[Ontology-editors] haspart documentation

[Midori Harris]

> - 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