immaterial entity

[zhengj2007]

From haen...@ohsu.edu on March 01, 2012 19:08:27

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: http://code.google.com/p/bfo/issues/detail?id=21

[zhengj2007]

From janna.ha...@gmail.com on April 29, 2012 02:13:44

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

Status: Done

[zhengj2007]

From alanruttenberg@gmail.com on May 01, 2012 01:11:46

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, https://code.google.com/p/bfo/source/browse/trunk/src/ontology/owl-schulz/bfo.owl r215

Status: Started

[zhengj2007]

From alanruttenberg@gmail.com on May 01, 2012 01:12:04

Labels: -Type-Defect Type-BFO2-Reference

[zhengj2007]

From alanruttenberg@gmail.com on May 07, 2012 21:10:48

Owner: ifo...@gmail.com

[zhengj2007]

From meli...@eagle-i.org on July 10, 2012 12:38:11

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

[zhengj2007]

From mcour...@gmail.com on July 10, 2012 12:53:44

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/specification/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 )

[zhengj2007]

From alanruttenberg@gmail.com on July 11, 2012 21:05:34

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.

[zhengj2007]

From bjoern.p...@gmail.com on July 17, 2012 08:10:52

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)).

[zhengj2007]

From alanruttenberg@gmail.com on July 17, 2012 10:00:29

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?