[Ontology-editors] OBO file format idea

[Jennifer Deegan (nee Clark)]

Should I put this on the wiki somewhere to store it for a later date 
when we might have time to do something?

Jen

Chris Mungall wrote:
> 
> 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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