_defined_hierarchy - Githubissues

Hi,

I started going through the current defined hierarchy and here are some notes:

1/ the _defined quality branch:
- asymptomatic : lots of typos, including in the label
- the definition of subclinical is unclear to me
- resistance quality is defined by low susceptibility, which seems strange:
should this be susceptibility quality then, or at least have a synonym to
that effect?

2/ _defined_infectious disease
- Is it planned to add some examples of usage later on? I tried to read the
"zoonotic disposition" definition and it is pretty hard to follow for example.
- should zoonosis also be linked to infection? There is no definition for
infectious disease, should all infectious disease be "derived_from" (or
other relation) infection? Infection itself has been obsoleted: is it
planned to add a note pointing to replacement terms for the obsolete terms?

3/ _defined_cellular component
- endotoxin: should LPS be expanded and moved to example of usage? maybe
"The prototypical examples of endotoxin are lipopolysaccharide (LPS) or
lipo-oligo-saccharide (LOS) found in the outer membrane of various
Gram-negative bacteria and is an important cause of their ability to cause
disease" from http://en.wikipedia.org/wiki/Endotoxin

4/ _defined material entity
- end reservoir of infectious organism is defined as organism bearing the
end of reservoir of infectious organism role. This role is not in the file.

5/ anatomical entity is used in several definitions and should probably be
mireoted from FMA (there is a note to that effect in the definition of
portal of entry of infectious organism role)

6/ _defined material entity
- Should antifungal etc be renamed antifungal material etc? I think this is
how we are planning to represent those in OBI too.
- microbicide:I am not sure what is the difference with antimicrobial: as
per the current definition, it would be that microbicide material is an
antimicrobial in the specific process of killing microorganisms. But
antimicrobial is defined as material bearing antimicrobial disposition,
which itself states " The disposition is realized in the killing and growth
inhibiting processes. "
Looking at microbistatic, it seems the difference is that in the first case
we specifically talk about "killing" - I think the realization should be
detailed in the definition of the disposition, and would therefore suggest
having 2 additional subclasses to the antimicrobial disposition.
- long term non progressor has no definition

7/  _defined organism
- I would suggest to add the prefix organism to the adjectives currently in
this hierarchy as well, in order to have noun as label for all classes.
There currently is "mutualist" sibling to "definitive host" or example.
- parasite is a role whereas antiparasitic is a disposition - should we
have parasitic as disposition (cf CHEBI:35442, antiparasitic drug = A drug
used to treat or prevent parasitic infections")
- infectious agent is defined as having the infectious disposition: I found
only infectious disposition of x relative to Y in the file: should we keep
just infectious disposition, and have relational dispositions (like there
are relational qualities)?
- emerging pathogen doesn't have a definition

Melanie
Original issue reported on code.google.com by mcour...@gmail.com on 2 Sep 2009 at 6:44
infectious-disease-ontology / infectious-disease-ontology-retired

_defined_hierarchy #10
