synonyms

[Pascale Gaudet]

This seems reminiscent of the mitosis/meiosis story.

I think there are two ways to deal with this:
1. Avoid using the same string in two terms
2. Accept that the same string means different things to different people 
and capture that in GO.

I think that solution #2 is closer to reality. I am sure that everybody 
working on these concepts are aware that other people use the same string 
to mean different things. They must encounter this every time they search 
PubMed. As far as their conception of GO is concerned, I think that these 
researchers  would be more understanding of conflicting use of the same 
term rather than what might seem as an omission in GO.

Pascale


At 08:55 AM 9/6/2005 -0400, David Hill wrote:
>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