Standardized Term Names

[J Clark]

Hi Chris,

If there was a way to mark the 'obol' synonym then I could 
easily assign the synonym type to that as I went along. 
Might this be a possibility with DAG-Edit John?

Thanks,

Jen

Chris Mungall wrote:

> Yes, this is correct. I can make Obol start using the synonyms. Naming
> policy certainly shouldn't be constrained by Obol!
> 
> What would be nice is if one synonym could be designated the 'formal'
> exact synonym, in the cases where a term already has an exact synonym. Not
> sure if Dag edit allows this yet. But this isn't super important, it
> should mostly be possible to automatically work out which synonym best
> communicates the actual meaning.
> 
> On Fri, 18 Feb 2005, J Clark wrote:
> 
> 
>>Hi,
>>
>>I asked Chris about this before and he said that it just
>>deals with term names just now. However, he said that I
>>could start adding the structured names as synonyms if they
>>are not suitable as term names, and that he would get obol
>>to parse those synonyms marked as being of interest at a
>>later date.
>>
>>So in other words, if I put these redundant term names in as
>>synonyms then they can be used by obol a bit later on, and
>>they will be out of the way of the biologists.
>>
>>Jen
>>
>>Midori Harris wrote:
>>
>>
>>>Chris will have to comment on obol's capabilities ... I've been under the
>>>impression that it deals only with term names at present, but I may be
>>>mistaken.
>>>
>>>m
>>>
>>>On Fri, 18 Feb 2005, Alexander Diehl wrote:
>>>
>>>
>>>
>>>>Jen and Midori,
>>>>
>>>>Thank you for your replies.  Yes, I would prefer these term names to
>>>>return to their original formulations.  I would also argue that it
>>>>should be unnecessary to change term names to enable obol to  figure
>>>>them out in cases where obol can easily read the term parentage as
>>>>well as any human.  I would expect this to be a part of the obol
>>>>algorithm already, though perhaps the program is not that
>>>>sophisticated.
>>>
>>>[snip]
>>>
>>>
>>>
>>>>-- Alex
>>>>
>>>>At 9:59 AM +0000 2/18/05, J Clark wrote:
>>>>
>>>>
>>>>>>better as a synonym than as the term name! so if obol needs it, OK
>>>>>>
>>>>>>(I do think Alex has a point, that actual human beings should be
>>>>>>able to suss it out ... but computers aren't as smart as us.)
>>>>>
>>>>>Cool. I'll wait for Alex to respond and if he's happy that I'll go ahead.
>>>>>
>>>>>Jen
>>>
>>>
>>>
>>

-- 
EMBL - European Bioinformatics Institute,
Gene Ontology Consortium,
and Wolfson College, Cambridge.
http://www.ebi.ac.uk/~jclark/