[Ontology-editors] plant-type terms etc.

[Midori Harris]

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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>>> 
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>