[Ontology-editors] plant-type terms etc.

[Midori Harris]

oooh, I like it ... anything with this typedef could be suppressed in 
AmiGO displays

On Mon, 1 Jun 2009, 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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>