[Ontology-editors] haspart documentation

[Karen Christie]

Hi,

Working my way through Midori's example and the logic for reasoning, I now 
have a question on the reasoning for part_of.

So, this one is fine:

If child term A (mitochondrion) is a subclass of term B (intracellular
organelle), and term B (intracellular organelle) is part of term C
(cell), term A (mitochondrion) is part of term C (cell).

My question is on this one:

Term A (mitochondrial membrane) part of term B (mitochondrion), and
term B (mitochondrion) is a term A (intracellular organelle),
therefore Term A (mitochondrial membrane) is part of term C
(intracellular organelle)

It seems odd to me, to describe a thing that actually exists in cells,
the mitochondrial membrane (term A) as being part of something that is
a grouping term for a variety of cellular structures. However, this
seems OK logically if it means that mitochondrial membrane is part of
AN intracellular organelle.

However, if I put a slightly different word 'ALL' in place of 'AN',
then this isn't true:
mitochondrial membrane is part of ALL intracellular organelle.

So, I just wanted some clarification about how to think about the logic.

thanks,

-Karen




On Wed, 17 Jun 2009, Midori Harris wrote:

>> - good examples for the has part transitivity rules
>
> As promised yesterday, here's an example drawn from SF 2784316, which 
> motivated the push to get has_part live.
>
> Briefly:
> 'something' = precatalytic spliceosome
> 'something else' = U4/U6 x U5 tri-snRNP complex
> 'another thing' = snRNP U5
>
> More detail:
> At present we have (greatly oversimplified):
>
>  spliceosome GO:0005681
>  [i] U2-dependent spliceosome GO:0005684
>  --[p] snRNP U5 GO:0005682
>  --[p] [several other snRNP U(n) terms]
>
> Or, as a sentence, "snRNP U5 part_of U2-dependent spliceosome is_a 
> spliceosome".
>
> We also have another CC term, 'U4/U6 x U5 tri-snRNP complex' (GO:0046540), 
> which is is_a snRNP and has no direct part_of parent.
>
> But it's now known that there are several more types of spliceosome, not all 
> of which are catalytically active, and many of which are formed sequentially 
> by the addition, removal, and rearrangement of various snRNPs. A given snRNP, 
> such as snRNP U5, can thus be part of any of several different spliceosomal 
> complexes, and the part_of relationship now in GO is wrong.
>
> In the has_part pilot project, the oversimplified example will become:
>
>  precatalytic spliceosome GO:new
>  --[hp] U4/U6 x U5 tri-snRNP complex GO:0046540
>  ----[hp] snRNP U5 GO:0005682
>
> "Precatalytic spliceosome has_part U4/U6 x U5 tri-snRNP complex has_part 
> snRNP U5".
>
> Thinking about this example, I now doubt that has_part is transitive over 
> is_a, though. The new term will be is_a spliceosome:
>
>  spliceosomal complex GO:0005681 [renamed]
>  [i] U2-dependent spliceosome GO:0005684
>  --[i] precatalytic spliceosome GO:new
>
> ... and not all spliceosomal complexes have the U4/U6 x U5 tri-snRNP complex, 
> or even just U5. So I don't think the has_part.is_a section has the correct 
> conclusion. (I think is_a is transitive over has_part, i.e. the is_a.has_part 
> section is OK.)
>
> hope this is useful ...
>
> m
>
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