Add annotations to 'realizes' and 'realized in'

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This issue is tricker than the others.

Unlike most of the ObjectProperties in ROCore, 'realizes' and 'realized in' 
have BFO IDs and are defined by the BFO developers. We should not add 
annotations that contradict bfo.owl. I suggest:

- because these relations don't have definitions in bfo.owl, just 
elucidations...
  - copy the 'elucidation' annotations from bfo.owl
  - add the IAO_0000600 'elucidation' AnnotationProperty to ROCore
- because the elucidations are too technical for the average reader, but we 
shouldn't just add our own definitions...
  - add 'rdfs:comment' annotations with simpler text and mark them as a "Paraphrase of elucidation"
- add rdfs:isDefinedBy annotations pointing to bfo.owl

I would like to add examples, but I think we should not.

Concrete steps:

IAO_0000600 elucidation
- add new AnnotationProperty
- add label: elucidation

BFO_0000054 realized in
- add rdfs:comment: Paraphrase of elucidation: a relation between a realizable 
entity and a process, where there is some material entity that is bearer of the 
realizable entity and participates in the process, and the realizable entity 
comes to be realized in the course of the process
- add elucidation from BFO2: [copied from inverse property 'realizes'] to say 
that b realizes c at t is to assert that there is some material entity d & b is 
a process which has participant d at t & c is a disposition or role of which d 
is bearer_of at t& the type instantiated by b is correlated with the type 
instantiated by c. (axiom label in BFO2 Reference: [059-003])
- add rdfs:isDefinedBy: http://purl.obolibrary.org/obo/bfo.owl

BFO_0000055 realizes
- add rdfs:comment: Paraphrase of elucidation: a relation between a process and 
a realizable entity, where there is some material entity that is bearer of the 
realizable entity and participates in the process, and the realizable entity 
comes to be realized in the course of the process
- add elucidation from BFO2: to say that b realizes c at t is to assert that 
there is some material entity d & b is a process which has participant d at t & 
c is a disposition or role of which d is bearer_of at t& the type instantiated 
by b is correlated with the type instantiated by c. (axiom label in BFO2 
Reference: [059-003])
- add rdfs:isDefinedBy: http://purl.obolibrary.org/obo/bfo.owl

Original issue reported on code.google.com by ja...@overton.ca on 22 Jan 2015 at 3:52

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I don't know if BFO already includes them, but examples of usage would be 
really helpful here too.

Original comment by rlwalls2...@gmail.com on 26 Jan 2015 at 8:26

[GoogleCodeExporter]

BFO_0000054 realized in
- move domain from ro-edit.owl to core.owl: realizable entity

BFO_0000055 realizes
- move range from ro-edit.owl to core.owl: realizable entity

Ramona: BFO2 does not include explicit examples. I emailed Barry to confirm 
that these are good examples:

A. this investigator role is realized in this investigation
B. this fragility is realized in this shattering
C. this disease is realized in this disease course

Original comment by ja...@overton.ca on 28 Jan 2015 at 2:32

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I just noticed that the "non-temporalized RO relations" section of the ROandBFO 
wiki page says that we were going to change these to RO IDs:

realized in BFO_0000054 ==> RO_0000054
realizes BFO_0000055 ==> RO_0000055

However:

1. the links on the wiki page point to other terms (RO_0000053)
2. those RO IDs are not used anywhere that I can see (RO_0000054, RO_0000055)
3. the BFO IDs are used in the RO OWL files.

So is this just a mistake on the wiki page?

https://code.google.com/p/obo-relations/wiki/ROAndBFO#non-temporalized_RO_relati
ons

Original comment by ja...@overton.ca on 28 Jan 2015 at 2:48

[GoogleCodeExporter]

Barry confirmed the paraphrase and examples. I think we should change the wiki 
page and not the IDs.

Here's the updated proposal.

IAO_0000600 elucidation
- add new AnnotationProperty
- add label: elucidation

BFO_0000054 realized in
- add rdfs:comment: Paraphrase of elucidation: a relation between a realizable 
entity and a process, where there is some material entity that is bearer of the 
realizable entity and participates in the process, and the realizable entity 
comes to be realized in the course of the process
- add elucidation from BFO2: [copied from inverse property 'realizes'] to say 
that b realizes c at t is to assert that there is some material entity d & b is 
a process which has participant d at t & c is a disposition or role of which d 
is bearer_of at t& the type instantiated by b is correlated with the type 
instantiated by c. (axiom label in BFO2 Reference: [059-003])
- add rdfs:isDefinedBy: http://purl.obolibrary.org/obo/bfo.owl
- move domain from ro-edit.owl to core.owl: realizable entity
- add example of usage: this disease is realized in this disease course
- add example of usage: this fragility is realized in this shattering
- add example of usage: this investigator role is realized in this investigation

BFO_0000055 realizes
- add rdfs:comment: Paraphrase of elucidation: a relation between a process and 
a realizable entity, where there is some material entity that is bearer of the 
realizable entity and participates in the process, and the realizable entity 
comes to be realized in the course of the process
- add elucidation from BFO2: to say that b realizes c at t is to assert that 
there is some material entity d & b is a process which has participant d at t & 
c is a disposition or role of which d is bearer_of at t& the type instantiated 
by b is correlated with the type instantiated by c. (axiom label in BFO2 
Reference: [059-003])
- add rdfs:isDefinedBy: http://purl.obolibrary.org/obo/bfo.owl
- move range from ro-edit.owl to core.owl: realizable entity
- add example of usage: this disease course realizes this disease
- add example of usage: this shattering realizes this fragility
- add example of usage: this investigation realizes this investigator role

Original comment by ja...@overton.ca on 5 Feb 2015 at 1:57

[GoogleCodeExporter]

This issue was closed by revision r400.

Original comment by ja...@overton.ca on 6 Feb 2015 at 4:37

• Changed state: Fixed