[Ontology-editors] plant-type terms etc.

[Jennifer Deegan (nee Clark)]

Hi,

I mean adding examples and deleting the synonyms.

Jen

Midori Harris wrote:
> If by "this" you mean adding examples and then deprecating sensu 
> synonyms, then yes.
> 
> m
> 
> On Mon, 1 Jun 2009, Jennifer Deegan (nee Clark) wrote:
> 
>> Excellent, thanks. If I hear no other objections I will plan to start 
>> this coming Monday.
>>
>> Are you happy for me to do this without consulting people outside this 
>> list?
>>
>> Jen
>>
>> Midori Harris wrote:
>>> no objection, then
>>>
>>> m
>>>
>>> On Mon, 1 Jun 2009, David Hill wrote:
>>>
>>>> I think if Jen adds the appropriate examples to the definition 
>>>> gloss, we could live without these.
>>>>
>>>>
>>>>
>>>> Jennifer Deegan (nee Clark) wrote:
>>>>> That might be nice actually, but I'd still like to make sure that 
>>>>> the terms stand alone without these synonyms. I think it is very 
>>>>> easy for those of us within the GO to rely on these synonyms as 
>>>>> clues, and the other users  have to manage without. I think if we 
>>>>> are not prepared to live without them then we need to think 
>>>>> carefully about why that is.
>>>>>
>>>>> Jen
>>>>>
>>>>> Chris Mungall wrote:
>>>>>>
>>>>>> 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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>>>>>>>>>>>>> Ontology-editors at geneontology.org
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>>>>>>>>>>>>>
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>>>>
>>>>
>>