[Ontology-editors] plant-type terms etc.

[Jennifer Deegan (nee Clark)]

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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>>>>>>
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