[Ontology-editors] plant-type terms etc.

[Midori Harris]

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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