[Ontology-editors] plant-type terms etc.

[Jennifer Deegan (nee Clark)]

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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>>>>>>>>>>>
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