The Concept

2018 Q3 Newsletter

The Content and Mapping team has had a busy and productive year as we make significant headway on a number of initiatives and work plan deliverables for 2018.
 
Before I specifically address these achievements, I would like to first convey my deep thanks and appreciation to my team who continually strive for the best possible results, are dedicated to our due diligence in achieving best quality outcomes and who always have international impact and the greater good in mind at the core of what we produce. Further recognition is owed to SNOMED International’s Technical Services team who take meticulous care in delivering functionality, analysis, scripts, reports and queries, always showing patience when we ask "Can you run that again?".  As well, a very special thank you to Dr. Jim Case for his continued support providing immeasurable guidance, value and direction to our staff and the success of SNOMED CT.
 
While you may hear me speak about delivering against initiatives and work plan items, of significance to note is that SNOMED International’s content and mapping activities are guided by a principle of continuous improvements. Regardless of ongoing projects or Quality initiative, every release cycle addresses the quality of content in SNOMED CT, with improvements seen each January and July.

Commitment to Requests
 
For each release, the organization maintains a commitment to the number of content requests it accepts and addresses. In the July 2018 release, the content team surpassed its targeted goal of 95%, with 99% of content requests received addressed.
 
In January 2018, as a necessary measure of actioning the Quality Initiative, the organization notified stakeholders that the service level agreement for the year would only include work that addresses a clinical critical need. However, taking on new ways of managing our work along with the ability of the team to adopt a flexible approach, we’ve been able to address the majority of requests for the January 2019 release.  The restrictions on the service level agreement will stay in place and we hope to continue to have progress as we address other priority demands.

Commitment to Quality
 
Since the January and July 2018 releases, and inclusive of January 2019 work to date, we’ve seen an encouraging 34% quality improvement to the core product. This number is representative of additions, modifications, description updates, and primitive to sufficiently defined concepts providing impacts on improved quality and overall concept growth. 

The scope of the Quality Initiative project is to address the majority of Structural Quality issues while addressing critical clinical errors as identified. Structural quality involves the internal structural consistency and compliance with editorial policy related to the stated modelling of content. As part of the Quality Initiative, a new concept model needs to be applied to the existing content using template-based transformation. While this applies to much of SNOMED CT, there remains concepts that are not applicable to template use. Only those with a model are in scope for the totality of the QI project touching approximate 90% of the approximate 349K concepts held in the International core.
 
The first area of focus was identified as Clinical Findings, being the broadest and most used area covering over 33% of SNOMED CT. Important to understand about this project is that once we correct one area, it subsequently corrects or identifies other areas, which require logical and or clinical corrections.  

For the initial first level hierarchy 404684003|Clinical finding (finding)| there are around 112,999 clinical findings and disorders. Of the 112,999 concepts there are 7014 which have no model (ie no inferred attributes) and are therefore out of scope. The remaining 105985 will be reviewed and remodelled in 2 phases, Simple and Complex. We have also commenced work on the 37 manageable sub-hierarchies containing 34543 concepts within the simple and co-occurrence categories within defined phase 1 scope.

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Major Projects
 
There is substantial work underway in a number of SNOMED CT areas.  

Content Quality Improvements

  • For the January 2018 release, the synonym of "occlusion" was inactivated from 26036001|Obstruction (morphologic abnormality) and added to 50173008|Complete obstruction (morphologic abnormality). 415582006|Stenosis (morphologic abnormality)| became a descendant of 25659002|Narrowed structure (morphologic abnormality). These changes resulted in a further 133 released concepts being reviewed and/or changed for the July 2018 release.
  • Added a new sufficiently defined concept of 763597000|Hereditary ataxia (disorder)| resulting in changes to 40 concepts.
  • Hierarchy review/remodel descendants of 248595008|Sputum (finding)| with changes to 59 concepts.
  • Review/remodel "Progressive" disorders with changes to approximately 200 concepts.  A new clinical course qualifier value has been created: 255314001|Progressive (qualifier value)| as a subtype of 90734009|Chronic (qualifier value)|. Can be used to fully define progressive disorders using 246454002|Occurrence (attribute)| = progressive (qualifier value)
  • Review/remodel of "Acquired" disorders with changes to 697 concepts. A new period of life has been created: 767023003|Period of life beginning after birth and ending before death (qualifier value)|. This allows for a distinction to be made between acquired vs. congenital concepts and also permits existing ‘acquired’ concepts to be sufficiently defined.
  • Addition of Bipolar disorder concepts which include the most recent episode information.
  • 36 new concepts added for genetic diseases which were not part of the Orphanet project.
  • Remodelling and re-terming of 110288007 |Joint tenderness (finding)|. Redefined Joint tenderness as IS_ A Tenderness (finding) + finding site=joint structure and all of the specific joint tenderness concepts using the same pattern. Renamed all joint tender(ness) concepts as Tenderness of x joint (finding).
  • Inactivated 202936005 |Ganglion and cyst of synovium, tendon and bursa (disorder) and used an analogous approach to inactivate the descendants with new replacement concepts.
  • Remodel 63491006 |Intermittent claudication (finding)| hierarchy. Added due to 86341008 |Vascular insufficiency (disorder)|. Removed parent of 22253000 |Pain (finding)| and added parents of 427935006 |Pain relief by rest (finding)| and 427341007 |Pain provoked by exertion (finding)|.
  • Review and remodel 11 viral disorder and related concepts.
  • 45 new clinical finding/disorder concepts added for Dentistry.
  • Inactivated out of scope |Allergy to X (disorder)| concepts, as identified by the Allergy/Hypersensitivity and Intolerance Clinical Reference Group.
  • Review and remodel of 520 fracture of lower limb concepts using a proximal primitive parent and creating stated defining relationships for those which were previously inferred relationships.
  • Intussusception disorder concepts were remodelled using the proximal primitive parent modelling approach with two relationship groups capturing the invagination and obstruction morphologic abnormalities of this disorder. The concept Intussusception (morphologic abnormality) was inactivated as a duplicate of Invagination (morphologic abnormality).
  • Machine Readable Concept Model (MRCM) -14 new MRCM rules and 10 updates to the existing MRCM in the MRCM refsets and authoring platform.
  • Veterinary Extension -15 concepts were moved to the Veterinary Extension.
  • Situation with Explicit Context New concepts added 64,143 concepts using the pattern 'OFFERED' or 'NOT OFFERED' were inactivated. Addition of new concepts for transplant donor and recipient Epstein Barr virus status. Work continuing on IHTSDO-703 Inactivation of 'unilateral' concepts. Work on the inactivation of unilateral concepts and the creation of left and right replacement concepts continue.
  • Social Context 26 new concepts were added as a subtype of 14679004|Occupation (occupation)|.
  • Assessment Scale - Review of 11 of assessment scale concepts for duplicates or correctness. Addition of 96 assessment scale, observable entity and procedure concepts to support use of assessment scales.

Anatomy

One subproject of the Anatomy project is to revise inferred IS A relationships in production of the body structure hierarchy. The revision is based on the inferred relationships from the new anatomy concept model in MySQL, OWL and Protege.

The target for the January 2019 release of the implementation of corrected areas of musculoskeletal systems 26107004|Structure of musculoskeletal system (body structure) which comprises 33% of the overall scope. Cardiovascular (113257007|Structure of cardiovascular system (body structure)|) is also in progress and will near completion this year with implementation in the following release.

Progress on the initial review of all IS A in the Anatomy relationships hits at the 80% mark (10,026) with changes in production sitting at 62%, (3,869) followed by an impact review at 40%(6,997), the fourth measure, a second impact review after production is completed at the final task. During this review, we also made changes in Clinical Content modeling to improve the quality.

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Convergent Medical Terminology

The scope of the project covers all content donated for review by Kaiser as part of the Convergent Medical Terminology (CMT) agreement. All content suitable for inclusion into the International Release will be accepted, with the remaining content referred to the NLM for inclusion into the US Extension.

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Orphanet

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Pharmaceutical/Biologic Product

At start of this project we assessed the 373873005 |Pharmaceutical / biologic product (product)| descendants (n≈17,500) as having primitive concepts, incomplete and inconsistent modeling and terming, and identified out of scope concepts. Nearing the conclusion of the project we have descendants (n≈22,500), including 763158003 |Medicinal product (product)| descendants (n≈18,800) seeing now sufficiently defined concepts conforming to editorial guidelines including proximal primitive modeling pattern and templated modeling and terming. Below we can provide an overview for interest, additional areas with defined scope include; Allergen extract and patch test products, Blood products, Clinical drug gap analysis, Dietary products, Reference set development, and Vaccines.

Review the topic, key deliverables, and status of applicable products here.

Substances

The main focus has been on flattening of the Substance hierarchy, as well as assignment of structural parents and dispositions to substance concepts. New structural and disposition groupers are being created as required. Priority has been given to the remodelling of substances associated with the definition of medicinal product concepts. Work in other areas, including review of INN/US/GB alignment (required for tool automation), case sensitivity assignments, duplicate synonyms, and fixing spelling errors are in progress. The project is also assisting the Allergies project in resolving dependency and clarification issues.

Read all Substances highlights here.

For 2019, scope of work includes:

  • Flattening of Substance hierarchy
  • Regular maintenance of substance hierarchy - Add missing structural parents and Disposition and Structure groupers
  • Review of the remaining existing JIRA tickets for Substance project
  • Review of the existing JIRA tickets for Allergies project
  • Replace Substance concepts with product concepts, where role concepts have been used to define procedures or findings
  • The retirement of role concepts
  • Gap analysis on selected national extensions Substances to support the product Active ingredients not in SNOMED - RxNORM, AM

SNOMED CT derived products

ICD-10 map
  • 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.
  • The map provided for the July 2018 release has been updated, and now represents a complete map from SNOMED CT International release to ICD-10 2016 version.1278 2092 new concepts added.
 
ICD-O map
  • There are 5 updates for the ICD-O Morphological abnormality map in July 2018 release.

Last, but certainly not least, in addition to the SNOMED International Edition, the following releases are now available

  • SNOMED CT Nursing Activities refset package – Production release now available
  • SNOMED CT Nursing Health Issues refset package – Production release now available
  • July 2018 SNOMED CT General Dentistry Diagnostic refset package Production release
  • SNOMED CT Odontogram refset package
  • The production release of the GMDN Linkage Table
  • July 2018 ICNP to SNOMED CT (Interventions) package Production release now available
  • July 2018 ICNP to SNOMED CT (Diagnoses) package Production release now available
  • July 2018 GP/FP SNOMED CT Reference Sets and SNOMED CT to ICPC-2 Map Production

More information on the 2018 advancements made in these and other projects, as well as plans for 2019 can be found here. Also please keep a close watch on the Early Visibility page for advanced notice of potentially impactful changes.
 
It’s been a privilege working with exceptional contributors, partners, and internal teams to continue the representative nature and overall quality of SNOMED CT.

For more information on SNOMED CT, the Quality Initiative and our approach to content, please contact us at info@snomed.org.  
 

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