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

[Tanya Berardini]

Hi Amelia,

>
> http://www.ebi.ac.uk/~aji/go/GO.ontology.relationships.shtml<http://www.ebi.ac.uk/%7Eaji/go/GO.ontology.relationships.shtml>


This looks really good.


>
>
> Questions:
>
> - are those examples OK?
>

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.

mitochondrion is_a cytoplasmic part part_of cytoplasm

instead of

mitochondrion part_of cytoplasm

I know that we can get the latter relationship by transitivity and the
introduction of the  xxx_part terms makes things a bit more complicated but
I wonder whether readers will be confused by the differences if we leave the
docs as they are.



> - should I make more of the difference between "has part" and "part of",
> and that one is from the perspective of the child, whereas the other is from
> the perspective of the parent?
>

Do you think it might be useful to color-code the parent and child terms in
the illustrations that only show two terms?  It would be an additional cue
to the differences, on top of the left vs. right arrangement of the terms.
(For part of, has part and regulates)

>
> - have any colours been thought of for the "has part" link?
>
> - in the has-part diagrams, I tried to make a visual difference between the
> "ALL x ... y" and "SOME x ... y" rules. Does it make it any clearer, or
> should I just redo those diagrams in the standard style?


I think the ALL lines are slightly bolder in the has part documentation vs.
ALL lines in the the part of (and regulates) documentation.  I like the
wider lines in has part better.

Am also not sure whether all chromosomes have chromatin.

Regulates doc:

" The Gene Ontology uses generic "regulation of ..." terms as a catch-all
for anything that regulates the parent term,"

perhaps better to say

" The Gene Ontology uses generic "regulation of ..." terms to encompass any
process that modulates the parent term,"

I can just see us getting pounced on for 'catch-all' :).

For regulates * part of:

I would drop this sentence.

" This rule is limited to the regulates relation."

That's it for now.

Thanks,

Tanya


-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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