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

Tue Jun 2 11:07:50 PDT 2009

"Gloss" seems to be favored by the more ontologically oriented for the 
bits of a definition that provide clarification to the definition for 
human readers, according to one of the definitions of the word:

gloss2
noun
a translation or explanation of a word or phrase.

The problem I have with "gloss" is that the word carries some negative 
connotations:
as a noun:  a superficially attractive appearance or impression ;
as a verb: ( gloss over) try to conceal or disguise (something 
embarrassing or unfavorable) by treating it briefly or representing it 
misleadingly.

I always feel a bit offended when Chris describes the interesting parts 
of a carefully crafted definition as its "gloss," although I understand 
his meaning is not pejorative.

-- Alex

Karen Christie wrote:
> Could we please stop using the word "gloss". It is completely 
> meaningless.
>
> 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.
>
> -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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>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
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>>>>>>
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-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
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