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

[Jane Lomax]

As an aside, ChEBI also had the parent/child nomenclature issue, and 
they now use "incoming" "outgoing" instead e.g.

http://www.ebi.ac.uk/chebi/searchId.do;9F09D4D09954F8AFEDE8721A3ECD91C0?chebiId=CHEBI:32816

Although not sure this is a great solution either.

I think the documentation looks great btw!

Jane

Amelia Ireland wrote:
> 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
> BBOP Plant Project: http://bbopgarden.blogspot.com
>
>
>
>
>
>
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-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
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