[Ontology-editors] plant-type terms etc.

[Jane Lomax]

Yep - I'd just go ahead. I'll be very glad to see the back of sensu!

Jane

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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-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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