[Ontology-editors] use of word "gloss" Re: plant-type terms etc.
Karen Christie
kchris at genome.stanford.edu
Tue Jun 2 11:14:15 PDT 2009
Yes, as someone who is more oriented towards annotation too, I also feel
offended by the use of the word gloss to describe the only part of the
definition that actually helps me annotate.
I would like to suggest that the ontologically oriented should stop using
a word that offends annotators, which constitute a major use community for
GO, and instead use a word that conveys meaning about the second part of
the definition.
-Karen
On Tue, 2 Jun 2009, Alexander Diehl wrote:
> "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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>
> --
> 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
> fax: +1 (207) 288-6131
>
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