Re: [Obo-format] Annotations in OBO

[Chris M. <cjm...@lb...>]

No. Residual mentions of this have been removed from the guide

On Feb 23, 2011, at 6:28 AM, Erick Antezana wrote:

> Chris,
> 
> is the [Annotation] stanza going to be part of the OBO spec (as from
> version 1.4)?
> 
> cheers,
> Erick
> 
> On 12 October 2010 23:21, Erick Antezana <eri...@gm...> wrote:
>> Yes, I agree that a mapping from GAF to OWL could do the trick.
>> 
>> if the [Annotation] and [Formula] stanzas will not longer be there,
>> could you delete the occurrences thereof in the OBO guide:
>> 
>> http://www.geneontology.org/GO.format.obo-1_4.shtml
>> 
>> cheers,
>> Erick
>> 
>> On 8 October 2010 23:00, Chris Mungall <cjm...@lb...> wrote:
>>> 
>>> On Oct 8, 2010, at 9:50 AM, Erick Antezana wrote:
>>> 
>>>> which ones were the original motivations (use cases) that promoted the
>>>> inclusion of that stanza?
>>> 
>>> unified syntax and semantics for ontologies and associated data.
>>> 
>>> that is still a motivation, it's just not clear that adding more constructs
>>> to obo-format is the way to go. for example, for GO annotations it may be
>>> simpler to map directly from GAFs to OWL.
>>> 
>>> In the deprecated obof1.3/obolog formal spec annotation stanzas were defined
>>> using the "that" construct in IKL, which provided a form of reification that
>>> allowed you to have seemingly contradictory statements in your knowledge
>>> base without inconsistencies. I recall something similar almost made it into
>>> OWL2.
>>> 
>>>> and what about the Formula stanza?
>>> 
>>> The original intent was to embed arbitrary FOL. The macro expansion tags
>>> give you the ability to do something similar for OWL2-DL, so moving from
>>> obof1.3 to 1.4, this stanza is no longer required.
>>> 
>>>> On 8 October 2010 18:05, Chris Mungall <cjm...@lb...> wrote:
>>>>> 
>>>>> I'm considering omitting these from the standard.
>>>>> 
>>>>> On Oct 7, 2010, at 12:46 AM, Erick Antezana wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> where can I find an example of the usage of the Annotations stanza?
>>>>>> 
>>>>>> is there any ontology making part (or not) of the OBO foundry that
>>>>>> already uses such stanza?
>>>>>> 
>>>>>> thanks,
>>>>>> Erick
>>>>> 
>>>>> 
>>> 
>>> 
>>