[Ontology-editors] use of word "gloss" Re: plant-type terms etc.

[Chris Mungall]

On Jun 2, 2009, at 6:52 PM, Karen Christie wrote:

> Could we please stop using the word "gloss". It is completely  
> meaningless.

Merriam Webster:
1 a (1) : a brief explanation or a translation or definition (as one  
appearing in the margin or between the lines of a text or in a  
wordbook based on the text) of a textual word or expression felt to be  
difficult or obscure (2) : an expanded interpretation of or commentary  
on a textual word or expression

> For the "logical" part of the definition, we have a word that  
> explains the type of information. "Gloss" does not do that. Could we  
> start calling this the "descriptive" part of the definition. Then  
> both aspects of the definition have a word that is descriptive as to  
> the type of information contained there.

sure, but would you not consider the logical part also descriptive?  
I'm not sure why you find the word gloss so offensive. I'll try and  
stick with "descriptive part of definition" but I am a very slow and  
lazy typist so sorry in advance if I occasionally slip into saying  
"gloss"

>
> -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
>>>>>>>>>>>>>>> _______________________________________________
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