[Ontology-editors] haspart documentation (meeting with Chris (fwd))

[Amelia Ireland]

Hi again all,

re: comments on ordering the terms in the diagrams: I can see both  
sides of the argument for the order in which the terms are displayed,  
but I think that for the sake of clarity and consistency, I am going  
to going to stick to the following conventions:

for vertical diagrams, the root nodes will be at the top, and the leaf  
nodes at the bottom (as in AmiGO and OBO-Edit)

for horizontal diagrams, the root nodes will be on the left, and the  
leaf nodes on the right (as in AmiGO's browse mode, where the child  
terms are indented with respect to the parents).

The arrowheads provide a visual cue as to whether the relation goes  
parent --> child or vice versa.


re: has part examples... our example for "has part" from ye olde  
documentation is

	nucleus has part chromosome

Is this definitely, unequivocally, 100% true? When I did the  
chromosome / chromatin example, I was trying to find something that  
all chromosomes have, but it seems that just about everything is  
expendable! Maybe chromosome has part DNA would be easiest...


Tanya said:
> I have a question about the examples in general. Do we want them to  
> reflect the GO as it stands or not?  For example, the very first  
> example on one term having two different relationships to two  
> different parents isn't quite right, if we look at the ontology  
> literally.
[snip]
I went for an example that was relatively easy for anyone with basic  
biological knowledge to understand. I think in general it's probably  
better to go for clarity rather than fidelity to the exact ontology  
structure (especially given that the structure changes over time). I  
also wanted to try to avoid the "artificial" GO terms like  
'cytoplasmic part'... at least for the first diagram!


I'll do the various suggested minor edits and send out a new version  
later on.

Cheers!

--
Amelia Ireland
GO Editorial Office
http://www.berkeleybop.org || http://www.ebi.ac.uk
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