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caro2 - issue #5

appendage examples requested


Posted on Oct 17, 2011 by Swift Dog

Term name: appendage Term URI: CARO_0010003 svn revision number: current textual definition (for this revision number): "An organism subdivision that protrudes from the body."@en current formal definition (please use OWL MS): none

Please state what is wrong with the current definition, how you suggest it could be improved and what you believe the practical implications of this change will be.

The relation "protrudes from" is not defined, and "body" is not in CARO2. Also, "body" is sometimes used to denote the whole organism, here we mean the, errrm, organism minus appendages...

I'm particularly interested in where the protrusion starts and the body ends. I have a concrete use case. Current ontologies differ massively in whether they consider girdles to be part of or overlapping the limb. The FMA introduces terms like "free limb" (excludes girdle region) and "limb" (includes). Limb isa "cardinal body part", and "free limb" isa limb segment.

Which of these are the appendages? Perhaps neither, perhaps the appendage itself extends part of the way into the girdle region. Perhaps both are appendages (as in VAO) but this would be very odd, as it would mean that 8 paired appendages, not 4!

Of course, there is a large degree of arbitrariness here, but even so I think CARO should have some kind of recommendation here to help unify the ontologies. My gut feeling is that we declare the free limb to be an appendage. The free limb + girdle would be an anatomical cluster or subtype thereof.

Comment #1

Posted on Oct 26, 2011 by Swift Dog

Discussed briefly on the VAO call. There was a general feeling that "the bit that sticks out" was the appendage (i.e. just the limb proper), whereas the limb+girdle was something else (probably an anatomical cluster, not sure if a more specific class is warranted).

On a related issue - skin adnexa/appendages (e.g. http://en.wikipedia.org/wiki/Skin_appendage - also MP:0010678) would not be considered appendages according to CARO (I don't think they would classify under "organism subdivision").

This is fine, but I wonder if it isn't worth signaling this clearly in the class name? i.e. renaming "appendage" in CARO to "organism appendage". This leaves the terminological path open to organ appendages (which would be organ subdivisions?) and even, if we desire, reserving "appendage" for the ultra-general grouping class (which I think David might consider worthless).

Status: Accepted