[Ontology-editors] plant-type terms etc.

[Chris Mungall]

What about adding a synonymtypedef 'historic', or 'deprecated'?

On Jun 1, 2009, at 9:07 AM, Jennifer Deegan (nee Clark) wrote:

> Hi,
>
> I think that for new users it is confusing to have them in place. We  
> no longer explain to users what 'sensu' means and they are likely to  
> look at the synonyms and assume that they are still current and  
> ascribe their own assumed meaning to them. I think it is very  
> important that they are either still supported and kept correct or  
> removed altogether.
>
> Jen
>
> David Hill wrote:
>> Jen,
>> How does it hurt to have the synonyms there?
>> David
>> Jennifer Deegan (nee Clark) wrote:
>>> Hi,
>>>
>>> Following on from this, I would like to start stripping out the  
>>> sensu synonyms from the live file.
>>>
>>> I am not planning to do it in one big deletion, but rather remove  
>>> them incrementally, checking in each case that no information is  
>>> lost. I envisage going through the terms on at a time, adding  
>>> examples as discussed here, and deleting the synonym when I am  
>>> happy that the meaning of the term is clear. I do not anticipate  
>>> that this will take very long.
>>>
>>> Would anybody have any objection to my starting to do that?
>>>
>>> Thanks,
>>>
>>> Jen
>>>
>>>
>>>
>>> Midori Harris wrote:
>>>> Yes, taking the issue of examples separately, there's no reason  
>>>> not to include more, and they would probaby be very helpful.
>>>>
>>>> m
>>>>
>>>> On Mon, 1 Jun 2009, Chris Mungall wrote:
>>>>
>>>>>
>>>>> I agree, no need to revisit the naming issue.
>>>>>
>>>>> However, these terms are in the minority. There are a larger set  
>>>>> of terms in which specific examples would be helpful. Examples  
>>>>> would always go in the gloss part of the definition, and ideally  
>>>>> have a citation. I think this is just clarifying existing GO  
>>>>> policy.
>>>>>
>>>>> On Jun 1, 2009, at 8:47 AM, Midori Harris wrote:
>>>>>
>>>>>> I seem to recall several annotators expressing a strong  
>>>>>> preference for the names like 'plant-type vacuole' when we  
>>>>>> discussed it at a GOC meeting. Given that these names got the  
>>>>>> full discuss-at-meeting treatment, and that the current names  
>>>>>> are thus a consensus meeting outcome (tm), I wouldn't change  
>>>>>> them without obtaining explicit approval from the larger GO  
>>>>>> group.
>>>>>>
>>>>>> m
>>>>>>
>>>>>> On Mon, 1 Jun 2009, Jennifer Deegan (nee Clark) wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> A proposal has been made as follows:
>>>>>>>
>>>>>>> Instead of putting modifiers like 'plant-type' in term names  
>>>>>>> to make the meaning of the more esoterically defined terms  
>>>>>>> clear, we should just put an example in the definition gloss.  
>>>>>>> For example this term:
>>>>>>>
>>>>>>> GO:0000325
>>>>>>> name: plant-type vacuole
>>>>>>> exact: vacuole, cell cycle-independent morphology
>>>>>>> def: A closed structure, found only in eukaryotic cells, that  
>>>>>>> is completely surrounded by a unit membrane, contains liquid,  
>>>>>>> and retains the same shape regardless of cell cycle phase.  
>>>>>>> [source: GOC:mtg_sensu, ISBN:0815316208]
>>>>>>>
>>>>>>> would become:
>>>>>>>
>>>>>>> GO:0000325
>>>>>>> name: vacuole, cell cycle-independent morphology
>>>>>>> def: A closed structure, that is completely surrounded by a  
>>>>>>> unit membrane, contains liquid, and retains the same shape  
>>>>>>> regardless of cell cycle phase. An example of this structure  
>>>>>>> is the vacuole of plant cells. [source: GOC:mtg_sensu, ISBN: 
>>>>>>> 0815316208]
>>>>>>>
>>>>>>> Would anybody have any objection to this change? The  
>>>>>>> advantages are that this policy would remove prominent taxon  
>>>>>>> information from the file but would still leave information in  
>>>>>>> the gloss to clarify the meaning of the term. The disadvantage  
>>>>>>> is that the less prominent clue to the meaning of the term  
>>>>>>> would leave users having to hunt a bit more to find what they  
>>>>>>> want.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Jen
>>>>>>>
>>>>>>>
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