Jim Case

Jim Case

•  Toni Morrison will provide link to the issue log

Substance hierarchy redesign

Substance disposition proposal (see attached document)

Comments from EAG regarding the proposal were sought.

BGO had a question about the use of the HAS DISPOSITION relationship; where would it be used? JCA stated it would be solely used for substances. WRT to substances associated with allergens, how would these be used when the substance had a disposition other than allergen. A substance has a disposition, whether it is being used in another context or not. Disposition is a defining attribute for substances.

•  Jim Case will prepare a briefing note for the MF to inform them of the proposed changes

Issue: In some cases, the representation of FINDING SITE at the proper level of granularity requires multiple body structures. E.g.:

Image Removed

The proposal under consideration is:

"If two body structures are needed to fully define the finding site for a condition, then a combined anatomic structure shall be created to represent that body structure."

For example: A new body structure "Bone structure of distal phalanx of great toe (body structure)" would be created to support the modeling of the concept above.

Discussion: PAM supported this approach by email. BGO supports this change as well. YGA was asked about his support and he also supported the new guidance.

•  Jim Case will send a edit to the Editorial guide editor to get this guidance implemented.
•  Monica Harry to work with technical writer to add this proposed (and accepted) wording to the guide where appropriate.

Create a table of mandatory grouping of relationships.  Rationale – needed for template based authoring, provides internal consistency of model patterns, allows for batch editing due to consistency.

See initial review from Daniel Karlsson and Yongshen Gao

The grouping patterns are currently being defined in the groups of templates, but there has been no general guidance for how relationships should/must be grouped. This would define mandatory grouping as well as addressing exceptions to grouping in particular subhierarchies. These would provide guidance for the templates being created.

This is project that is currently not resourced, but will be put on the list of needed edits for the revision of the editorial guide.

•  Jim Case will address this when the technical writer comes on board to begin the comprehensive editorial guide review.

•  Jim Case A summary of the options for "Disease in remission" from the Inception document and the pros and cons for each including modeling examples will be developed for additional review.

Jim Case

Suzanne Santamaria Toni Morrison

Discussion:

• A question arose as to whether attributes that would represent origin/destination or in/out relationships could be generalized for other uses as well. Not always a 1:1 relationship in anatomy.
• So far, no resolution on how to distinguish between "device" and "equipment". Put on hold for now. Bruce Goldberg recommended getting rid of the distinction within SNOMED CT.

• Editorial policy for simple co-occurrence Editorial policy for simple co-occurrence.pptx
• Traumatic and non-traumatic injury - follow-up Injuries.pptx
• Gout - follow-up Secondary disorders and gout.pptx
• Sources of truth - Jeff PiersonBruce Goldberg
  • KP clinical library

Discussion:

• Simple co-occurrence - three scenarios where the use of the pattern can be justified. The distinction between syndromes and diseases with multisystem involvement requires that intermediate primitives be used in the latter. The definition being developed was discussed and the scope of what should be included as an approved co-occurrence pattern.
• Traumatic and non-traumatic injury -

•  Bruce Goldberg to submit co-occurrence edits to the ed.guide
•  Bruce Goldberg to test the use of DUE TO "event" and full modeling of condition for pathologic fractures as a result of an underlying condition (e.g. osteoporosis)

7

Following a panel discussion at the ICBO conference in Buffalo Aug 1-2, an agreement in principle for SNOMED to collaborate with the OBO community was reached. Much of the discussion revolved around the current representation of diseases as subtypes of clinical findings. There is a clear, mutually exclusive separation in BFO and other disease ontologies based on BFO between "diseases", which are specifically dependent continuents and clinical observations (i.e. findings), which are considered occurrents. The challenges in implementing this notion in SNOMED is explained in https://www.academia.edu/26897896/Scalable_representations_of_diseases_in_biomedical_ontologies.

As we had initially discussed, one differentiating feature of what we are calling findings is the notion of temporality, i.e a findings is made at a point in time (an occurrence) whereas a disease is persistent. This is similar to the notions in BFO, but they (and all other disease ontologies) refer to diseases as dispositions (i.e. a realizable entity that is manifested as some abnormal process or structure. For terminologies like SNOMED that do not seek to define diseases, but to identify when a realization of the disease disposition occurs in a patient, this logical representation breaks down.

At the ICBO conference, a paper was presented in which an attempt was made to "BFOize" ICD-10. It was clear to the authors of that paper of the conundrum we face, i.e. that the use of the terms in ICD-10 as dispositions was not appropriate because they had been realized and so they modeled their ICD-10 ontology as processes (i.e. occurrents). This was criticized by a number of the ontologists, but no practical solution to the need for representation of realized dispositions in clinical recording were proposed.

Regardless, it would be of some benefit, in light of our desire to resolve the findings/disorders issue, to attempt to align as closely as possible with top level ontologies. One area where this would be of great use is the move by SNOMED to improve coverage of genomics. This would be greatly enhanced by an ability to integrate with the genome ontology.

A draft document is being developed by members of the MAG as a response to the issues surrounding the lack of alignment between SNOMED and BFO: https://docs.google.com/document/d/1HcBj5bVIg8lB_uyORZU9A_FWKFsw0sxmB6Xg4UYKygk/edit

Discussion:

Neuralgia – finding or disorder.pptx

Findings and Disorders thread.doc

Comments:

Keith Campbell expressed concern regarding "the notion that finding vs diseases may be differentiated by the notion of temporality, I believe there will be great difficulty applying such rules, and it will result in a false dichotomy… And will also result in no practical benefit the use of SNOMED in any way…"

Continued to next call...

Update on ongoing issues with ECE

Discussion:

Complications and Sequellae

Proposal made by BGO to model both "Complications" and "Sequellae" using the combined disorder patterns and following the FSN naming conventions for those concepts. Add descriptions that include the terms "Complication" or "Sequellae" as synonyms (or preferred terms where required) and retire the top level concepts of "Complication" and "Sequellae". This is still being discussed within the ECE. JCA leaned towards eliminating the primitive concept "Complication" due to its inconsistent use and to also look at the relationship of these to "Secondary disorders". Whether this fits with Sequellae needs more discussion. Bruce will update after the next ECE call.

Allergy model:

A revision to the proposed allergy model using the application of the HAS REALIZATION attribute to model "Allergy to X". A quesion about how the current concept model for Substances might impact this proposed model. BGO said he did not think it would have a deleterious effect. There would be some value is using the HAS DISPOSiTION attribute in substances to limit which substances might be used as values for "Allergy to X"; however, this might be an unnecessary complication.

Awaiting additional input from Stefan Shultz on the representation of the top level concepts of hypersensitivity condition, allergic condition and pseudoallergic condition.