[Ontology-editors] plant-type terms etc.

[David Hill]

The examples would be great.

David

Jennifer Deegan (nee Clark) wrote:
> Hi,
>
> Yes, I think I got my explanation wrong now I think about it. I am 
> bringing a mostly-formed thought from quite a complicated discussion.
>
> Some of the terms really benefit from saying 'plant-type' in the name 
> line, but there are others that could just do with an example in the 
> def to clarify things. I would like to check that people would be 
> happy for me to add these examples. I don't think that taking the 
> 'x-type' out is necessary.
>
> Thanks,
>
> Jen
>
> 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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-- 
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