[Ontology-editors] plant-type terms etc.

[Jennifer Deegan (nee Clark)]

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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