[Ontology-editors] plant-type terms etc.

[David Hill]

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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-- 
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