Infection and inflammation #3885
Replies: 11 comments
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The asserted parent is due to mirroring ncit, but we can override these I agree it would be good to be more consistent here. |
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How should we go about making this more consistent? Should we remove the equiv axiom that uses 'disease has inflammation site' from:
Maybe instead use 'disease has location'? |
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@cmungall please see my question above |
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Yes, change the relation |
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@nicolevasilevsky @cmungall |
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@paolaroncaglia re: MONDO:0021666 ear infection: All of the children terms are infections of some kind. I feel like this classification make sense. Do you agree? |
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@nicolevasilevsky I do not disagree with the classification of children of MONDO:0021666 'ear infection', because they are all indeed infections, though for 'otitis externa' this is only clear from the textual definition. Also, MONDO:0021666 'ear infection' is a Subclass of 'infectious disease of the nervous system'. This doesn't feel entirely correct and may be a similar issue to #747? Thanks again, |
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@paolaroncaglia - I share your concerns. I haven't had time to look fully. To me the most logical solution is always to separate inflammation terms from infection terms, and link with a causal relation where appropriate (from infection to inflammation, if this is an all-some). But for some diseases the conflation may be too deeply part of the medical lexicon. |
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@nicolevasilevsky |
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sorry, still have not had time for this |
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I was looking at the 'inflammatory disease' branch and I noticed some infection terms.
E.g. MONDO:0000369 'abdominal tuberculosis' http://purl.obolibrary.org/obo/MONDO_0000369 has the axiom:
tuberculosis and (disease has inflammation site some abdomen)
which makes 'abdominal tuberculosis' an inflammatory disease.
This makes sense.
'tuberculosis', however, is not an inflammatory disease in MONDO. I guess that is because inflammatory diseases in MONDO are logically defined based on their location:
disease or disorder and (disease has inflammation site some anatomical structure)
and that would be harder to state for generic tuberculosis.
So, even though most infectious diseases cause inflammation, I could see why one wouldn't want to generalize.
However, MONDO:0021666 'ear infection' http://purl.obolibrary.org/obo/MONDO_0021666 has the axiom:
infectious disease and (disease has location some ear)
and the asserted parent 'inflammatory disease'.
Where do you draw the line between infectious diseases and inflammatory ones? An infection may not produce inflammation, e.g. in its very first stage, but once it becomes "visible" and/or is diagnosed, that's often because inflammation is observed. Do I understand correctly that the strategy in MONDO is to link infection to inflammation when an inflamed anatomical location can be established? If so, is this done consistently?
Thanks!
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