immaterial entity

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Is it possible to include 'immaterial entity' as a sibling class to 'material 
entity'. Ideally site and boundaries would be subclasses of 'immaterial 
entity'. 

In order to have anatomical space and anatomical boundaries classify as 
immaterial anatomical entities this would be nice to have. Barry suggested that 
the anatomical spaces should be sites. The anatomical boundaries would then be 
subclass of 'object boundary'? Or is 'object boundary' meant to be material? 
The examples given for boundaries can be construed as either material or 
immaterial. Can you tell me, are they intended to be sites of gene expression? 

For example, here is how we are currently defining material anatomical entity:
'material entity' and ('is part of@en' some organism) and ('has quality@en' 
some mass)

ideally we'd have the parallel construction:
'immaterial entity' and ('is located in@en' some organism) and not ( 'has 
quality@en' some mass)

I am sure this has been discussed, please let me know how we might accommodate 
this using the new bfo.

Cheers
Melissa

Original issue reported on code.google.com by haen...@ohsu.edu on 2 Mar 2012 at 12:08

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Immaterial entity is in the BFO 2 Reference and in the BFO 2 OWL working 
version. 

Original comment by janna.ha...@gmail.com on 29 Apr 2012 at 9:13

• Changed state: Done

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Reverted status to open. Janna correctly notes that the class hierarchy in BFO2 
reference reflects the desired class hierarchy but the other questions 
regarding relations are not verified.
"BFO 2 OWL working version" is non-referring.
The intended referent is, I believe, 
http://code.google.com/p/bfo/source/browse/trunk/src/ontology/owl-schulz/bfo.owl
 r215

Original comment by alanruttenberg@gmail.com on 1 May 2012 at 8:11

• Changed state: Started

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Original comment by alanruttenberg@gmail.com on 1 May 2012 at 8:12

• Added labels: Type-BFO2-Reference
• Removed labels: Type-Defect

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Original comment by alanruttenberg@gmail.com on 8 May 2012 at 4:10

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Its much better, thanks. However, I find the the difference between a 
"three-dimensional spatial region" and a "site" a bit confusing. Is the 
difference that a site can itself move through space? simply that it is bounded 
on one or more side by a material boundary or surface? This seems to be in the 
text definition (as an aside, why is the BFO text definition using a new 
annotation property "elucidation", I see it is from IAO?) but there is no axiom 
to this effect. What is the purpose of making this distinction?

Also, we will define material boundaries and surfaces in CARO if they are not 
in BFO, which is fine, but it would seem such things could potentially be used 
to define a "site" above. We need these material entities to record gene 
expression, for example, the midbrain hindbrain boundary is a three dimensional 
"plane" (not a plane in the mathematical sense, but a material bona fide 
boundary) in which specific gene expression occurs.

Also, anatomically, "site" is poor label as it is used in the material sense 
very often (site of gene expression, site of hemorrhage, tumor site). We'll 
undoubtedly have to either relabel or not use for anatomy (depending on 
consideration of the above).  

Thanks for considering all of this.
Melissa

Original comment by meli...@eagle-i.org on 10 Jul 2012 at 7:38

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I also have issues with site and 3D spatial region, see 
https://code.google.com/p/bfo/issues/detail?id=69 and thread at 
https://groups.google.com/forum/?fromgroups#!topic/bfo-devel/rZpINfrPry8 
We added extra annotations: see the file 
https://code.google.com/p/bfo/source/browse/trunk/src/ontology/owl-group/specifi
cation/non-reference-annotations.lisp, which includes an annotation "A site can 
move through spatial regions.  Consider the hold of a ship (site).  As it 
sails, the hold is moving through space, and changing its spatial region 
continuously.  Ditto for the captain's quarters, passenger rooms, etc. Spatial 
regions don't pass through one another"
I would love to hear (and include more info in the file) as the rationale for 
distinction.

The elucidation annotation is for those terms that are so primitive that a 
definition would be circular (see 
https://code.google.com/p/bfo/issues/detail?id=38#c8)

Original comment by mcour...@gmail.com on 10 Jul 2012 at 7:53

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Hi Melissa,

There are other issues with site that aren't addressed yet - it isn't well 
defined as far as I'm concerned, but the distinction between space and site is 
at least clear. But I think that can be repaired. 

I think that CARO should define "anatomical material boundary" and "anatomical 
surface" as there will be nuances that change from domain to domain. The 
unqualified terms seem too general for CARO.

Can you suggest an alternative to using the terms site here, and give some 
examples of the alternate use you see in anatomy?

All the cavities etc in anatomy will be sites, not spatial regions. In fact, 
from a physics point of view it isn't even clear that spatial regions exist in 
any useful sense. The terms are included, IMO, more as a way to define BFO than 
to be used in domain ontologies. 

We tried hard to retain only site and jettison spatial region (Bjoern led the 
charge) but failed to convince Barry, in the end.

I don't know if you have read much of the BFO2 Reference draft, but it does 
have discussion of this issue. I'm working on including it more in the OWL file 
but in the interim you can read the draft at

https://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx

This kind of discussion is the reason I emphasized that the upcoming public 
release of bfo2 will be a draft for public comment - we'll have done as much as 
we can in the smaller group here, but that doesn't mean the design is finalized 
- we need to have wider review before implying it is a stable release.

There have been a couple of terms added to IAO in order to accommodate the BFO 
development process, Elucidate is one of them. There was a question of whether 
we should have both definitions and elucidations and a vote found most people 
preferring both.

Original comment by alanruttenberg@gmail.com on 12 Jul 2012 at 4:05

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As Alan pointed out, I remain unconvinced that there should ever be a use of 
'spatial region'. I don't want to hold things up though, and the present state 
is not worse than the old BFO version. It would at least be helpful though if

a) examples of 'spatial region' and 'continuant fiat boundary' would be 
included in the owl file
b) the term 'frame' in the definition of 'spatial region' is explained in some 
way. 
In particular it is not explicitly stated that BFO assumes one canonical frame 
for spatial regions. (It needs to; If not, then the statement that 'sites move 
through each other and spatial regions do not does not help distinguish them. 
(E.g. the spatial region marked by certain GPS coordinates move through spatial 
regions marked by a celestial coordinate system)). 

Original comment by bjoern.p...@gmail.com on 17 Jul 2012 at 3:10

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> As Alan pointed out, I remain unconvinced that there should ever be a use of
> 'spatial region'. 

I'm also fairly confident that anyone who used spatial region directly in an 
ontology would be making a mistake. Win some, lose some ;-)

> I don't want to hold things up though, and the present
> state is not worse than the old BFO version. It would at least be helpful
> though if
>
> a) examples of 'spatial region' and 'continuant fiat boundary' would be
> included in the owl file

I believe there are some in the reference now and they will be included in my 
next OWL checkin.

> b) the term 'frame' in the definition of 'spatial region' is explained in
> some way.

I think we should simply point to WIkipedia or another reasonable source for 
people who are curious. Anything else would be premature. 

> In particular it is not explicitly stated that BFO assumes one canonical
> frame for spatial regions. 

It doesn't. It can't. For one thing, it isn't clear whether the business of 
frames is in the frames or the relative differences.

(It needs to; If not, then the statement that
> 'sites move through each other and spatial regions do not does not help
> distinguish them. (E.g. the spatial region marked by certain GPS coordinates
> move through spatial regions marked by a celestial coordinate system)).

It can be fixed with: 

sites can move through each other, and do so in any frame of reference, whereas 
and spatial regions do not move with respect to each other in any frame of 
reference.

Agreed?

Original comment by alanruttenberg@gmail.com on 17 Jul 2012 at 5:00