johnbeve
commented
4 years ago If we could get the developers of TRANS involved that would be ideal. They may have reasons for not having worried about circularity, or they may have overlooked it, etc.
Barry suggested "natural reservoir" and "susceptible host" were redundant if we used "source", which I agree with. I went further and removed "source" too since it seemed too vague. My thinking was that the children classes could specify the source, so it wasn't too important to include them in the textual definition.
I think my dropping off any specification of the source in this process might avoid people thinking the class is restricted to host-host transmission. The definition I'm proposing only indicates a pathogen is transmitted to a host, but doesn't mention where it's coming from. Am I misunderstanding the concern?
PhiBabs935
Original TRANS definition: A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
The current suggested revised definition for our new version of IDO Core: Process during which a pathogen is transmitted directly or indirectly to a new host.
It is suggested by the Apollo SV team (https://pubmed.ncbi.nlm.nih.gov/27538448/) that the original TRANS definition is circular, because it defines "transmission process in terms of a pathogen being transmitted, with no definition of transmitted.
I think that the worry about circularity is a result of the misleading original label, transmission process. If the term was intended to cover transmission in general (not just pathogen transmission), then there would certainly be circularity. But it seems to me from the definition that they only intended to cover a pathogen transmission process, and the notion of transmission more generally is being taken as a primitive in TRANS. What do you think?
Or maybe we should ask TRANS, or another higher level ontology, to add a more general term for transmission processes, and then define pathogen transmission process as "Transmission process during which..."
Another issue. What was the rationale for deleting from the textual definition the reference to natural reservoirs? My worry is that since the new proposed definition only talks about being transmitted to a new host, to some people's ears this may seem to imply that pathogen transmission process is always a process in which the pathogen moves from a previous host to a new host. And that could lead to an issue as a natural reservoir need not be a host organism. According to various definitions, natural reservoirs (reservoirs of infection) can also be environments such as bodies of air or water.
Incidentally, IDO has the term reservoir of infectious agent role, which is borne by a material entity that serves as the habitat in which infectious agents can persist. This term of course will need curation given that we no longer classify viruses as infectious agents--assuming, that is, that viruses also have reservoirs of infection.