Introduction

 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.

Purpose

This document provides a summarized description of the content changes included in the July 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 July 2019 International Edition release.

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.

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 July 2019 International Edition release.

Content Development Activity

Summary

Continuous quality improvement and enhancement of existing content is an ongoing process by SNOMED International for every release. The July 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.

Content Quality Improvement

Anatomy 

New anatomy concepts: 451

The initial review was completed for over 12,000 hierarchical relationships that are different between the production release and new anatomy model for body structures. For this release, the focus for the Anatomy project is quality improvement for the cardiovascular, digestive and genitourinary systems. Review of the remaining systems is planned for the 2020 January release.

• • Changes to hierarchical relationships:
    Cardiovascular system: 1363   
    Digestive system: 906
    Genitourinary system: 510

• • Reviewed potential impact to other hierarchies e.g. disorder, procedure and addressed most issues.
    Cardiovascular system: over 8600 
    Digestive system: over 7200
    Genitourinary system: over 6800

Other Content Quality Improvements:

• • In the body structure hierarchy a branch of a specified artery is not subordinate to its origin but has an IS_A relationship to a more regional artery. Any relationships that did not fulfil this rule have been corrected.
  • Similarly in the body structure hierarchy a tributary of a specified vein is not subordinate to the vein it drains in to, but has an IS_A relationship to a regional vein that covers the entire anatomical boundaries of every tributary of that vein. Any relationships that did not fulfil this rule have been corrected.
  • In the body structure hierarchy the vascular structure of an organ is composed of vessels that lie within and are part of the organ and the vessels that lie outside which supply it. So the kidney has glomerular arterioles within the kidney and a renal artery and renal vein that supply and drain the kidney. These relationships have been implemented for most organs and the remaining organs e.g. liver, stomach will be rationalized in the subsequent release.
  • In the body structure hierarchy a distinction has been made between the abdominopelvic structure and its constituent components: structures of the abdomen proper and those subsumed by pelvic structure. In general clinical concepts using the word ‘abdominal’ usually mean ‘abdominopelvic’ but in some specific circumstances a distinction is required; for example the uterus is located in the true pelvis (pelvis major) and not within the abdomen proper.
  • Skin appendage structures have been placed under skin structure.
  • Revision made to digital nerves of toe and its subconcepts.
  • Updates to free margin of eyelid and its subconcepts.
  • New additions of lumen concepts for the gastrointestinal tract and joint region concepts to support work for the Quality Initiative.
  • Updated content for the internal part of the mouth region.
  • Revision of subconcepts of lateral half of face.
  • Updated and validated release file for the lateralizable body structure reference set.
  • Updated and validated release files for the SEP refsets.

Clinical finding

New concepts for clinical findings and disorders: 1206

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 and July 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.

Total count of changes for the QI project: 

• • Stated: A total of 25508 concepts had changes made to the Stated relationships in their models. 
  • Inferred: A total of 14887 concepts affected by inferred changes.
    

Changes to 64572001 |Disease (disorder)| hierarchy - A bulk operation has been run against 17308 concepts in the << 64572001 |Disease (disorder)| hierarchy which has copied any inferred attributes into the stated view where they did not already exist.  In addition where the Proximal Primitive Parent could be correctly calculated to be 64572001 |Disease (disorder)| the existing immediate fully defined parents have been inactivated and replaced with Disease.This process brings these concepts into line with SNOMED International's Editorial Policy of using a Proximal Primitive Parent where all appropriate attributes are stated and classification ensures that the correct parents are assigned in the inferred view.   This is considered to be an efficient authoring style as the hierarchy is maintained mostly automatically by the classifier, rather than requiring authors to manually curate parent child relationships within hierarchies.

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.

Work continues 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:

• Revision of 7890003 |Contracture of joint (disorder)| - Contracture of joint and its subtypes have been remodeled to more precisely represent the anatomical structures associated with contracture.  Joint contractures are due to abnormal shortening of the soft tissues surrounding a joint as opposed to an abnormal morphology of the bony structure of a joint, so the finding site has been changed to "Structure of X joint region". This has resulted in the removal of the previously inferred parent of "Arthropathy" and replaced by "Disorder of joint region" and "Finding of joint movement".
  
• Revision of 298180004 |Finding of range of joint movement (finding) - The concepts under the subhierarchy 298180004 |Finding of range of joint movement (finding)| are being remodeled to represent the finding site of <<785818007 |Structure of joint region (body structure)| instead of <<39352004 |Joint structure (body structure)|. Range of movement of a joint region can be impacted by both bone and soft tissues, therefore the use of 39352004 |Joint structure (body structure)| was too restrictive and caused issues in other areas of the terminology.  These changes will be made over the course of two releases due to the number of affected concepts.
• Review of the hierarchy with parent concept of 432119003 | Aneurysm (disorder). It was noted that there were 4 potential ways of expressing the presence of an aneurysm:
  • Aneurysm of xxx artery
  • Unruptured aneurysm of xxx artery
  • Non-ruptured aneurysm of xxx artery
  • Nonruptured aneurysm of xxx artery
    The number of concepts using either unruptured, non-ruptured or nonruptured were 13/1/4 respectively. There are 97 'Aneurysm of xxx artery' concepts. A decision was taken to inactivate those concepts of the form 'unruptured/non-ruptured/nonruptured aneurysm of xxx artery' as duplicates and point to their 'aneurysm of xxx artery' equivalents where available and to create new concepts where they were not.

• Inactivations were made to remove many classification-derived concepts in the disorder hierarchy concerning late effect or sequela of injuries.  The naming was updated to comply with current editorial advice.  Relationships were added when possible to improve the definition of the concepts. Concepts from the injuries subhierarchy were remodeled when applicable when associated with the sequela/late effect counterpart.  Revisions will continue for the January 2020 release.

• Review of medical eponyms with Nazi affiliations. Removed references to "Wegener's" and "Reiter's" from FSNs to support a request to minimize the use of medical eponyms with Nazi affiliations. The terms were retained as synonyms for searching. From the article: "Eponyms and the Nazi Era- Time to Remember and Time for Change."

• Reactive arthritis was a synonym on two concepts:
  67224007 |Reiter's disease (disorder)|  67224007 |Reactive arthritis triad (disorder)| 239783001 |Post-infective arthritis (disorder)|.  As part of the removal of Nazi-related names, this area was reviewed:

  • Reactivated Reactive arthritis and model as a primitive with a parent of 724606001 |Peripheral spondyloarthritis (disorder)| and due to infectious disease.
  • Removed synonym of reactive arthritis from 239783001 |Post-infective arthritis (disorder)|.
  • Added Reactive arthritis as a parent of this concept.

  
  

Convergent Medical Terminologies (CMT)

New CMT concepts: 702

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

• • • • CMT Ophthalmology - 285
      • CMT Mixed Domains - 410
      • CMT Musculoskeletal - 7

Procedure Hierarchy

New concepts for procedure hierarchy: 215

• • Diagnostic imaging - 72 requests were received for new imaging procedure concepts with various imaging modalities.
    • • Plain X-ray 63 new concepts.
      • Magnetic resonance imaging 3 new concepts.
      • Ultrasound 5 new concepts.
      • Computed tomography 1 new concept.
        
        
  • Addition of 6 laparascopic pectopexy concepts.
    
    Other Content Quality Improvements:
    
    
  • Colorectal excision -changes have been made in either modeling, description, or addition of over ten procedure hierarchy concepts concerning the excision/resection of colon and/or rectum, anal anastomosis, colostomy, and/or creation of intestinal pouch.  
    
  • 80093006 |Enophthalmos (disorder)| and subtypes have been remodeled.
  • 121278003 |Drug measurement (procedure)| has been inactivated for the 2019-July Release and descendant concepts have been updated accordingly (n≈150). Because exposure to the substance being measured may or may not be due to the substance being used in a medicinal product, the grouper was inactivated as Ambiguous with Possibly equivalent to relationship to 430925007 |Measurement of substance (procedure)|.
    

  • 80 descendants of 784396007 |Graft of skin to skin (procedure)| were remodelled to fix issues identified in the previous 304040003|Skin grafting| sub-hierarchy. A consistent modelling plan with one role group was adopted and the FSN and PT terming pattern adapted to match "[skin graft material substance] to [skin structure]." Skin graft procedure concepts were updated and now use the same terming throughout. Subsumptions that were expected but previously did not exist have been achieved through the development of a sub-hierarchy 420934007 Graft of skin (substance) and 32 descendants specifically for use in these procedures. A Template is currently under development.

• • Created new and remodelled Implantation and Insertion qualifier values and procedures:
    • Inactivated: 71861002 |Implantation (procedure)| - replaced with new 782902008 |Implantation procedure (procedure)|; Retained as subtype of introduction for use with non-biological devices.
    • Created new concept: 770651008 |Insertion procedure (procedure)|.
    • Reactivated 129336009 |Implantation - action (qualifier value)| as subtype of 424832003 |Surgical introduction - action (qualifier value).
    • Made 129337000 |Re-implantation - action (qualifier value)| a subtype.
    • Made 129407005 |Grafting - action (qualifier value)| a subtype.
    • Made 129406001 |Transplantation - action (qualifier value)| a subtype.

Collaboration/Harmonization Projects

Orphanet

As a result of collaboration with Orphanet (http://www.orpha.net/consor/cgi-bin/index.php) 306 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. 

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.

Event

New concepts added: 6

Content Quality Improvement:

Sexual assault (event) - Definitions were added to some of the sexual assault concepts within the event hierarchy. Forcible sexual assault is sexual assault that involves force, threat of force, or injury. A new concept was added to distinguish sexual assault described as incapacitated when the victim is unable to give consent due to incapacitation. |Sexual assault and rape| was inactivated.

Work completed on the following Content Projects:

• • IHTSDO-1071 - 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.
    
    
    

Record Artifact

New concepts added: 7

Organism

New organism concepts added: 141

• Changes made to the organism hierarchy as result of member requests:
  Added 141 new organism concepts.
  Updated FSN (and parent) for 266 concepts resulting from taxonomic names changes.
  
  
• Clarification, simplification and correction of the top levels of the SNOMED CT Organism hierarchy to enhance accurate retrieval and aggregation of organism classes important for defining infectious disease and for laboratory findings for infectious disease:
  Upper levels of the organism hierarchy above the following three (they are at the level of "Organism" and the Domains Prokaryota and Eukaryota).
  Upper levels of the Kingdom Bacteria hierarchy.
  Upper levels of the Virus hierarchy.
  Upper levels of the Kingdom Fungi.

Pharmaceutical / biologic product

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

 Veterinary Extension

11 concepts were moved to the Veterinary Extension. 

 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_20180731.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)|.

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.

 Mapped content for July 2019

The map provided for the July 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

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

ICD-O Map

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

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

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 the Snomed CT July 2018 International edition, the following Known Issues were identified, and agreed to be resolved in the next editing cycle (to be published in July 2018):

 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 the latest release - in this case the July 2018 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 the Snomed CT July 2018 International edition can be found here:

Technical updates

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.

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.

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.

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 will deprecate 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.

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:  Early Visibility - Planned changes to upcoming SNOMED International Release packages

IMPORTANT CHANGE 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 stated relationship file will be replaced by the OWL Axiom refset files, that will include all logical definitions and other features specified in the SNOMED CT logic profile specification. The stated relationship file will NOT be included in the international release; however, it may still be available on request to support migration to the OWL Axiom refset.

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

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.