Closed PhiBabs935 closed 4 years ago
PhiBabs935
commented
4 years ago Similarly, 'infectious agent portal of exit role', currently defined as 'Role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent exits a host' should be changed to: 'Role borne by an anatomical entity in virtue of the fact that it contains a site through which an infectious agent exits a host.
johnbeve
commented
4 years ago With respect to CARO, I think they simply have a confusing textual definition. What they mean is that anatomical entity is a material entity that may have immaterial parts (they don't intend any anatomical entity to be entirely immaterial). They say as much in the definition. That's aligned with BFO since such an entity would still be a material entity, as that only requires having material parts.
With respect to the site issue, I'd adopted the textual definition from the original IDO, and was thinking infectious agent portal of entry - a material entity - can serve as a site because it has an immaterial part that is a site. But your proposal captures the intent better and should be adopted. Thanks!
Why looking at the new term 'pathogen portal of entry site' John added to IDO Core, I thought related terms already in IDO need minor curation.
infectious agent portal of entry =def Anatomical entity bearing an infectious agent portal of entry role.
infectious agent portal of entry role =def Role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent enters a host.
The latter definition seems problematic to me. It implies that an anatomical entity, which is classified as a material entity in IDO Core, can serve as a site. But how can a material entity serve as a site if a site is immaterial? A rock can serve as a paperweight, but only because both are material entities.
I think that there is a simple fix here, which would be modelled after the definition of 'source of infection role' =def Role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted. This role is borne by an IDO Core 'source of infection'
Following the definition for 'source of infection role', I suggest the following revised definition for 'infectious agent portal of entry role': =def Role borne by an anatomical entity in virtue of the fact that it contains a site through which an infectious agent enters a host.
I think that this definition for the role also gels more nicely with John's revised OWL definition for 'infectious agent portal of entry' which includes the condition that it has part some 'pathogen portal of entry site'.
By the way. So what’s the deal with ‘anatomical entity’? Is the CARO definition problematic? Should we ask them to get rid of the disjunctive ‘is either an immaterial entity or a material entity’? If not, this class shouldn’t be a subclass of material entity as it is in IDO, right? John you touched on this issue in your comment on the term in the OWL file.