Welcome & apologies

@Daniel Karlsson

• Remember recording!

Conflicts of interest

@Daniel Karlsson

None stated

Minutes from previous meeting

@Daniel Karlsson

Mental Function observables

@Jim Campbell

@Piper Ranallo PhD

Piper Allyn Ranallo is  doing a mental health clean up based on Mental & Behavioral CRG work - she has submitted some requests for editing and applying the observable entity model to existing content: 285231000 |Mental function (observable entity)|, 8373002 |Nervous system function (observable entity)|, 4065008 |Affect, function (observable entity)|311465003 |Cognitive functions (observable entity)|. Need advice on applying the model to these function observables.

Hello Daniel and Suzanne

I have now received a reply from Piper to Daniel's questions:
https://prod-request.ihtsdotools.org/#/requests/preview/745434?kb
The new comment is:
Hi Nicki, Regarding the relationship between functions --

• both mental and cognitive functions are specific kinds of central nervous system (CNS) functions.

• Motor functions and sensory functions are specific kinds of nervous system functions, with some motor and sensory functions inhering only in the PNS (peripheral nervous system). others inhering in only the CNS, and others inhering in both the PNS and CNS.

• A cognitive function is generally thought to be a more specific kind of mental function, although I don't know whether there's a clear consensus among scientists about how to unambiguously define the line between a mental and a cognitive function. In general, most scientists describe a cognitive functions as higher level, or more complex, mental function -- functions related to things like consciousness.

• 'Executive cognitive functions' are an even more specific (i.e., more complex, higher level) kind of cognitive function that includes reasoning, memory, attention, etc.

• The relationship between cognitive and intellectual function is unclear to me. An intellectual function may be synonymous w executive cognitive functions. I just don't know.

• Regarding the body structure in which the functions inhere - we'll need to look in more detail at the literature and consult with cognitive neuroscience experts.

• Regarding the process that the functions realize, we will need to work on defining that more specifically.

• In terms of modeling these concepts, one thing that is unclear to us is the distinction between processes in the qualifier hierarchy and processes in the observable hierarchy.

• Another question we have relates more generally to different needs for modeling mental and behavioral phenomena (v. biological phenomena). While biological phenomena can be meaningfully defined in terms of body structures and physiologic processes, most mental, behavioral, and social phenomena are more appropriately defined in terms of functional systems that may or may not have clearly defined biological underpinnings. This is a topic that MBH-CRG would like to explore with the folks working on the Observable and Investigation Model Project. Thanks you, Piper

2020-04-20:

@Daniel Karlsson participated on MBHCRG call 2020-04-08. A central issue is two aspects of mental function observables, e.g. Folstein MMT asks about the current date, but the function studied is the ability to orient in time. The raw value is a date, but the clinical value is about function. Observables preferably should allow representation of both aspects.

2020-06-15:

Need for clarification of what "function" means in function observables.

Other MBHCRG issues.

2020-07-20:

@Jim Campbell presented a hierarchy of "neuropsychological" processes. We agreed to contact the MBHCRG through the liaison Paul Amos to start getting agreement on such a hierarchy, likely to be a central piece in definition of MBH observables.

2020-08-17:

With participation from the Mental and Behavioural Health CRG, @Jim Campbell presented the neuropsychological processes. @Piper Ranallo PhD asked the group how to progress the work that MBHCRG needs to do to better define both Clinical findings and Observables in the MBH space. One concern is the demarcation of process observables on the one hand and process qualifier values on the other. Due to a large legacy of existing not always well-represented Observables, trying to make sense of the current MBH observables is likely not a worthwhile effort. It was suggested to focus on use cases that need to be represented in SNOMED and then see what concepts are needed both to define Observables and Clinical findings and to allow those respective hierarchies to reflect the intended meaning.

@Daniel Karlsson Send email to @Former user (Deleted) and @Piper Ranallo PhD (CC @Jim Campbell) to initiate discussion about Nebraska mental process hierarchy

Dentistry observables

@Daniel Karlsson

At a Dentistry CRG meeting 2020-08-05 it was requested that the Observables PG discussed observables for count of teeth with caries of various types (active and arrested particularly), likely children of 251319000 | Decayed tooth count (observable entity) |. See Dentistry page.

Discussion will be held next call (2020-09-21)!

2020-09-21:

Slides on use of component for defining count of carious teeth: https://docs.google.com/presentation/d/10t0zEBwtR5-RpUN4nAwS281HZdsavecZ5aXS4RufnfM/edit?usp=sharing

Definitions both in the Observables model and Evaluation procedure model needs to aligned and updated.

Target observables

@Daniel Karlsson

The issue of representation of target observables has been raised again in a Jira ticket.

The question the group needs to answer is whether targets and observables need to be seperated or to be kept apart. In practice, is there a requirement to query for both observables and "settings" alternatively is there a risk in having targets and observations mixed up?

One solution would be to (minimally) add a primitive parent "setting observable" (or just "setting") to all targets, settings, parameters, etc. in the current observables hierarchy.

2020-09-21:

@Suzanne Santamaria shared with the nutrition group, will share with @Jim Case

Process observable attributes

X

The use of attribute | process output | for intake observables is at least mildly confusing. Is there a need for updated guidance or clarification?

Open

2020-02-24:

Guidance needs clarification. This particular attribute is difficult to explain and often needs re-explaining(!). Alternatives | process target |?

2020-03-16:

Check existing use of the attribute in the SNOMED release as well as in the LOINC linking results.

2020-04-20:

Deadline for MRCM changes has passed, so more time is available for analysis. All LOINC expressions with | process output | are also | characterizes | = | excretory process |. The other | process output | Observables are <<364075005 | Heart rate (observable entity) | and <<86290005 | Respiratory rate (observable entity) |.

2020-05-18:

Use case from histopathology: representation of invasion.

Open

Slides

2020-06-15:

Update of range of | process output | to include Products.

2020-07-20:

Slides updated. Use cases presented compared to other ontology work, primarily the Relations Ontology of BFO. The use case from CSRPG (specifying the anatomic structure into which a neoplasm has proliferated) seems not to be supported by any single attribute. Recommendation is to use | process output | until this issue is resolved and a batch update can be made.

2020-09-21:

(More than) Time to decide on new attributes: https://docs.google.com/presentation/d/1zdM5Ld4H74GCmelaH0K1a5DlnK7ETSQpVFezgpdUEDY/edit?usp=sharing

Tumor observables

X

Around 200 observable entity concepts include "tumor" in the FSN and around 50 observable entity concepts include "neoplasm" or "neoplasia" in the FSN. "Tumor" is considered ambiguous by SI (described in the specific disorder modeling section of the SNOMED CT Editorial Guide here: https://snomed.atlassian.net/wiki/display/DOCEG/Specific+Disorder+Modeling). However, "tumor" is used in this morphologic abnormality modeling section of the Ed guide: https://snomed.atlassian.net/wiki/display/DOCEG/Morphologic+Abnormality+Modeling.

Tumor observable entity content has been considered for use in the Cancer Synoptic Reporting Project work; 395531003 |Tumor observable (observable entity)| is one of the high level concepts that currently subsumes much of their content being developed in an extension which will be a candidate for promotion to the international release in the future. Scott Campbell brought up the issue of what to do with the tumor observable content as he tends to think "tumor" is ambiguous. CAP uses "tumor" in their worksheets but it specifically means "primary malignant neoplasm." Scott will try to obtain some usage data on the current SNOMED CT tumor observable concepts. An initial conversation with one CAP representative revealed that he did not see much of an issue with using "tumor" in the FSN of the content because tumor and neoplasm are equivalent in his mind.

Some initial options to consider:

1. Leave tumor observable content as is in respect to terming and use it in their work. **We would still need to decide upon a morphologic abnormality concept (e.g., neoplasm, mass, proliferative mass) to define this observable concept.

2. Inactivate FSN of tumor observable content and create new FSNs with "neoplasm"

3. Inactivate tumor observable content and replace with new content that uses "neoplasm" or "primary malignant neoplasm" in FSN

4. Leave tumor observable content as is in respect to terming; create new content with "neoplasm" or "primary malignant neoplasm" as subtypes

Consider providing early release notice or BN if any option involving inactivation of content is chosen.

2020-07-20:

JIRA ticket: https://projects.jira.snomed.org/browse/OBSERVABLE-4

Jim Case have given go ahead to change FSN of Tumor observable to Neoplasm observable and to author a new concept Proliferative mass observable, a super concept of Neoplasm observable. The definition of this new observable might need a GCI to represent that the neoplasm can have different roles in different observables, e.g. | inheres in | or | component |.

Observables and Evaluation procedures

X

Since Observables were introduced into SNOMED CT the demarcation between Observables and Evaluation procedures has been a potential source of variability of SNOMED CT use. In order to progress this issue the group need to agree on what knowledge is needed to inform any future decision.

2019-11-18:

<<404684003 |Clinical finding (finding)| : 363714003 |Interprets (attribute)| = << 386053000 |Evaluation procedure| ==> 7148 concepts

...but also

1350 hits for <<386053000 | Evaluation procedure (procedure) |: [2..*] { 260686004 |Method (attribute)| = <<129265001 |Evaluation - action (qualifier value)| }

3 hits for <<386053000 | Evaluation procedure (procedure) |: [2..*] { 260686004 |Method (attribute)| = <<129266000 |Measurement - action (qualifier value)| }

611 hits for <<386053000 | Evaluation procedure (procedure) |: [2..*] { 246093002 |Component (attribute)| = * }

2019-12-16:

Some more exploration of existing Evaluation procedure content:

(<<386053000 |Evaluation procedure (procedure)| : [2..*] { * = * }) MINUS <<363679005 |Imaging (procedure)|

10 000-ish Evaluation procedures have 2 or more role groups...

<<386053000 |Evaluation procedure (procedure)| : [2..*] { 246093002 |Component| = * }

611 have 2 or more Components, indicating that it could be a panel. However, many examples are just strangely modeled and likely not intended to be panels. Thus, it's not straight forward to identify panel-like procedures among the Evaluation procedure. Sometimes, e.g. 442553005 | Measurement of chloride in peritoneal fluid specimen (procedure) |, additional Components are inherited from ancestors.

(<<386053000 |Evaluation procedure (procedure)| : [2..*] { 246093002 |Component| = * }) MINUS <<122869004 |Measurement procedure|

Even non Measurement procedures have multiple Components...

<<386053000 |Evaluation procedure (procedure)| : [3..*] { 246093002 |Component| = * }

A few have 3 or more components, many of which are in fact panels, but again likely not all of them. E.g. see <67899004 | Complement component, classic pathway (substance) |.

Briefing note should include:

• Current status in regard to overlap

  • Actual concepts

  • Concept models

• Current status in regard to modeling of Evaluation procedures

• Orders and results use of SNOMED CT

  • Actual use of Evaluation procedure concepts for reporting results

  • Actual use of Evaluation procedure concepts for ordering

• Panels vs. single-measurement observables/procedures

2020-01-28:

The issue of panel concepts (sets of distinct Observable entities) was discussed. The current Observables model, by design, does not allow representation of panels.

Many examples of panels are not well-defined, e.g. a Complete Blood Count may contain different observables in different laboratories. The benefit of adding content on the international level is likely limited. However, SNOMED CT should provide the means to represent such panels when there is agreement on meaning on a national, regional or local level.

Several Evaluation procedure concepts contain multiple groups, but all are not correctly modelled.

2020-02-24:

Aim to get feedback from members about usage of Evaluation procedures.

Further aim to identify candidates for Procedure-to-Observables transfer, i.e. Procedure concepts which represent observations which has a single, distinct result/value.

Some gaps exist in creating observables corresponding to those procedures, most notably techniques are missing.

2020-03-16:

The topic has been lifted in the Modeling Advisory Group.

Panels (aka observables without values): Examples of types of panels are groupers for lists, screening and function tests. Naming today is insufficient to distinguish from e.g. totals (e.g. amino acid panel vs. total amino acid etc.).

Definition and naming of panels (observables OR evaluation procedures).

2020-04-20:

EAG + MAG meeting to be planned. Preparation meeting held (slides).

Next meeting

@Daniel Karlsson

Next meeting is 2020-10-19 20.00UTC

AOB

@Daniel Karlsson