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

Tue Jun 2 14:00:39 PDT 2009

Interesting that there is actually a definition that is non-pejoritive and 
relevant to the context it is being used in here, though from Amelia's 
comment it seems that we are using too much text for that meaning to 
actually be appropriate.

I find the word offensive because when I look it up on my default web 
based dictionary (www.dictionary.com), these are the defs at the top of 
the page, several of which use words such as 'false' or 'superficial', 
though there is also one def relating to the meaning Amelia isn't so fond 
of ;)

noun
1. 	a superficial luster or shine; glaze: the gloss of satin.
2. 	a false or deceptively good appearance.
3. 	Also, glosser. a cosmetic that adds sheen or luster, esp. one for 
the lips.
verb (used with object)
4. 	to put a gloss upon.
5. 	to give a false or deceptively good appearance to: to gloss over 
flaws in the woodwork.

And responding to the question, do I find the 'logical' definition to also 
be descriptive, no, I don't. I find the logical def to be a text statement 
of things I can see from the graph, but it does not describe the relevant 
biology to me.

I'm not tied to the word 'descriptive' if someone has another suggestion.

thanks,

-Karen

On Tue, 2 Jun 2009, Chris Mungall wrote:

>
>
> 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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