[Ontology-editors] haspart documentation

[Chris Mungall]

On Jun 17, 2009, at 7:03 AM, 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

This is inverted. Remember, we ready from bottom-right to top-left

(this is why I am in favour of abandoning parent/child nomenclature,  
it just leads to confusion with the introduction of has_part)

I'm also in favour of eliminating denormalized tree type displays such  
as the one above for anything except is_a, part_of, develops_from and  
select others. It's less confusing if hp is written as sentences or  
drawn as a graph

precatalytic spliceosome has_part U4/U6 x U5 tri-snRNP complex
U4/U6 x U5 tri-snRNP complex has_part snRNP U5


>
> "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.)

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.

[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


>
> hope this is useful ...
>
> m
>
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