2020-11-16 - OBSERVABLE Meeting

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Sarah Harry Daniel Karlsson

Evaluation procedures to Observables (E2O) transfer evaluation

• A summary of the meeting was presented
• Farzaneh Ashrafi make sure that any issue regarding the agreement is addressed

Daniel Karlsson 

Suzanne Santamaria

A review of existing Editorial Guide for Observables is due. Some pages seem dated. Comments to pages are done in a Google Doc here.

• Sarah Harry terming guidelines needs updating
• Many pages seem dated, e.g. Relationship between Observable Entities and NPU codes, Representing LOINC Terms with the SNOMED CT Observable Entity Model, Test Observable Entity Naming Conventions
• Wording of guidelines could be lighter on the jargon
• Examples from existing Observables as well as from the LOINC tech preview could be added
• Process for approval of changes discussed

• Daniel Karlsson make Google Doc of the comments

X

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:

James R. 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, James R. Campbell presented the neuropsychological processes. Piper Allyn Ranallo 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 Paul Amos and Piper Allyn Ranallo (CC James R. Campbell) to initiate discussion about Nebraska mental process hierarchy

Daniel Karlsson

• Daniel Karlsson check for use of Component in the LOINC expression ontology
• Daniel Karlsson compare and suggest updates to Component definitions

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

2020-11-16:

Release of content postponed to July 2021.

• Suzanne Santamaria talk to Jim Case about setting observables (updated NUTRITION-54 - Getting issue details... STATUS  with query for Jim Case on 22 September)

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

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.

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

• Daniel Karlsson to update guidance.
• Talk to Jim Case about attribute name changes.
• Daniel Karlsson Check existing uses of the attribute process output
• Suzanne Santamaria check "process acts on" is fine with nutrition group. Created  NUTRITION-57 - Getting issue details... STATUS  for input from Nutrition Group and they said this is fine.

Daniel Karlsson