[Ontology-editors] plant-type terms etc.

[Karen Christie]

I have no objection to removing the sensu synonyms and I am all for having 
more descriptive information in the description.

-Karen


On Tue, 2 Jun 2009, Jennifer Deegan (nee Clark) wrote:

> Great, thanks. If I don't hear any objections I'll start on Monday then.
>
> Jen
>
> Jane Lomax wrote:
>> Yep - I'd just go ahead. I'll be very glad to see the back of sensu!
>> 
>> Jane
>> 
>> Jennifer Deegan (nee Clark) wrote:
>>> Excellent, thanks. If I hear no other objections I will plan to start this 
>>> coming Monday.
>>> 
>>> Are you happy for me to do this without consulting people outside this 
>>> list?
>>> 
>>> Jen
>>> 
>>> Midori Harris wrote:
>>>> no objection, then
>>>> 
>>>> m
>>>> 
>>>> On Mon, 1 Jun 2009, David Hill wrote:
>>>> 
>>>>> 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
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Ontology-editors mailing list
>>>>>>>>>>>>>> Ontology-editors at geneontology.org
>>>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>>>>>>>>>> 
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Ontology-editors mailing list
>>>>>>>>>>>>> Ontology-editors at geneontology.org
>>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>>>>>>>> 
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Ontology-editors mailing list
>>>>>>>>>> Ontology-editors at geneontology.org
>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>>>> 
>>>>> 
>>>>> 
>>> _______________________________________________
>>> Ontology-editors mailing list
>>> Ontology-editors at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>> 
>> 
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>