[Ontology-editors] plant-type terms etc.

[David Hill]

OK this makes sense.

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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>>>>>
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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