synonyms

[David Hill]

Yes, but in a lot of cases, it is not even as clearcut as embryologists 
vs neuroscientists. I really don't think the sensu solution is a good one.

David

J Clark wrote:

> 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
>>>
>>>
>>
>>


-- 
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