[Ontology-editors] plant-type terms etc.

[Jennifer Deegan (nee Clark)]

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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