[Ontology-editors] plant-type terms etc.

[Jennifer Deegan (nee Clark)]

Hi,

Yes, I think I got my explanation wrong now I think about it. I am 
bringing a mostly-formed thought from quite a complicated discussion.

Some of the terms really benefit from saying 'plant-type' in the name 
line, but there are others that could just do with an example in the def 
to clarify things. I would like to check that people would be happy for 
me to add these examples. I don't think that taking the 'x-type' out is 
necessary.

Thanks,

Jen

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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