[Ontology-editors] plant-type terms etc.

[David Hill]

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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>>>>>>>>> Ontology-editors at geneontology.org
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>>>>>>>>>
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>>>

-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430