Add annotations to 'part of' and 'has part'

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For historical reasons these terms have BFO IDs, but they belong to RO and are 
not in BFO2 OWL.

These terms are notoriously problematic. First, they are ambiguous between 
occurrent parthood and continuant parthood. Second, they are ambiguous between 
class and instance level, since the RO2005 paper works at the class level but 
OWL works at the instance level. Third, it's hard to handle time at the 
instance level because OWL forces us to use binary relations.

See the ROAndTime wiki page.

I don't want to rehash the whole debate, but we need to include some 
annotations to warn users of these problems. My suggestion is to add an editor 
note with a link to an RO wiki page, and add more details to the wiki page.

# Background

BFO developers have been working on these problems in this document:

https://code.google.com/p/bfo/source/browse/trunk/docs/OWL-TIME/

They distinguish three categories of parthood for continuant:

"Temporary Generic Relatedness (TGR)
Informally: for all instances a of A there is some time t and some instance b 
of B such that a is related to b at t.
Examples:
(a) for all apple seeds there is some apple such that the seed is part of the 
apple at some time;"

"Permanent Generic Relatedness (PGR)
Informally: for all instances a of A there is, at all times t for which a 
exists, some instance b of B such that a is related to b at t, but not 
necessarily always the same b at all times t.
Examples:
(a) all cells have a water molecule as part at all times, but not always the 
same water molecule;"

"Permanent Specific Relatedness (PSR)
Informally, for all instances a of A there is, at all times t that a exists, an 
instance b of B such that a is related to b at t; in this case it is the same b 
at all times t. Examples:
(a) a human being has a brain as part at all times, and it is necessarily the 
same brain;"

RO specifies has part and part of as inverses, and both as transitive, which is 
even stronger than these. Essentially, RO (as expressed in OWL) requires us to 
think of continuant parthood at a single instant.

# Anntotations

BFO_0000050 part of
- add textual definition: a relation between two continuants or two occurrents, 
the part and the whole, in which the part is located within and belongs to the 
whole
- add example of usage: this day is part of this year (occurrent parthood)
- add example of usage: my brain is part of my body (continuant parthood, two 
material entities)
- add example of usage: my stomach cavity is part of my stomach (continuant 
parthood, immaterial entity is part of material entity)
- add editor note: A continuant cannot be part of an occurrent: use 
'participates in'. An occurrent cannot be part of a continuant: use 'has 
participant'. A material entity cannot be part of an immaterial entity: use 
'has location'.
- add editor note: Occurrents are not subject to change and so parthood between 
occurrents holds for all the times that the part exists. Many continuants are 
subject to change, so parthood between continuants will only hold at certain 
times, but this is difficult to specify in OWL. See 
https://code.google.com/p/obo-relations/wiki/ROAndTime

BFO_0000051 has part
- add textual definition: a relation between two continuants or two occurrents, 
the whole and the part, in which the part is located within and belongs to the 
whole
- add example of usage: this year has part this day (occurrent parthood)
- add example of usage: my body has part my brain (continuant parthood, two 
material entities)
- add example of usage: my stomach has part my stomach cavity (continuant 
parthood, material entity has part immaterial entity)
- add editor note: A continuant cannot have an occurrent as part: use 
'participates in'. An occurrent cannot have a continuant as part: use 'has 
participant'. An immaterial entity cannot have a material entity as part: use 
'location of'.
- add editor note: Occurrents are not subject to change and so parthood between 
occurrents holds for all the times that the part exists. Many continuants are 
subject to change, so parthood between continuants will only hold at certain 
times, but this is difficult to specify in OWL. See 
https://code.google.com/p/obo-relations/wiki/ROAndTime

Original issue reported on code.google.com by ja...@overton.ca on 2 Feb 2015 at 4:01

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I'm not sure that we would all agree on a definition of part-of given it is 
primitive.

The proposed one seems just unsatisfactory... belongs? Also we have located_in 
already, po isn't defined by located_in, and located_in doesn't work for 
occurrents.

What about synchronizing with SIO here?

Alternatively, taking something directly from a mereology text

Original comment by cmung...@gmail.com on 3 Feb 2015 at 4:11

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Lots (most?) of the relations in ROCore are primitive, but I haven't been 
distinguishing primitives from non-primitives. I've been proposing IAO_0000115 
'definition' annotations for (almost) everything. We could use IAO_0000600 
'elucidation' for primitive relations, if we distinguish them. I'm happy to do 
that, but I'd like to have clear instructions.

Original comment by ja...@overton.ca on 3 Feb 2015 at 4:41

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The point about 'located in' and 'belongs' is well taken; the definitions I 
proposed aren't good.

SIO says: "has part is a transitive, reflexive and antisymmetric relation 
between a whole and itself or a whole and its part." and "is part of is a 
transitive, reflexive and anti-symmetric mereological relation between a whole 
and itself or a part and its whole." I would like to keep the continuant and 
occurrent distinction from what I proposed. RO asserts transitivity but does 
not assert reflexivity or anti-symmetry. New suggestions:

- textual definition (or elucidation) for 'part of': a mereological relation 
between two continuants or two occurrents, the part and the whole
- textual definition (or elucidation) for 'has part': a mereological relation 
between two continuants or two occurrents, the whole and the part

both terms
- add editor note: A whole is considered part of itself, so this relation is 
reflexive.

Original comment by ja...@overton.ca on 3 Feb 2015 at 4:47

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The Stanford Encyclopedia of Philosophy is a good resource, and they have an 
article on mereology: http://plato.stanford.edu/entries/mereology/

Original comment by ja...@overton.ca on 3 Feb 2015 at 4:52

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Why is it important to specifically name continuants or occurrents?  are there 
other entities that don't fall into these two categories in which the relation 
could apply?

Original comment by michel.dumontier on 3 Feb 2015 at 5:27

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I believe that it's important to say "two continuants or two occurrents", to 
make it clear that you can't have occurrent parts of continuants or continuant 
parts of occurrents.

I've also proposed editor notes to remove this ambiguity. Maybe the editor 
notes are sufficient.

Original comment by ja...@overton.ca on 3 Feb 2015 at 5:37

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I think it works well to just add it as an editor note. the 
continuant/occurrent thing is very BFO.

Original comment by michel.dumontier on 3 Feb 2015 at 11:29

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I would tend towards a separate note too. If we want to be complete it would be

 between an independent continuant and an independent continuant or
 between an dependent continuant and an dependent continuant or
 between an occurrent and an occurrent

Which becomes a wee bit of a mouthful

w.r.t constraints I would like to have both

  X SubClassOf part_of only X

And the weaker but EL++

  X DisjointWith (part_of some X')

for all X in {IC,DC,O}, for all distinct pairs X,X'

Would these belong in core? Maybe the weaker axiom in some optionally imported 
auxhiliary ontology (for Elk users)?

Original comment by cmung...@gmail.com on 4 Feb 2015 at 1:15

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the subClassOf part_of only X is exactly what i have in SIO too. good idea to 
have aux ontology.

Original comment by michel.dumontier on 4 Feb 2015 at 2:13

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Revised to:

1. use SIO definitions (dropped 'is' from 'is part of'; added 'mereological' 
for 'has part)
2. add more detail on allowed pairings in editor notes

It still bothers me that we're saying "reflexive and anti-symmetric" in the 
textual definitions without asserting those logical characteristics, but I've 
been avoiding changes to logic.

BFO_0000050 part of
- add textual definition: part of is a transitive, reflexive and anti-symmetric 
mereological relation between a whole and itself or a part and its whole
- add example of usage: this day is part of this year (occurrent parthood)
- add example of usage: my brain is part of my body (continuant parthood, two 
material entities)
- add example of usage: my stomach cavity is part of my stomach (continuant 
parthood, immaterial entity is part of material entity)
- add editor note: Occurrents are not subject to change and so parthood between 
occurrents holds for all the times that the part exists. Many continuants are 
subject to change, so parthood between continuants will only hold at certain 
times, but this is difficult to specify in OWL. See 
https://code.google.com/p/obo-relations/wiki/ROAndTime
- add editor note (two paragraphs): Parthood requires the part and the whole to 
have compatible classes: only an occurrent can be part of an occurrent; only a 
process can be part of a process; only a continuant can be part of a 
continuant; only an independent continuant can be part of an independent 
continuant; only an immaterial entity can be part of an immaterial entity; only 
a specifically dependent continuant can be part of a specifically dependent 
continuant; only a generically dependent continuant can be part of a 
generically dependent continuant. (This list is not exhaustive.)

A continuant cannot be part of an occurrent: use 'participates in'. An 
occurrent cannot be part of a continuant: use 'has participant'. A material 
entity cannot be part of an immaterial entity: use 'has location'. A 
specifically dependent continuant cannot be part of an independent continuant: 
use 'inheres in'. An independent continuant cannot be part of a specifically 
dependent continuant: use 'bearer of'.

BFO_0000051 has part
- add textual definition: has part is a transitive, reflexive and antisymmetric 
mereological relation between a whole and itself or a whole and its part
- add example of usage: this year has part this day (occurrent parthood)
- add example of usage: my body has part my brain (continuant parthood, two 
material entities)
- add example of usage: my stomach has part my stomach cavity (continuant 
parthood, material entity has part immaterial entity)
- add editor note: Occurrents are not subject to change and so parthood between 
occurrents holds for all the times that the part exists. Many continuants are 
subject to change, so parthood between continuants will only hold at certain 
times, but this is difficult to specify in OWL. See 
https://code.google.com/p/obo-relations/wiki/ROAndTime
- add editor note (two paragraphs): Parthood requires the part and the whole to 
have compatible classes: only an occurrent have an occurrent as part; only a 
process can have a process as part; only a continuant can have a continuant as 
part; only an independent continuant can have an independent continuant as 
part; only a specifically dependent continuant can have a specifically 
dependent continuant as part; only a generically dependent continuant can have 
a generically dependent continuant as part. (This list is not exhaustive.)

A continuant cannot have an occurrent as part: use 'participates in'. An 
occurrent cannot have a continuant as part: use 'has participant'. An 
immaterial entity cannot have a material entity as part: use 'location of'. An 
independent continuant cannot have a specifically dependent continuant as part: 
use 'bearer of'. A specifically dependent continuant cannot have an independent 
continuant as part: use 'inheres in'.

Original comment by ja...@overton.ca on 5 Feb 2015 at 3:14

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There's good reasons not to use a reflexivity characteristic in ontologies 
(unless you are sure the relation is applicable to every thing in the 
universe). And anti-symmetric isn't available.

Anyway, I just meant that there's no reason RO and SIO couldn't converge on the 
same def, not that the existing one has to be the one we choose. I'm not 
massively keen on listing the characteristics - seems too incomplete for a 
formal def (where we might just use the technical term 'primitive') and too 
formal for a user-friendly def. But I'm not sure it matters so much.

How about trimming it down to "A core relation that holds between a part and  a 
whole."

And leaving it to individual ontologies to add their own specific annotations?

If we think it important to list characteristics in the def, how wbout spelling 
them out as in at the top of section 2.1 of the stanford entry:

(16)    Everything is part of itself.
(17)    Any part of any part of a thing is itself part of that thing.
(18)    Two distinct things cannot be part of each other.

Original comment by cmung...@gmail.com on 9 Feb 2015 at 4:00

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Updates to proposal:

BFO_0000050 part of
- add textual definition: A core relation that holds between a part and its 
whole.
- add editor note: Everything is part of itself. Any part of any part of a 
thing is itself part of that thing. Two distinct things cannot be part of each 
other.

BFO_0000051 has part
- add textual definition: A core relation that holds between a whole and its 
part.
- add editor note: Everything is part of itself. Any part of any part of a 
thing is itself part of that thing. Two distinct things cannot be part of each 
other.

Original comment by ja...@overton.ca on 10 Feb 2015 at 3:02

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This issue was closed by revision r410.

Original comment by ja...@overton.ca on 11 Feb 2015 at 2:16

• Changed state: Fixed