[Ontology-editors] OBO file format idea

[Chris Mungall]

I like the idea of having more consistency in the definitions, but I  
the solution below would require a change in the obo format spec and  
all downstream software to modify how it displays definitions.

My choice for structuring of the definitions is as follows:

"A" / "An" <genus> "that" <differentium> "." <optional gloss>

Note the differentium is typically a relation-term pair. In your  
example below this would be something like "acquires features of neuron"

it should be possible to parse noun phrases that correspond to the  
above grammar without the help of tags. The presence of the first  
"that" keyword and the closing "." should be sufficient.

Note that obol is capable of generating definitions, given a grammar.  
This could be useful for the trivial cross-product cases, where you  
are basically following a template anyway.

More generally, I think it would be good to have OE highlight phrases  
that correspond to names or synonyms of other terms (in the same or  
separate ontologies), highlighting them in the same manner as the  
spell-checker.

On Apr 23, 2009, at 7:32 AM, Jennifer Deegan (nee Clark) wrote:

> Hi Chris,
>
> Now that we are going to have intersection tags, do you think it  
> might be possible to also have tags that differentiate between the  
> parts of the text definition so that we can retrofit changes more  
> easily, and edit in a more sophisticated way in OBO-Edit? I was  
> thinking something like this:
>
> [Term]
> id: GO:0030182
> name: neuron differentiation
> namespace: biological_process
> def: "<genus>The process whereby a relatively unspecialized cell  
> acquires specialized features of a </genus><differentium>neuron</ 
> differentium><genus>.</genus><gloss>A neuron is a type of cell  
> that...</gloss>" [GOC:mah]
> is_a: GO:0030154 ! cell differentiation
> relationship: part_of GO:0048699 ! generation of neurons
>
> I think that if we had these tags then there could be new features  
> in OBO-Edit that would let us quickly improve swathes of  
> definitions. We could still have the option to quickly check each  
> change by eye, but without having to type each new def in manually.  
> These features could be similar to those that cascade override  
> methods to is_a child classes in Eclipse.
>
> Jen
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