Re: [Obo-anatomy] muscle divisions in UBERON

[Melissa H. <ha...@oh...>]

few additional thoughts.
On May 26, 2012, at 1:58 PM, David Osumi-Sutherland wrote:


On 26 May 2012, at 15:09, Melissa Haendel wrote:

Perhaps we should define a general attachment term for cases, like muscle attachments, where there is no continuity of structure?
I think this is what Chris is proposing, that a new 'connected_to' relation would be the parent property of 'articulates_with' and/or 'attached_to'? where the specific system connection properties would be further refined in that way. Some examples would be:

Not sure how to define - perhaps on continuity of material entity (granularity can be a problem for this, but perhaps it is enough to appeal to common sense in making judgment calls regarding its use).\
Yep I think you hit the nail on the head - A lot of the distinctions in these examples depend on that. If we end up with some sort of system-specific interpretation of the parent property, this will vary.


muscle attachment
Agree
bone articulation at a joint
Maybe - although in this case isn't there a gap filled with synovial fluid?
cell adhesions
Agree
gap junctions
Agree
tissue perfusion by a blood vessel, or the relationship between that blood vessel and the tissue (a connection? or rather a surrounded_by relation?)

Not sure perfusion is right word here.  Also not sure that connectedness is useful here.  I think I'd prefer to use contained_in:
X contained_in some Y expands to X located_in some site that part_of some Y
e.g. 'vasculature of brain' contained_in some brain
sure, I guess I was thinking more about how some larger blood vessel was connected to some distant tissue that it perfuses, as opposed to the vasculature contained within a tissue. In some senses this seems similar to the neural issues you are dealing with.

the neuronal relations that david put in, such as:
 'in neural circuit with'
Nope - this is a a transitive relation cover synapsing - it explicitly does not require connection.  Note - transitive is excessive here.  Probably needs to be replaced with a relation that limits the number of connections it can jump over.

'fasiculates_with'
No again, this is a subproperty of overlap.
only if intended to be neuron to nerve bundle, right? but if neuron-neuron would be similar to synapsed_by? (sorry haven't read about your treatise on these relations)
'synapsed_by'
Agree.

- David

Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library
http://www.ohsu.edu/library/
Department of Medical Informatics and Epidemiology
Oregon Health & Science University
ha...@oh...<mailto:ha...@oh...>
skype: melissa.haendel
503-407-5970