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COVID-19 Content Changes - Interim Release March 2020 (and subsequently in the July 2020 International Edition Release)

An INTERIM International Edition Release has been created as part of the ongoing global effort to tackle the Coronavirus outbreak and includes the updated Coronavirus descriptions for Members and implementers.

The full International Edition Release package containing changes to the content detailed in the news item (https://www.snomed.org/news-and-events/articles/changes-coronavirus-descriptions) under the following conditions:

1. Following SNOMED International's critical incident policy, there will NOT be a recall of the January release, simply an update in response to international renaming, to ensure that SNOMED CT is current when assisting with the global Coronavirus effort.
2. Implementers are encouraged to update to the new edition, however, they are NOT obliged to do so as the concept modelling and identifiers are not being modified.
3. The entirety of these changes will also be incorporated into the upcoming July 2020 International Edition Release.

A set of new components have been added for the March 2020 Interim release:

• • 840534001   3950925017 COVID-19 vaccination 
  • 840544004   3950926016 Suspected COVID-19 
  • 840535000   3947177019 Antibody to severe acute respiratory syndrome coronavirus 2 (substance) 
  • 840535000   3947178012 Antibody to severe acute respiratory syndrome coronavirus 2 
  • 840535000   3947179016 Antibody to SARS-CoV-2 
  • 840536004   3947180018 Antigen of severe acute respiratory syndrome coronavirus 2 (substance) 
  • 840536004   3947181019 Antigen of severe acute respiratory syndrome coronavirus 2 
  • 840536004   3947182014 Antigen of SARS-CoV-2 
  • 840539006   3947183016 Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder) 
  • 840539006   3947184010 Disease caused by severe acute respiratory syndrome coronavirus 2 
  • 840539006   3947185011 COVID-19 
  • 840546002   3947186012 Exposure to severe acute respiratory syndrome coronavirus 2 (event) 
  • 840546002   3947187015 Exposure to SARS-CoV-2 
  • 840546002   3947188013 Exposure to severe acute respiratory syndrome coronavirus 2 
  • 840533007   3947189017 Severe acute respiratory syndrome coronavirus 2 (organism) 
  • 840533007   3947190014 SARS-CoV-2 
  • 840533007   3947191013 Severe acute respiratory syndrome coronavirus 2
  • 840534001   3947192018 Severe acute respiratory syndrome coronavirus 2 vaccination (procedure) 
  • 840534001   3947193011 SARS-CoV-2 vaccination 
  • 840534001   3947194017 Severe acute respiratory syndrome coronavirus 2 vaccination 
  • 840544004   3947195016 Suspected disease caused by SARS-CoV-2 
  • 840544004   3947196015 Suspected disease caused by severe acute respiratory coronavirus 2 
  • 840544004   3947197012 Suspected disease caused by severe acute respiratory coronavirus 2 (situation) 
    
    

March 2020 Interim International Release

+ ALSO IN THE

July 2020 International Edition Release

July 2020 International Edition Release format

The current plan is to publish the formal July 2020 International Edition with the March 2020 Interim release as the official "previous published release". 

This means that all COVID-19 content published in the March 2020 release will be present in both July 2020 Snapshot and Full files, with an effectiveTime of 20200309. The Delta files will be relative to March 2020, containing only new contentfrom the July 2020 editing cycle, and will not duplicate the Delta file content from the March 2020 release.

1. For those users who consumed the March 2020 Interim Release:
   1. It causes no issues for these users who want to use either the Full, Snapshot or Delta to update to July 2020.
      
      
2. For those users who did NOT consume the March 2020 Interim Release:
   
   1. It may require some workarounds only for those users who want to use the Delta files, as they will not see the new Coronavirus content from March 2020. 
   2. They should therefore use one of the following methods to update:
      1. The best approach is to first apply the March 2020 Interim Release Delta files, and after that apply the July 2020 Release Delta files.
      2. Use the Snapshot files to update to July 2020 - this approach will also be supported going forward, for all future releases (even continuous delivery)
      3. Use a new Rollup Delta package that we will publish alongside the July 2020 Release:

         1. This July 2020 Rollup Delta package would be a separate resource with clear documentation.  It would include all changes since January 2020, with the actual, official effectiveTime. Therefore all of the new Corona content would have an effectiveTime of 20200309. The rest of the content will have an effectiveTime of 20200731.

         2. This rollup package would include instructions on how to cope with multiple effectiveTimes (per componentID), as this will be a necessary feature of rollup Delta files) - for example if a concept has been added in March 2020, and then inactivated in July 2020, both records will exist in the same Delta file for this rollup period.

         3. We may also use this Rollup package as an opportunity to trial the new proposal for the Delta file naming conventions - containing the effectiveTime of BOTH the current Delta, and also the release that the Delta is taken from - for example, if a Delta is from Jan 2020 to March 2020:
            

            1. 1.  sct2_Concept_Delta_INT_20200131_20200309.txt 

         
         

3. This proposal ensures that both deltas are consistent, and this therefore a) preserves RF2 protocols, and b) pushes forward the prep for continuous delivery.

PLEASE PROVIDE ANY FEEDBACK ON THIS PROPOSAL ASAP, IN ORDER TO FACILITATE COMPREHENSIVE PLANNING FOR THE JULY 2020 RELEASE.

Browse Content Changes for the January July 2020 Release

The daily build is available to review changes made to content for the January July 2020 release https://dailybuild.ihtsdotools.org/

Forthcoming concept inactivations, new concepts and changes to existing concepts can be reviewed using the tab 'Daily build.'

Implementation of the new anatomy concept model

The completion of the revision of hierarchical relationships provides stable anatomy content and improves the quality of classification results in other hierarchies.

Over forthcoming releases, the plan is to implement the new anatomy concept model and release the changes in January 2021. There are almost 35,000 anatomy concepts and they will be modeled by different types of 'part of' relationships. The new model will enable us to automatically generate hierarchies to further improve quality and consistency. 

Information about the work completed in previous release for

revision of IS_A relationships can be viewed here:

https://confluence.ihtsdotools.org/display/IAP/Revision+of+IS-A+relationships+for+anatomy

July 2020 International Release and future releases

Revision of the cell hierarchy

Over forthcoming releases, descendants of 4421005 |Cell structure (cell structure)| will be updated according to the SEP model.

SEP description patterns will be applied to the existing content. Descendants of 362837007 |Entire cell (cell)| will be updated to include the word ‘entire’ in all descriptions.

The semantic tag ‘(cell)’ will be changed to ‘(cell structure)’. Descriptions for the rest of the concepts will be updated to include the word ‘structure’. 

This modeling improvement will address the missing relationship between structure and entire concepts. 

Please contact info@snomed.org with any inquiries or to submit feedback.

July 2020 International Release and future releases.

MRCM Changes

Please see:

MRCM changes in for the January July 2020 release

Quality Initiative

Information about the project can found here - Quality Initiative - Progress

Note: There are changes to the Service Level Agreement for the CRS as a result of the Quality Initiative:

https://www.snomed.org/SNOMED/media/SNOMED/documents/Early-Visibility-of-Changes-to-Service-Level-Agreement-International-Content-Request-Service-(CRS).pdf

Changes to Case Sensitivity

Over 31,000 descriptions have been reviewed and approximately 5,402 descriptions across 2806 concepts have had their case significance settings corrected as appropriate.   
The changes are across all SNOMED CT hierarchies but in particular disorder concepts (1774), procedure (978) and qualifier values (736). 

The Editorial Guidance on case significance related to descriptions containing numeric values and special characters has been updated for the January 2020 release.

Top level groupers/Allergen classes in substance hierarchy

Based on recommendation by the Allergies CRG, deprecation of top level groupers/Allergen classes in substance hierarchy, which has been partially done for Jan 2019 release, will be completed for July 2020 release.

Changes to Subtypes of 419199007 |Allergy to substance (finding)

As part of the QI project review of the 419199007 |Allergy to substance (finding)| sub-hierarchy and per the Allergies CRG recommendation, the concepts in this sub-hierarchy that represent allergy to "role groupers" and "Structure + role groupers" will be inactivated starting from the July 2020 release.

A few examples of these concepts are provided below:

• • 294450008 Allergy to anthelmintic agent (finding)
  • 294461000 Allergy to antibacterial drug (finding)
  • 294869008 Allergy to anticoagulant (finding)
  • 293857007 Allergy to anticonvulsant (finding)
  • 294263000 Allergy to antidote (finding)
  • 294340008 Allergy to antifungal agent (finding)
  • 294616009 Allergy to antileprotic drug (finding)
  • 294387001 Allergy to antimalarial agent (finding)
  • 294605002 Allergy to antimycobacterial agent (finding)
  • 293739003 Allergy to antineoplastic agent (finding)
  • 293863003 Allergy to barbiturate antiepileptic (finding)
  • 294430009 Allergy to biguanide disinfectant (finding)
  • 294603009 Allergy to hydroxyquinoline antiprotozoal (finding)
  • 294991000  Allergy to thiazide diuretic (finding)
  • 293757002  Allergy to triazene antineoplastic (finding)

Content Improvements in the Substance and Product Hierarchies

Please see briefing notes here Drugs Project

Please contact info@snomed.org with any inquiries.

Content Improvements in the Physical object Hierarchy

Please see briefing notes here https://confluence.ihtsdotools.org/display/IAP/Devices+Project

Please contact info@snomed.org with any inquiries.

WAS_A

Inactivation reason of LIMITED/WAS_A is not allowed for any new content inactivations after the July 2018 release. The WAS_A association refset has not been updated thereafter.

At the Editorial Advisory Group meeting in April 2019, agreement was reached to discontinue the maintenance of WAS_A relationships when inactivating concepts that have a historical association to an inactive concept. When changes are made to a historical relationship for a concept that was previously inactivated using WAS_A, effort will be made to assign a new historical relationship that facilitates traceability of the concept (e.g. DUPLICATE or AMBIGUOUS) as opposed to NON-CONFORMANCE TO EDITORIAL POLICY.

Existing WAS_A relationships will be inactivated in a future release once a plan for batch reassignment of historical relationships has been developed. Until then, SNOMED International will not continue to use or maintain WAS_A relationships.

Known Content Issues July 2019 Release

Approximately 149 text definitions are missing either a US or GB spelling variation. These are all legacy issues that will be rectified in the January 2020 release.

A small set of disorder concepts have been identified with descendants that have a semantic tag of clinical finding. A further small set of concepts have been identified that have a semantic tag of disorder but are not descendants of 64572001|Disease (disorder)|. These concepts are all legacy issues that will be rectified in the January 2020 release.

Release validation rules have been enhanced to prevent recurrence of legacy issues for future content additions.

Changes for 'On examination' (O/E) and 'Complaining of' (C/O) conceptsJan 2020 release:

• Addition of approximately new 230 concepts to cover content identified (to date) as having no base concept.
• Continued analysis of O/E and C/O content to determine replacement content (current suitable concept, new or no value in replacing)

July 2020 release:

• Addition of any further required content
• Inactivation of the O/E and C/O content (Batch change) for return to the UK.

Content being inactivated will use the reason - component moved elsewhere. 

Note: some concepts will not have a replacement concept as they are groupers. For example:
On examination - sign irregular (finding)
On examination - neurological reflex (finding)

Inactivation of 33359002 |Degeneration (morphologic abnormality)|

In order to distinguish the degenerative process from the structure, 33359002 |Degeneration (morphologic abnormality)| has been inactivated as a DUPLICATE, SAME AS 107669003 |Degenerative abnormality (morphologic abnormality)|.

All morphologies in the disorder hierarchy have been replaced accordingly.

107669003 |Degenerative abnormality (morphologic abnormality)|

33359002 |Degeneration (morphologic abnormality)|

Inactivation of 23583003 |Inflammation (morphologic abnormality)

In order to distinguish inflammatory process from structure, 23583003 |Inflammation (morphologic abnormality)| has been Inactivated as DUPLICATE, SAME AS 409774005 |Inflammatory morphology (morphologic abnormality)|.

All concepts in the Inflammatory disorder hierarchy have been remodeled accordingly. 

IACR have released ICD-O-3.2 as a listing of all new additions, changes and revisions to ICD-O-3.1 in Excel format. The new version, ICD-O-3.2, is recommended for use from 2020.  ICD-O-3.2 is not yet available online or in book format. In preparation for the update, the changes have been divided into types and are being investigated/addressed in the ICD-O-3.2 update project. The priority is being given to those that have an impact on clinical safety, e.g., changes of behaviour (benign, malignant etc.) and adding new content for SNOMED CT morphologies, this refers to the 400177003 |Neoplasm and/or hamartoma (morphologic abnormality)| hierarchy.

The descriptions with [obs] have been inactivated as outdated because they are artefacts of descriptions from the ICD-O-3 print version for their history tracking. 

The maps to ICD-O-3.1 are being updated only for error correction purposes for the January 2020 release. The maps to ICD-O-3.2 are out of scope for the January 2020 release and are planned for a future release.

Over the Counter

Concepts referring to “over the counter” status have been inactivated. 

Concepts referring to regulatory status or characterization (e.g. over the counter) are out of scope for the International Release since the meaning may vary by jurisdiction and is not consistent internationally.

Antigens Required for the Vaccine Products

As a Vaccine project work item and based on requests submitted mutually by Argentina and Canada, new antigen concepts (~150) have been added to the Substance hierarchy to be used in the modeling of vaccine products in a future release.

Vaccine Poisoning

Concepts referring to vaccine poisoning have been inactivated from the International release and moved to the NHS extension per their request.

The notion of vaccine poisoning has persisted in ICD 10 under T50 but it is not included in ICD-11; the poisoning aspect seemingly referred to the adjuvants and carriers that are included in the vaccines as opposed to the biological component itself.

Traumatic Dislocation

Traumatic dislocation concepts are being remodeled according to the new representation using DUE TO "Traumatic event".

This work has been partially completed for the Jan 2020 release, resulting in the remaining subhierarchies moving from under "Traumatic dislocation of joint" to "Dislocation of joint". These remaining subhierarchies will be remodeled for the July 2020 release.

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.

Spinal Cord Syndrome

A new concept 840721004| Incomplete spinal cord syndrome (disorder) has been created as a grouper parent to thefour major subtypes of this syndrome:

282785008 |Anterior cord syndrome (disorder)|

27982003|Brown-Séquard syndrome (disorder)|

282786009 |Posterior cord syndrome (disorder)|

282787000 |Central cord syndrome (disorder)|

In prior releases these syndromes had been modeled with an ASSOCIATED MORPHOLOGY = 19130008|Traumatic abnormality (morphologic abnormality)|; however, these syndromes may present due to non-traumatic etiologies such as space filling lesions (tumors, etc.) or vascular compromise (occlusions, ruptures, etc.).

These syndromes have been remodeled with ASSOCIATED MORPHOLOGY = 52988006|Lesion (morphologic abnormality)|.

Incomplete cord syndromes with a traumatic cause have been remodeled to specifically represent773760007 |Traumatic event (event)| as the DUE TO value as well as any other relationships to describeassociated disorders (e.g. fractures or dislocations).

Other Occupations

Concepts representing "other" occupations e.g. 79445009 |Other clerk (occupation)| have been inactivated for the July 2020 release as these represent classification constructs.

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

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

• SNOMED DL Profile Enhancements
• SNOMED CT Logic Profile Specification
• SNOMED CT OWL Guide (OWL Refsets specification)
• 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

For any questions, please contact SNOMED International at support@snomed.org with “OWL Axiom refset files implementation question” in the subject line.