Creating an OWL file containing SNOMED CT - https://youtu.be/sfFbMMioA_4

3.3.8. Document links

All links provide information that is correct and current at the time of this Release.  Updated versions may be available at a later date, but if so these will need to be requested from the relevant SNOMED International teams.