Jim Case

Jim Case

Jim Case

• From Freshdesk ticket
• There was an agreed set of editorial principles accepted in 2014 by the Microbiology Reporting project group for concepts representing "X, not Y (organism)" i.e. when a laboratory report indicates a class of organisms described by the exclusion of specific Linnaean or non-Linnaean classes. The guideline specifies "accommodating these in the Organism hierarchy (based on reasonable use cases to avoid a combinatorial explosion), but making them primitive super class in between the species (or species subtype e.g. Haemophilus influenzae, not B)
• The current content does not conform to these guidelines
• Need to define what is meant ontologically by "X, not Y (organism)" in light of the limitations of our DL profile

Observable Entity and Microbiology Test Results

Discussion:

• Suggested that the use of disjoint classes may resolve this issue. Prior testing of this axiom resulted in poor performance for classification.
• Consensus that these concepts need to be in the Organism hierarchy
• Requested Farzaneh Ashrafi solicit additional information from submitter as to the intended meaning of X, not Y. Does this mean "Any X species except Y" or is it just a specific exclusion?
• Non-Linnaean concepts not specifically discussed.

• Farzaneh Ashrafi - Solicit additional information from submitter on the intended meaning of X, not Y

• Follow-up of fracture model from last call
• Simple co-occurrence (with Paul Amos ) - follow-up discussion from August 28 call
  • 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.
  • Question posed as to the need for the "Multisystemic manifestation" concepts for disorders named by their primary clinical sign, if that primary clinical sign is always present? What is the need to call out these other signs specifically in another subhierarchy?

• Fractures_follow-up.pptx
• Injuries.pptx
• Editorial policy for simple co-occurrence.pptx

8

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…"

Discussion 2019-09-25: Tabled for lack of time. Will be discussed in KL