[Ontology-editors] haspart documentation

[Midori Harris]

some clarifications ...

On Wed, 17 Jun 2009, Chris Mungall wrote:
> On Jun 17, 2009, at 7:03 AM, Midori Harris wrote:
>
>> 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
>
> This is inverted. Remember, we ready from bottom-right to top-left

I did wonder whether to put in a tree at all. But the point is to provide an example

> It's less confusing if hp is written as sentences or drawn as a graph

erm, I did include exactly the same sentence as you put in ...


>> 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.)
>
> has_part is transitive over is_a, but don't worry, it doesn't lead to the 
> erroneous conclusion. If you draw the example as a graph, or invert the tree 
> above such that the implication always flows from bottom right to top left 
> then this should become apparent.

I must have the R1-transitive-over-R2 wording backwards in my head ... but 
that's for me to sort out. The important thing is that for has_part and 
is_a, it works one way round but not the other (in contrast to part_of + 
is_a, which allows inference either way round).

>
> [1] precatalytic spliceosome has_part U4/U6 x U5 tri-snRNP complex
> [2] precatalytic spliceosome is_a spliceosomal complex
> [3] U4/U6 x U5 tri-snRNP complex has_part snRNP U5
>
> From [1]+[3] and transitivity of has_part we infer:
> precatalytic spliceosome has_part snRNP U5
>
> but we don't infer anything about spliceosomal complexes

That's my point - there's a bit in the doc draft that *does* the 
equivalent of making an inference about spliceosomal complexes, so it 
needs fixing.

m