[Ontology-editors] plant-type terms etc.

[Midori Harris]

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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>>> 
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