2019-10-28 & 30 MAG Face to Face Meeting, Kuala Lumpur

Meeting Introduction

@Peter Williams

10

Start GTM Recording

Welcome to Karim Nashar

Previous meeting (summer full call): 2019-07-15 - Full MAG Meeting (Conf call)

DL Enhancements

@Yongsheng Gao

30

Open

Feedback from members

Review the OWL Guide. The key changes:

• Ontology header in section Edition, Modules and Ontology Import Statement.

• Section for Referenced component for an Axiom

• Punning for Class and Property in section Representation of |is a| Relationships

Concrete Domains 

@Peter Williams

30

Concrete Domains

SNOMED International Proposal for Representing Concrete Domains in RF2

Update on Consultation

Unified Test List for pathology SNOMED content development

@Karim Nashar

10

Modelling for the UK Unified Test List for pathology SNOMED content development and a proposed cognitive model that could be transposable to a potential SNOMED observable entities concept model for reporting pathology and lab test results.

Open

Terminology Management Working Group update

@Rory Davidson

@Yongsheng Gao

40

Strategic options (to be considered by GA at October Conference) looking for 2020 - 2025.

Basic Formal Ontology

@stefan.schulz (Unlicensed)

@Daniel Karlsson (Unlicensed)

@Yongsheng Gao

20

MAG discussion here: Basic Formal Ontology Discussion

Review the draft response at https://docs.google.com/document/d/1HcBj5bVIg8lB_uyORZU9A_FWKFsw0sxmB6Xg4UYKygk/edit#heading=h.izs8q5fkm2

Basic Formal Ontology Discussion See also https://en.wikipedia.org/wiki/Open_Biomedical_Ontologies and https://en.wikipedia.org/wiki/Gene_ontology

@Former user (Deleted) you may be able to join remotely. I think this is 18:00 PDT

This topic received substantial coverage at Monday's EAG meeting. Recording available TBC.

Introduction

@Peter Williams

5

Zoom + Start Recording

Requirements and recommendation for representing SNOMED CT in a standalone OWL file

and

Annotating concepts, axioms, and ontology

@Former user (Deleted)

@Yongsheng Gao

@Kai Kewley

40

Use Cases: Repetitional risk, desirable to be able to assert correct canonical / sanctioned representation. Classifier research - allows for reproducible results.

Specification for representing SNOMED CT in OWL

SNOMED CT Annotations

Open

Note: It is possible and efficient to create a language refset that specifies "by exception", but few SNOMED browsers are able to work with an array of language refsets ie take a first preference, and then a fallback position if not found.

Degree of Synonym

@Jim Case

20

Requirement for a new description type (as discussed by EAG) for terms that are not very synonymous.

TRAG items of potential interest

@Peter Williams

@Jim Case

10

Reference set metadata See Agenda item 17 and consider in wider context of machine readable metadata item 11. Traction has been lost, is a sub-group needed to progress?

FSNs greater than 255 characters eg for vaccine concepts. Steer from SI is that we don't want to be changing RF2 description limits for the sake of a single use case.

Additional item: some refsets should not contain inactive concepts. This should be part of the metadata.

ISO language/dialect code where applicable

Versioning of Templates

@Guillermo Reynoso

5

From the EAG: Templates are becoming first class citizens and would be useful to other members. They should be given unique identifiers, packaged and versioned like any other RF2 component.

Revisit "Negative Delta"

@Peter Williams

@Andrew Atkinson

5

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

See TRAG agenda item #TBC

Use cases:

Two categories: 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. Does that become more or less of a problem with frequent releases? Fixed quicker, but we lose ability to recall and re-publish.

GR: If the fault can be subsequently fixed in the Snapshot eg by restating the correct state with a new effectiveTime, then that could be considered sufficient.

Introduction

@Peter Williams

0

Start Recording

Modularizing the core and/or Migrating content to a dependant module

@Peter Williams

@Jeremy Rogers (Unlicensed)

45

Check for EAG discussion on same.

@michael lawley is the previous work you did on module composition (as opposed to dependency) available?

Use cases:

1. Return of content to the UK Edition,

2. Separation of clinical core from "Community Content"

Content would need to be inactivated in the International Edition and then the same identifiers would be re-activated in the next UK Edition using their own module. FYI @Jeremy Rogers (Unlicensed)

The apparent "break in time" can be resolved by detection of the "Concept Moved Elsewhere" inactivation indicator and the historical association to the concept representing the receiving namespace.

Actually, it's easier to move to another edition than it is to move within the same release. Would we end up with an active concept in one module, and an active inactivation indicator in the other?

The receiving module should inactivate both the inactivation indicator and the historical association - agree?

The inactivation and reactivation in a new module within a single package is going to be very noisy. Can we make a clean cut and just restate the new modules?

Previous work on Module Composition - discussion including link to my proposal https://snomed.atlassian.net/wiki/x/eIL8Bw

What's the best way to support query of historical records?

@michael lawley

@Jeremy Rogers (Unlicensed)

45

1. Multiple queries run against successive releases of SNOMED with results collated.

2. Update the EHRs to the latest concept using historical associations

3. Create an enhanced transitive closure table containing inactive concepts at their last known position (but not children?)

4. Augmented solution checks the position of replacement to determine concepts inactivated due to wrong placement.

Option here for a % confidence level and/or reason for inclusion to annotate results.

Should ECL / hosted services support this natively?

Is guidance around the issues and options (pros cons gotchas) the first thing to be done?

As always, soliciting the specific use cases would be very useful.

SPLG discussing changes to specifying substrate and access to the "Target" field in refsets eg the historical association.