2021-10-20 Full MAG Meeting (Conf call)

Meeting Introduction

@Peter Williams

10

Start recording

Summary of previous meeting : 2021-04-19 Full MAG Meeting (Conf call)

New MAG Members:

• Francisco Sanchez Laguna, Spain's GA Rep.   

• Marcelo Carrascal, Argentina 

• Saranya Raviprakash, India NRC

Thanks to MAG Members rolling off - Harold Solbrig and Brandon Ulrich!

Review ECL 1.7 Proposal

@Former user (Deleted)

20

ECL 1.7 Adds support for including results from historical associations (so the targetComponentId, or in the case of a map, the mapTarget) . This is somewhat in line with our work in Historical Analytics

2021-10-07 - SLPG Meeting  See also http://snomed.org/ecl

Comments:  BU: Timeline - Linda hoping to have syntax out by the end of the year.

AP: Query about more complex ECL.   Answer is that HISTORY (in curly braces) will apply to the whole results of the expression by default

GR: Very much in agreement.   Concern about content eg WAS_A where they meant different things at different points in time.  WAS_A was often the stated parent rather than inferred.   Linda responded that they've been talking to the Historical Inactivation Subgroup.

ML: Question about transitivity.  PW said that historic associations are maintained and replaced as required such that the target is always an active concept so transitivity should not exist (or this will be the case after a small amount of data clean-up!)

JS: Performance impact.  KK was reasonably confident that performance would be acceptable with no impact to existing queries.

Proposed new Map Refset

@Former user (Deleted)

20

Redesigning Map Reference Sets to Support Maps in Either Direction

Comments:  KWF : Useful to avoid confusion.   A lot of meaning is being stored in the map type name.   Suggested super-set format where fields could be left unpopulated where not required. LB didn't think that empty fields would improve understanding.

GR: RF1 at least had metadata to say what the code systems being mapped were.  Mechanisms were not included in RF2 due to time pressures.   This is a specific fix for Medra but is not building extensibility into the solution.   Ways to express things like mapping to expressions and so on.   Next Generation mapping mechanism is required.

LB Suggestion to discuss broader refset extensibility in future meetings.

Concrete Domains

@Peter Williams

@Yongsheng Gao

5

Any final comments - experience of implementation?

GR: Used in several drug extensions, no issues (>20K concepts) also performance fine.

ML: Update AU Tooling while retaining backward compatibility, very smooth.

Issues with decimal places.  Potential classifications issues with 5.0 and 5 not being considered equivalent (although the Snowstorm ECL implementation would see these as mathematically equal).

DMc: Human rendering a separate question from storage and computation.

SNOMED CT representation of annotation properties and values

@Yongsheng Gao

30

Please add comments to SNOMED CT Annotations  

ML: Current approach to annotations is to formally define a new reference set.   Being able to add new annotations just by creating a new attribute seems less disciplined.  Eg inactivation reason exists as a small enumerated type which are concepts and therefore have translations and so on.

GR: Disagreed with language tag, need to find internationalization option.   Also issues with including HTML eg carriage returns.

DK: Important to allow population of OWL with correct syntax.

Alignment with BFO

@stefan.schulz (Unlicensed)

@Former user (Deleted)

1

Publication still dependent on sample concept discussion (with comparison to modelling patterns of other disease / phenotype ontologies). This is being prepared by the coauthor Catalina Martínez-Costa. Stefan Schulz presented some elements of the BFO alignment work in a keynote speech at ICBO & FOIS ("SNOMED CT x BFO: can the gap between legacy terminology and foundational ontology be bridged?"). Feedback from BFO people was positive and the effort of SNOMED becoming more "ontological" was generally acknowledged.

Slides and recordings available: [pdf] [mp4] 

Historic Analytics

@Peter Williams

@Former user (Deleted)

1

Historical Analytics

Module Dependency Refset

@Peter Williams

@Andrew Atkinson

20

The Core is dependent on the Model Module, but the Root Concept (referred to by model module concepts) is not visible in the Model Module.  Should we move the Root concept?

DMc Vaguely desirable but not worth the upheaval due to existing mutual-dependency.

YG: suggested we put it out to the NRCs to check for impact.

GR: Questions if there is a sufficient use case.

Moving to frequent releases, it becomes more likely that any two dependencies used will be based on different releases of the international edition.   How should implementers cope with combining archives that have different dependencies.   Answer:  make the changes to other's content in their own module to update them all to the most up-to-date dependency.

Composition mechanism proposed in TRAG (JSON list of module to be included with the 'main' module associated with an Edition or Extension).

AA: TRAG agreed to not introduce transitivity (ie where we'd state minimal dependency and allow higher dependencies to be inferred from the MDRS of the first parent dependency) and continue to fully list out dependencies.   Going forward with JSON based list of modules expected to include

Metadata working group proposed - volunteers? @michael lawley @Guillermo Reynoso @Peter Williams

Refset Descriptor Refset - Mandatory / Optional / Transitvity

@Peter Williams

0

5.2.4.1 Reference Set Descriptor

(Generate page for discussion)

AOB

0

Next meeting - conference call in January 2022.

AOB / Items outstanding

@Peter Williams

5

Concept model for a condition without condition (@Jim Case and @Yongsheng Gao)

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Role Grouping, Post Coordination (impact of DL changes),   further ECL filtering.

Concept model for conditions caused by substances or products - to be circulated before January @Yongsheng Gao (incl. other AGs and Member Forum)

Yong's further items to discuss (quick chat if time allow, or create page to continue)

• Qualifying Attributes - we've called them that, but they're being used as defining attributes

Metadata & Annotations

@Guillermo Reynoso

@Ronald Cornet (Unlicensed)

@Karim Nashar

@stefan.schulz (Unlicensed)

Metadata (including specifying aliases for langrefsets and some overload with Annotations in OWL): Capture, Interrogation and Publish

Was there a proposal for language refset aliases?

Refset Metadata

This topic comes from SNOMED on FHIR

Also TRAG item: Reference set metadata See Agenda item 17 and consider in wider context of machine readable metadata item 11

In fact, this metadata may be more widely useful when applied to a module.

Suggestion that we could use the FHIR standard which already defines metadata. DM suggests a JSON format which would be extensible unlike a column based solution.

Where are we at with this? Checking with @Andrew Atkinson ...

Relationship Grouping

@stefan.schulz (Unlicensed)

Google Document, editable

Presentation

OWL file with RGs interpreted as includes

Role group issues

@stefan.schulz (Unlicensed) (20211021): The role group topic has become an important issue in the BFO * SNOMED alignment manuscript, which offers a solution for the meaning of role groups in the clinical findings hierarchy (see agenda item 6, Oct 2021 meeting). Regarding the other hierarchies, a thorough analysis of the role groups is still pending

Revisit "Negative Delta"

@Peter Williams

At request of EAG - need to revoke/delete a published component. Comments added to Negative Delta.

See TRAG agenda item #

Notify @Andrew Atkinson

Use cases:

Two groups: where audit is desired (eg technical issue) and where it is not (IP, un-processable characters)

1. Removing IP - suggestion to blank out particular field ("~") while leaving row.

2. Conflicting Rows ie no clear state (technical issue, not content) - suggestion to subsequent delta clarifying row.

3. Clinically dangerous historical error in before-previous release.

Review the representation for product role

2019-April-EAG-Product-Roles.pdf

Discussion of options eg move role concepts into a separate module.

General requirement for flexible composition.