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Improvement to the Release file naming convention for the Asssociation Reference file

In order to improve the description of this file, we will be updating the file naming convention from:

'der2_cRefset_AssociationReferenceSnapshot_INT_*.txt'

to:

'der2_cRefset_AssociationSnapshot_INT_*.txt'

....as of the January 2018 International Edition

January 2018 International Edition - COMPLETE
ItemsProposed improvement

Planned Release date

(*this is provisional only and is subject to change)

1LOINC timeline changes - please refer to Roadmap link here LOINCJuly 2018 and potentially other future releases .- On hold
2

Revision of IS A relationships for anatomy concepts 

The new anatomy concept model has implemented the new enhanced Description Logic features, e.g. reflective reflexive and transitive propertyproperties, general concept additional axioms, for consistent logical modeling. However, the new model cannot be implemented in production because these DL features currently are not available in production. The implementation of them will depend on the enhanced logic profile for SNOMED CT which is under development by the Modeling AG. Yet, the inferred IS A relationship The inferred IS A relationships from the OWL anatomy ontology can be have been reviewed and the changes have been implemented in the production. This will utilise the outcomes of the new anatomy model as well as evaluate the design of the new model. In particular, it is important to review the changes of IS-A relationships in anatomy for quality assurance and minimise  The potential impact to other hierarchies, such as disorders, procedures, observables, situations etc are also reviewed as part of the project.

The first subject area for revision is the revision of sub-hierarchy of skin structure. The majority changes have been made in the January 2018 26107004|Structure of musculoskeletal system (body structure)| has been planned for the January 2019 release. The rest body systems will be completed in July 2018 release.revised in the future releases.

The For July 2018 release, the subject area for revision of IS A relationships will be determined and updated in the following confluence page.

July 2018 January 2019 International Edition
3

Summary of Drugs changes

Groupers Chemical structure

  • Most existing concepts remodeled, with modeling and terming updated per editorial guidelines
  • Top level groupers 763760008 | Medicinal product categorized by structure (product) and 767102007 | Medicinal product categorized by chemical element (product) created; this is an incremental improvement and there may still be missing subtypes

Groupers Dispositions

  • Most existing concepts remodeled, with modeling and terming updated per editorial guidelines
  • Top level grouper 766779001| Medicinal product categorized by disposition (product) created; this is an incremental improvement and there may still be missing subtypes

Groupers Intended site

  • All existing concepts remodeled, with modeling and terming updated per editorial guidelines

Medicinal product (MP)

  • Most existing concepts remodeled (>3400), with modeling and terming updated per editorial guidelines
  • Semantic tag updated to (medicinal product)
  • Terming update to include "product" in Preferred Terms in progress but not visible in alpha release 

Medicinal product form (MPF)

  • Most existing concepts remodeled (>1300), with modeling and terming updated per editorial guidelines
  • Semantic tag updated to (medicinal product form)

Clinical drug (CD)

  • Existing concepts are in the process of being remodeled and are not ready for review at this time
  • Preview of these concepts will be made available at a later date

Pharmaceuticaldose form

  • Most existing concepts remodeled, with modeling and terming updated per editorial guidelines
  • Semantic tag updated to (dose form)

General

The Alpha Release is a snapshot of the work-in-progress authoring environment; not all concepts are in scope for review at this time. Feedback given for concepts noted as out of scope will be rejected.

For drugs:

  • Review should be limited to sufficiently defined inferred descendants of 763158003 | Medicinal product (product)
  • Primitive concepts are out of scope for review
  • Concepts with semantic tag (clinical drug) are out of scope for review
  • Concepts with semantic tag (product) and containing product strength are out of scope for review

For dose forms:

  • Review should be limited sufficiently defined inferred descendants of 736542009 | Pharmaceutical dose form (dose form)
  • Primitive concepts are out of scope for review
  • Concepts without semantic tag (dose form) are out of scope for review
  • Documentation:
  • Editorial Guide draft version for the Medicinal Product Hierarchy available for review
  • Editorial Guide draft version for the Pharmaceutical Dose Form Hierarchy available for review

Briefing

Briefing note - Use of Additional Axiom Functionality and Remodeling Product Roles.pdf

(disposition, structural)

  • Preferred terms updated for existing concepts (n≈500)
  • Synonyms matching FSN removed for existing concepts (n≈500)

MP-containing

  • Preferred terms updated for existing concepts (n≈3800)
  • Synonyms matching FSN removed for existing concepts (n≈3800)

MP-only New concepts created (n≈3800)

MPF-containing

  • Preferred terms updated for existing concepts (n≈2800)
  • Synonyms matching FSN removed for existing concepts (n≈2800)

MPF-only New concepts created (n≈2800)

Clinical drug Synonyms matching FSN removed for existing concepts (n≈4900)

Role:

  • New additional axioms to model therapeutic role (n≈TBD; currently expect hundreds)
  • Populated new 766941000 |Therapeutic role (role)| hierarchy (n≈TBD; currently expect hundreds)
  • Created new 773830008 |Consumer product (product)| hierarchy as sibling of 763158003 |Medicinal product (product)|. Relocated descendants of 763087004 |Medicinal product categorized by therapeutic role (product)| as appropriate (e.g. Aftershave, Deodorant, Perfume) (n≈25)
  • Inactivated role concepts representing body site or body system (e.g. Gastrointestinal drug, Genitourinary drug) (n≈15)
  • Relocated 43747001 |Drug excipient (product)| as sibling of 763158003 |Medicinal product (product)|. Relocated descendants of 763087004 |Medicinal product categorized by therapeutic role (product)| as appropriate (e.g. Drug additive, Drug flavoring) (n≈15)

New semantic tags, attribute and hierarchies added and MRCM change made to support National Extension Model.

  • New top level concept added (for use by national extension model but not for International Release)
    • 781405001 |Medicinal product package (product)| 
  • New semantic tags added (for use by national extension model but not for International Release)
    • (product name)
    • (packaged clinical drug)
    • (real clinical drug)
    • (real medicinal product)
    • (real packaged clinical drug)
    • (supplier)
  • New attributes added (for use by national extension model but not for International Release)
    • 774158006 |Has product name (attribute)|
    • 774159003 |Has supplier (attribute)|
    • 774160008 |Contains clinical drug (attribute)|
    • 774161007 |Has pack size (attribute)|
    • 774163005 |Has pack size unit (attribute)|
  • New hierarchies added (for use by national extension model but not for International Release)
    • 774164004 |Supplier (supplier)|
    • 774167006 |Product name (product name)|

Updated briefing: Briefing note - Implications of describing liquid dose form product concepts using presentation strength.pdfv2, can be found on second table of this page Reference Documentation - Drug Model

January 2019 International July 2018 International Edition
4

Summary of Substances Changes

Top Level

  • Allergen class subhierarchy. The work to inactivate the allergen class subhierarchy has not yet started and so will not be evident in the Alpha release data. It is anticipated that the initial work on this will be evident in the July 2018 release.
  • Dietary subhierarchy. To remove context of use from the substance concepts and manage the situation where substances can be both a pharmaceutical ingredient and a foodstuff 80 substances that had a tag of “- dietary” in the Fully Specified Name (FSN) and the Preferred Term (PT) were inactivated. Replacement concepts concept without  "-dietary" in the FSN and PT were created. The top level concept "Dietary substance (substance)" has been inactivated and replaced with a new concept "Edible substance (substance)".
  • Radioactive isotope substances. These concepts have been remodelled and the terming normalised to provide consistent representation without the use of carats.
  • Cancer related substance. The subhierarchy has now been removed. Some concept have been inactivated. Some have been moved within the substances hierarchy.

Disposition groupers

  • Disposition groupers within the substance hierarchy have been modelled as fully defined concepts. The creation of the new top level substance concept of "Substance categorised by disposition" will allow these to be modelled by proximal primitive authoring.
  • Existing disposition grouper concepts in the substances hierarchy have been retained where appropriate and have been remodelled to conform to SNOMED CT Editorial policy. Examples as below.
    •  Substance with angiotensin-converting enzyme inhibitor mechanism of action (substance)
    •  Substance with beta-1 adrenergic receptor agonist mechanism of action (substance)
    •  Substance with phosphodiesterase inhibitor mechanism of action (substance)
  • Currently there are in excess of 200 disposition groupers in the substances hierarchy that have been remodelled.
  • Work to remodel existing substance disposition groupers is ongoing.
  • New concepts will be added as identified.

Role groupers

Role groupers within the substances hierarchy are being inactivated where this is possible without creating disruption in other hierarchies. At the start of this work there were approximately 600 role groupers. Currently in the region of 100 role grouper substance concepts have been inactivated or remodelled.This work is ongoing.

Many of these role grouper concepts remain in the substances hierarchy pending a solution for the roles concepts within the terminology as a whole and so will still be present in the July 2018 release.

Structural groupers

Structural groupers within the substance hierarchy have been modelled as primitive concepts.

Existing structural grouper concepts in the substances hierarchy have been retained where appropriate and have been remodelled to conform to SCT Editorial policy.

New structural grouper concepts have been added.

Groupers that identify X or derivatives where X is a specific substance will be inactivated. Some of these concepts have already been inactivated. As the implementation of the IS Modification attibute is carried out the remainder of these concepts will be inactivated.

Structural groupers that reference a chemical group will be retained.

e.g. Amides and derivatives (substance)

Where the structural group name also refers to a specific chemical the grouper has been re-termed “Substance with X structure” 

e.g. Substance with tetracycline structure (substance)

Combined groupers

Combined groupers that include a role will be inactivated where this is possible without causing disruption in other hierarchies. Inactivation of some of these concepts in the substances hierarchy is waiting on a solution for the roles concepts within the terminology as a whole and so will still be present in the July 2018 release.

Groupers of disposition + structure will be retained in the substance hierarchy. Existing concepts have been remodelled to conform to SCT Editorial policy. Examples as below.

Antimony compound with antiprotozoal mechanism of action (substance)

Quaternary ammonium compound with anticholinergic mechanism of action (substance)

Piperidine derivative with histamine receptor antagonist mechanism of action (substance)

New concepts will be added as required.

Use of the Is Modification attribute

The implementation of the IS Modification attibute has been started. This has achieved a flattening of the substance hierarchy. Priority has been given to the remodelling of substances associated with the medicinal products. This work is ongoing.

The following guidelines have been developed.

1. Substances may have zero to many Is modification attribute(s). e.g  Iodine (131-I) labelled monoclonal antibody (substance) has 2 IS MODIFICATION attribute values.

2. Salts have a IS MODIFICATION relationship to the base e.g. Doxepin hydrochloride (substance) IS MODIFICATION of Doxepin (substance)

3. Hydrates have a IS MODIFICATION relationship to the unspecified salt e.g. Caffeine hydrate (substance) IS MODIFICATION of Caffeine (substance)

4. Anhydrous salts have a IS MODIFICATION relationship to the unspecified salt e.g. Theophylline anhydrous (substance) IS MODIFICATION of Theophylline (substance)

5. Stereoisomers are subtypes of the unspecified substance. e.g.. Dextrothyroxine IS A thyroxine. 

6. There is no IS MODIFICATION relationship between stereoisomers.

Further guidelines will be added to the published documentation as they are developed.

The initial population of the IS MODIFICATION attribute is still subject to manual authoring input to ensure compliance to Editorial guidelines and so some areas of content may appear to be non-conformant in the Alpha release data.

July 2018 International Edition
5

Internal QA

Test and procedure status: Inactivated 143 concepts in the Situations and Findings hierarchies with pattern "Test/procedure OFFERED" and "Test/procedure NOT OFFERED" as these represent an administrative status.

6

Internal QA

Inactivation of Agencies and organizations (qualifier value) and subtypes: moved to UK extension i.e. 66 concepts inactivated.

7

Improvement to the Release package naming convention

In order to ensure that the status of each package is correctly identified, we will be capitalising the third element of the naming convention. For example therefore, instead of the January 2018 International Edition release package being called:

SnomedCT_InternationalRF2_Production_20180131T120000Z.zip

It will instead be called:

SnomedCT_InternationalRF2_PRODUCTION_20180131T120000Z.zip

Alpha/Beta releases will be called:

SnomedCT_InternationalRF2_ALPHA_20180131T120000Z.zip

SnomedCT_InternationalRF2_BETA_20180131T120000Z.zip

This should have no impact on most users, this is provided for visibility of anyone who's upload routine might be case-sensitive.

January 2018 International Edition - COMPLETE

    • Flattening of Substance hierarchy: Implement/updated “Is modification” attribute where applicable
    • Regular maintenance of substance hierarchy:
      • Add new substances required for creation of new medicinal products
      • Add new dispositions and structural grouper concepts to model existing content
      • Update modelling for existing concepts by adding "has disposition" where applicable
    • Improve substance concepts in the areas of 
      • Updating case sensitivity based on editorial guidelines
      • Alignment to the International Nonproprietary Name
    • Changes in the substance hierarchy as the result of Allergy project requirements:
      • Inactivate top level groupers/Allergen classes in substance hierarchy by reassigning their children to appropriate structural and/or functional parents:
        • 414052000 | Drug allergen by structure |
        • 414058001 | Drug pseudoallergen by function |
        • 414057006 | Drug pseudoallergen |
        • 414053005 | Drug allergen or pseudoallergen |
      • Inactivate “Allergy to X” concepts where X is a modification of a base substance and replace it with Allergy to the base substance
January 2019 Release
5

Remodeling of hypersensitive conditions

  • Immunoglobulin E-mediated allergic contact hypersensitivity process (qualifier value) and Non-immunoglobin E-mediated allergic contact hypersensitivity process (qualifier value) have been created.
  • Hypersensitivity, allergy and pseudoallergy condition classes will be moved under 404684003 |Clinical finding (finding)| and modeled using GCIs in order to encompass allergic disorders, dispositions and processes (reactions).
  • Hypersensitivity, allergy and pseudoallergy dispositions (the latter renamed as Non-allergic hypersensitivity based on feedback from the Allergy CRG) will be moved under 404684003 |Clinical finding (finding)| and remodeled using proximal primitive parents with a role group consisting of 719722006 |Has realization (attribute)| with a value of 472963003 |Hypersensitivity process (qualifier value)| or an appropriate subtype and a causative agent relationship to a substance and follow a naming pattern of Hypersensitivity/Allergy/Non-allergic hypersensitivity to X (finding).
  • 414029004 |Disorder of immune function (disorder)| will be remodeled and fully defined using a pathological process of 769247005 |Abnormal immune process (qualifier value).
  • A new hierarchy of Intolerance to substance (finding) will be created.

Hypersensitivity, allergy and pseudoallergy condition are modelled by general concept inclusion (GCI) axioms. The relationships in the GCIs are sufficient conditions which are excluded from the inferred relationships. The GCIs in the OWL axiom refset must be used with stated relationship file to enable correct classification for hypersensitivity conditions.

In addition to the changes to the concept model, the FSNs and Preferred terms will be updated to ensure consistent description patterns. The changes are word order in descriptions and they do not change the meaning. For example, Amoxicillin allergy (disorder) would be changed to Allergy to amoxicillin (disorder).

changes in the substance hierarchy as the result of Allergy project requirements (Allergies-30 and Allergies-32):

  • Inactivate the following two top level groupers/Allergen classes in substance hierarchy by reassigning their children to appropriate structural and/or functional parents :
    • 414052000 | Drug allergen by structure |
    • 414058001 | Drug pseudoallergen by function

6

Summary of Organism Changes

  • Improve Organism concepts by
    • Applying consistent case sensitivity to organism descriptions containing "Taxon Rank"
    • Fixing spelling mistakes in FSN and synonyms
  • Correct Influenza virus descriptions
January 2019 Release
7

Quality improvements on Clinical Findings

  • 125666000|Burn
  • 416462003|Wound (including closed and opened wound)
  • 125605004|Fracture of bone
  • 34014006|Viral disease
  • 95896000|Protozoan infection
Jan 2019 International Edition
8

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.

July 2018 International Edition
9

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 of the Release Notes for the relevant link.

July 2018 International Edition
10

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

Following the feedback, the normal stated relationship file will still be available in the January 2019 release package and the partial OWL axiom refset will include all description logic features that cannot be represented in the stated relationship file.

The complete OWL axiom reference set, which includes all logical definitions and the enhanced DL features, will be available on request in the January 2019 release.

In the July 2019 release, the stated relationship file will be replaced by the complete OWL Axiom refset file. 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.

Note
titleIMPORTANT NOTE FOR USERS
Users should carefully analyse any potential impact to their systems (upload routines, etc) and make provisions for these changes urgently (if not already done), in order to prevent any issues when these changes come into effect in January 2019.  Please contact SNOMED International at support@snomed.org with “OWL Axiom refset files implementation question” in the subject line.    

  

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. 


8January 2019 International Edition