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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

New hierarchies 766940004 | Role (role) and subhierarchy 766941000 | Therapeutic role (role) created with additional subtypes to be added in future releases

New semantic tags (role)

Attribute types New attributes created:

  • 766953001 |Count of active ingredient (attribute)|
  • 766954007 |Count of base and modification pair (attribute)|
  • 766952006 |Count of base of active ingredient (attribute)|
  • 763032000 |Has unit of presentation (attribute)|
  • 766939001 |Plays role (attribute)|

Grouper concepts representing disposition, intended site, and/or structure Grouper concepts representing disposition, intended site, and/or structure sufficiently defined by modeling to proximal primitive concept, adding defining attributes, and updating descriptions per editorial guidelines (n≈550).

New high level grouper concepts created as an incremental improvement with additional subtypes to be added in future releases:

  • 766779001 |Medicinal product categorized by disposition (product)|
  • 763760008 |Medicinal product categorized by structure (product)|
  • 767102007 |Medicinal product categorized by chemical element (product)|

Groupers (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
Product role concepts Concepts representing product role relocated as stated
  • descendants of 763087004 |Medicinal product categorized by therapeutic role (product)
with definition status = primitive and attributes inactivated (n≈ 400)
  • | 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:

For further details see Briefing Note Use of Additional Axiom Functionality and Remodeling Product Roles

Medicinal product (MP) concepts - MP-containing concepts sufficiently defined by modeling to proximal primitive concept, adding defining attributes, and updating descriptions per editorial guidelines (n≈ 3750). Includes the following attributes:

  • Has active ingredient (n≈4650)

Medicinal product form (MPF) concepts - MPF-containing concepts sufficiently defined by modeling to proximal primitive concept, adding defining attributes, and updating descriptions per editorial guidelines (n≈2100). Includes the following attributes:

  • Has active ingredient (n≈2400)
  • Has manufactured dose form (n≈2150)

Clinical drug (CD) concepts - CD-containing precisely concepts sufficiently defined by modeling to proximal primitive concept, adding defining attributes, and updating descriptions per editorial guidelines (n≈ 4850). Includes the following attributes:

  • Count of base of active ingredient (n≈4850)
  • Has basis of strength substance (n≈5600)
  • Has concentration strength denominator unit (n≈1450)
  • Has concentration strength denominator value (n≈1450)
  • Has concentration strength numerator unit (n≈1450)
  • Has concentration strength numerator value (n≈1450)
  • Has manufactured dose form (n≈4850)
  • Has precise active ingredient (n≈5550)
  • Has presentation strength denominator unit (n≈4750)
  • Has presentation strength denominator value (n≈4750)
  • Has presentation strength numerator unit (n≈4750)
  • Has presentation strength numerator value (n≈4750)

Documentation Notification for Briefing Notes, Editorial Guidelines, and other documentation updates are posted on the project group website as they become available; see Drug Model Working Group - Directory for details

Briefing

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

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

  • 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.

Substance groupers including Disposition, Structure and Combined groupers have been remodelled and additional grouper concepts created as required. The inactivation of role groupers in the substances hierarchy has been initiated.

Disposition Groupers had been updated, modeled and fully defined in Jan2018 release. Just under 50  additional Disposition concepts have been created in the July 2018 data.

  • Existing Disposition groupers for substances have been remodeled in the July 2018 data.
  • Additional Disposition Groupers for substances have been created. A total of approx. 300 Disposition grouper substances.
  • A new substance top level concept of “Substance categorized by disposition (substance)” has been created to allow substances with dispositions to be modeled as proximal primitive.

Structural Groupers have been retained as primitive concepts.

  • Additional Structural Groupers have been created. Approx 20.

Chemical element groupers Inactivated and recreated to avoid the use of AND/OR and provide consistent modeling.

Combined Groupers (Structure + Disposition) be have been remodeled in the July 2018 data

The "Is modification" of attribute has been implemented resulting in a to flattening of the substances hierarchy.

Role Groupers in the substances hierarchy have been reviewed. In the region of 100 substance Role grouper concepts have been inactivated and others replaced. This work is ongoing. The retention of some role based groupers in the substances hierarchy means that some substances are not classifying correctly.

General content updates

  • Radiopharmaceutical concepts have been remodelled and the terms updated to provide consistent representation of these concepts.
  • Dietary subhierarchy. To remove context of use from the substance concepts 80 substances inactivated. In some instances replacement concepts have been created without  “ – dietary” tag. The concept “Dietary substance (substance)" has been inactivated and replaced with a new concept "Edible substance (substance)“
  • Overall 447 new concepts added to the substances hierarchy. Just over 460 substance concepts have been inactivated in the release.

Documentation Notification for Briefing Notes, Editorial Guidelines, and other documentation updates are posted on the project group website as they become available; see Project Status Substance Hierarchy for details

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