synonyms

[J Clark]

Hi,

I think normally we'd just give sensu endings to the term name and synonym. 
However in some cases the sensu string would have to be something like 'in the 
sense used by developmental biologists' versus 'in the sense used by 
neuroscientists' rather than just a taxon name in the usual way. That makes it 
more difficult with our current system.

Would you say that's right David?

Jen

Midori Harris wrote:

> Hi David,
> 
> I don't think there's any question that GO should have terms for both 
> usages (assuming that both correspond to legitimate GO concepts). The 
> issue is what to name the terms, and I favor solutions like your second 
> alternative, in which we don't use the same string as the name of one term 
> and a synonym of another.
> 
> m
> 
> On Tue, 6 Sep 2005, David Hill wrote:
> 
> 
>>Hi Midori,
>>
>>This does go beyond neurogenesis because we just discussed it about 
>>myogenesis as well. The issue is that there are cases like neurogenesis 
>>and myogenesis that are used in two ways in the community. One solution 
>>to this would be to create terms for each. In the case of neurogenesis, 
>>it would be to create a term "neurogeneis" that describes a 
>>neurobiologists strict definition of the term. We would also use 
>>neurogenesis as a synonym for a more global term describing the 
>>formation of nervous tissue, a developmental biologist's view of the 
>>term. Alternatively, we could have created two separate terms that both 
>>have synonyms neurogenesis. What are people's thoughts on this?
>>
>>David
>>
>> Midori Harris wrote:
>>
>>
>>>Hi,
>>>
>>>Jen has brought it to my attention that this comment (made on SF 1262241) 
>>>should go to a wider audience, because neurogenesis is not the only term 
>>>affected:
>>>
>>>I've never been keen on using the same string as both a term name and a
>>>synonym (of any type/scope) for another term, because it gives a
>>>misleading impression that the two GO terms have the same meaning (if they
>>>did, they'd be merged). We've actively avoided doing it elsewhere in the
>>>ontologies, so it would be good to do the same for development-related
>>>terms.
>>>
>>>Admittedly, this is not in the synonym documentation, but it can easily be 
>>>added. One permissible exception is where one term is obsolete; an 
>>>obsolete term string may be used as a synonym for an 'active' term.
>>>
>>>Cheers
>>>Midori
>>>
>>>
>>>
>>> 
>>>
>>
>>
>>-- 
>>David P. Hill, Ph.D.
>>Senior Scientific Curator
>>Gene Expression Database
>>Gene Ontology Consortium
>>Mouse Genome Informatics
>>The Jackson Laboratory
>>600 Main Street
>>Bar Harbor, ME 04609-1500
>>tel:207-288-6430
>>htpp://www.informatics.jax.org
>>
>>
> 
>