request for reviewing ontology using BFO 2.0 OWL converted from BFO 1.x

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Beta Cell Genomics Ontology (BCGO) is an application ontology built for the 
Beta Cell Genomics database (http://genomics.betacell.org/gbco/). The ontology 
is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for 
Biomedical Investigations (OBI) as ontology framework and integrated subsets of 
multiple OBO Foundry (candidate) ontologies. BCGO contains 2384 classes 
referencing to 24 various OBO Foundry ontologies (BFO, 20 reference ontologies, 
and 3 application ontologies) and over thousands of logical axioms (not class A 
subClassOf class B) defined in OBI, UBERON, CL, and PATO. Details of BCGO 
ontology, please see 
http://code.google.com/p/bcgo-ontology/ 

BCGO was converted to BFO 2.0 (graz release) using BFO converter developed by 
He Group (http://bfoconvert.hegroup.org/). The mapping file of BFO1.1, BFO 
pre-graze version, and OBO-REL to BFO 2.0 is:
https://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/obi-view/obi-bfo2
/TermsMapping-BFO2.xls 

For temporal relations, 'at some time' were used except 'has continuant 
part/part of continuant' which used 'at all time' for keeping transitive 
characteristics desired for most of OBO Foundry ontologies. 

Details of conversion has been reported on 2013 BFO meeting, see 
http://ontology.buffalo.edu/bfo/2013/BFOconverter.pptx

The BFO 2.0 graz release compatible BCGO OWL file is avaiable on:
http://bcgo-ontology.googlecode.com/svn/trunk/release/20130214/bcgo_basis_bfo2.o
wl 

We would like BFO OWL developers can review this OWL file to see whether it is 
biological and logical correct. I think it would help us to see whether OBI, 
UBERON, CL and PATO can use BFO 2.0 and expand to other OBO Foundry ontologies.

Original issue reported on code.google.com by zhengj2...@gmail.com on 3 Jun 2013 at 5:27

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Stefan will look.
Barry will with some help from his friends.
Earlier versions in release directory
http://code.google.com/p/bcgo-ontology/source/browse/#svn%2Ftrunk%2Frelease%2F20
130214

Original comment by alanruttenberg@gmail.com on 5 Jun 2013 at 6:01

• Changed state: Accepted
• Added labels: Milestone-BFO2-Release

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Here is the result of my review. Not all observations are related directly to 
temporalized. I do not distinguish between the sources of the axioms.  

1. There are numerous relations between continuants for which an all times / at 
some time distinction should be required:

- connects and subclasses
- continuous with
- distal_to and subclasses
- dorsal_to
- ventral_to
- posteriorly_connected_to and subclasses
- secreted_by
- secretes (should be at some time)
- concretizes (could be at all times)
- isAbout

2. The role chain for develops from is problematic: 

   'part of continuant at all times' o develops_from -> develops-from

This axiom is not true for anatomical entities which develop from distinct 
origins, e.g. the placenta:

- placenta subclassOf develops_from uterus
- chorionic artery  subClassOf 'part of continuant at all times' some placenta, 
but the chorionic artery does not develop from uterus

3.
There are axioms that anticipate of the existence of future entities
- future_brain subClassOf  develops_into some brain
- eye_primordium eq primordium and develops_into some 'camera_ type_eye'
  (108 uses of develops into)

4.
subrelations of has_part / part_of not classified as such and not temporally 
qualified
- has_muscle_nerve
- has_plasma_membrane¬_part
- preaxial_part_of
- postaxial_part_of
- subdivision_of

5.
"lacks" relations as object properties (between individuals) are not meaningful:

- Erythrocyte subClassOf lacks_part some ribosome
- 'erythroid lineage cell' and (lacks_part some nucleolus) and  
  (lacks_plasma_membrane_part some 'CD19 molecule') …  

(145 uses of lacks* )

6. 
Dispositional meaning implicitly embedded in the object property, produces 
wrong existential assertions:

- Mammary gland equivalentTo Gland and secretes some Milk
- 'erythroid lineage cell'  subClassOf 
       (capable_of some 'erythrocyte differentiation')…
(108 uses of capable_of, 

7. 
Category problems:
Inceased_nucleus_size subClassOf Nucleus

8. 
General observation about anatomical entities:
Most anatomical entities can maintain their identity even severed from the 
whole they are part of in vivo. In most cases they are no longer functional, 
but may be subject to lab investigations and manipulations. As a consequence, 
one could argue that nearly all part-of relations between anatomical entities 
are of the type "continuant_part_of_at_some_time",  unless the meaning is 
restricted to entities in vivo. Even in this case "kindney subClassOf 'part of 
continuant at all times' some abdomen" would be incorrect due to the 
possibility of transplants (generic permanent parthood). 

One could consider axioms like

A and bearer_of some in_vivo subClassOf part_of_at_all_times some (B and 
bearer_of some in_vivo)

to express anatomical hierarchies (however, with the exception of anatomical 
entities that can be transplanted) 

Original comment by steschu@gmail.com on 25 Jun 2013 at 4:39

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Stefan, thanks for your review.

The issue 1 is the problem of automatic BFO version convertor. Need to be taken 
care in the future.

The other issues are more related to UBERON and CL ontologies. The reason we 
use 'at-all-time' because UBERON and CL would like to keep transitive property 
of relations (e.g. part of/has part) that defined in BFO 1.1. And it is the 
main issue for them to transit to BFO 2. It might be worth to let Chris look at 
it.

Original comment by zhengj2...@gmail.com on 25 Jun 2013 at 9:48

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uberon tracker: http://purl.obolibrary.org/obo/uberon/tracker
cl tracker:  http://purl.obolibrary.org/obo/cl/tracker

thanks for the review stefan. I transferred some issues that were not to do 
with TRs to the relevant trackers

http://code.google.com/p/cell-ontology/issues/detail?id=76 - increased nucleus 
size
http://code.google.com/p/cell-ontology/issues/detail?id=77 - lacks
http://code.google.com/p/cell-ontology/issues/detail?id=78 -    Dispositional 
meaning implicitly embedded in the object property, produces wrong existential 
assertions

Original comment by cmung...@gmail.com on 25 Jun 2013 at 10:36

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http://purl.obolibrary.org/obo/uberon/tracker/282 Truth of assertions 
concerning non-canonical anatomy

Original comment by cmung...@gmail.com on 25 Jun 2013 at 10:57

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Wierd issue that one. Recorded on the uberon tracker, but closed to comment?

My comment: if we need a generic part of true when "in vivo", this could be 
defined as a different relation. BFO defines some but not all relations that 
ontologies need. 

However, I doubt even that is always true.

FWIW. I'd need to check, but I believe that the approach I gave for generic 
parthood could be adapted to say this.

Original comment by alanruttenberg@gmail.com on 26 Jun 2013 at 6:57