2019-04-08 - OBSERVABLE Face-to-face Meeting

1

Welcome & apologies

@Daniel Karlsson

• Remember recording!

2

Conflicts of interest

@Daniel Karlsson

• None stated

3

Susceptibility observables

@Daniel Karlsson @Farzaneh Ashrafi @Suzanne Santamaria

Background

Draft editorial guidelines: Editorial Guidelines for Diagnostic Products Used for Susceptibility Testing

It was decided to recommend representation the physical form of the susceptibility test product, and also to use the | has presentation strenght... | attributes (as opposed to other strength attributes).

Two issues were discovered while re-reading the Inception/Elaboration document for susceptibility testing: 1. "oral form antibiotic susceptibility" exists as components in LOINC tests. 2. when other methods than culture are used, e.g. PCR or sequencing, to determine susceptibility, we might need to use another way of modeling, e.g. beta-lactamase producing ~ resistance towards beta-lactam antibiotics.

While the Susceptibility test products are needed for the mycobacteria tests (with strength-specified antibiotics), we might reconsider the approach for other cases, and use substances where products are not needed, together with a role chain | towards | o | ingredient | → | towards |.

Rob: Aren't all susceptibility tests strength-specified, even though the strength is not part of the definition?

Xavier: EUCAST breakpoint for diffusion disks : http://www.eucast.org/clinical_breakpoints/ the xls is at http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/Preliminary_v_9.0_Breakpoint_Tables_for_consultation.xlsxbreakpoint requires a definite antibio amount in the disk.

Most tests (mycobacteria tests being an exception) are based on there being a concentration gradient (e.g. disk diffusion, etest, MIC procedures) and thus not a single concentration.

2019-02-11:

An OWL ontology with Diagnostic test products and susceptibility observables is attached.

The combination substances are to be inactivated, so modeling cannot rely on use of such concepts.

2019-03-25:

An alternative version not using combination substances was presented and discussed.

Current objective

Presentation

Give recommendations on representation given two alternatives: (1) use | Susceptibility test product | as values of the | towards | attribute OR (2) use Substance together with | direct substance | = | Susceptibility test product | only when needed.

2019-04-08:

Presentation of alternatives for susceptibility observables modelling.

Has use with information models, e.g. FHIR Observation, been tested? No, but given that the observables are expression representations of LOINC content, for which there is ample experience, that is assumed not to be a problem.

Can Susceptibility test products be categorized as Pharmaceutical products, and thus be placed under 373873005 | Pharmaceutical / biologic product (product) |?

Comparison with allergy tests (skin or blood) can be explored further.

The project group voted to have a full example of using Test products as values for towards presented at next meeting (Motion: @Jim Campbell , second: @r.dash. Against: 0, Abstain: 1, For 5). @Former user (Deleted) to be invited to discuss placement of Susceptibility test products.

@Daniel Karlsson will produce a new version of the ontology according to the "towards test product" and present at next meeting, including retrieval use cases.

4

@Jim Campbell

(Cognitive) Function observables

See this page.

2019-04-08:

Presentation of work done by @Jim Campbell et al. at UNMC. Observables had been developed for MMSE (Mini-mental state examination). Process, scale type, and property concepts had been created in order to define the MMSE observables. Also, the section about function observables in the Observables I/E document was expanded.

The level of detail of Observables for individual instrument parts, such as the individual questions of MMSE, was discussed. Alternatively, generic observables, not specific to the instrument, could be used. UNMC preferred having specific observables.

The function observables are, according to the current pattern, defined by reference to the processes which are realized by the function, e.g. Orientation in time is realized by the function Ability to orient in time. Other observables can be defined by reference to the processes, e.g. performance of processes. Alternatively, these observables could be defined in terms of the function rather than the process.

5

@Jim Campbell

@Daniel Karlsson

Lab observables interoperability

See this page.

2019-04-08:

@Jim Campbell presented a request to SNOMED International to publish an OWL ontology including the LOINC expressions and expressions for any other lab terminology (e.g. NPU Terminology or the NHS pathology subset and content in SNOMED to allow classification, and comparison, of lab content.

The group was supportive of the proposal.

6

Next meeting

@Daniel Karlsson

• Next meeting will be 2019-05-20

7

AOB

@Daniel Karlsson

Bullet points for the closing plenary presentation:

• Almost concluded susceptibility observables

• Cognitive function observables, joint with MBH CRG, next steps identified

• Agreement of use of Observables model for international lab interoperability