Some upper respiratory diseases are not classified as infectious diseases

[allenbaron]

Is your request related to a specific disease? Please describe.
'common cold' (DOID:10459) and 'scarlet fever' (DOID:8596) are not properly classified in the infectious disease branch (should be viral and bacterial respectively).

Original request from Brenna Lee, [email protected]

[allenbaron]

These are both children of 'upper respiratory tract disease' (DOID:974) that for some reason are indeed lacking classification as infectious diseases. We should probably check other children of this disease to determine if they are also affected by this issue.

[allenbaron]

'common cold' is caused by more than 200 viruses in a variety of different taxonomic groups. I added https://medlineplus.gov/commoncold.html as a reference supporting the definition and the subClassOf axiom 'has material basis in' some Viruses to indicate it's causative agent. It will now be classified appropriately as a 'viral infectious disease' via reasoning.

[allenbaron]

'scarlet fever' is one of a number of diseases caused by Group A Strep, most commonly Streptococcus pyogenes. NCBITaxon has an unclassified Streptococcus sp. 'Group A' but given it has no definition and many sources treat S. pyogenes as equivalent with Group A strep, particularly with regard to scarlet fever, the following axiom has been used to classify it as a child of 'bacterial infectious disease' (DOID:104): 'has material basis in' some 'Streptococcus pyogenes'.

[allenbaron]

'laryngeal tuberculosis' (DOID:0050598) is also not classified as an infectious disease and needs to be classified as a descendant of tuberculosis.

[allenbaron]

On review, it looks like a number of updates to tuberculosis and its descendants are needed. I'll open a new issue for the review to avoid cluttering this one.