Standardized Term Names

[Jennifer I Clark]

Hi Chris,

I was thinking more about the cell differentiation things. I reckon your 
obol parser would be okay without the synonyms as long as I tell you a 
few more naming rules.

We have the following kinds of differentiation terms:

x cell differentation
xblast differentation
xphil differentation

where the word endings 'blast' and 'phil' are synonyms for the word 
'cell' in the first example. If I just tell you about these extra rules 
then could you add them to the pareser? That way I wouldn't need to to 
bother with the synonyms. I could add documentation to the website to 
say that where these endings are in a term we don't add the word 'cell' 
since it is redundant.

Thanks,

Jen

Chris Mungall wrote:

>Whichever way we do it, I don't think we should mark up things in the
>ontology just to suit a particular piece of software.
>
>We should only do this if it doesn't impact curation time and if the
>notion of a 'formal' synonym for a term is useful to humans.
>
>Here are the criteria for a formal synonym:
>
>- it must be an exact synonym
>  [ and would still be designated as such in the obo file, it
>    would just have an additional qualifier ]
>
>- the existing term name is some kind of colloquial shorthand
>  that is readily recognised by most biologists, yet the naming
>  style of the shorthand is different from the consistent naming
>  style employed for similar terms
>
>- the existence of the synonym is a genuine rephrasing of the
>  term name, and does not exist by virtue of alternate spellings
>  of words.
>
>- the formal synonym must employ canonical spellings
>
>Why would this be useful to humans too? Well, sometimes it may be useful
>to organise a set of terms such that either the formal synonym (or just
>the name if there is no designated formal synonym) is used as the primary
>label. Thus the term with name "methanogenesis" will be listed as "methane
>biosynthesis" and will have consistent labeling style with other "X
>biosynthesis" terms.
>
>If this isn't useful then we shouldn't bother.
>
>If we don't, then what I do think will be useful (and what will be quite
>sufficient for obol) is to separate the useful exact_synonyms from the
>exact_synonyms that are derivable from the exact_synonyms of sub-terms.
>
>An example is "sulfite reduction/sulphite reduction". This is only useful
>for the purposes of searching, and could be handled automatically.
>Displaying this synonym is of no use to the user.
>
>Cheers
>Chris
>
>On Fri, 18 Feb 2005, John Day-Richter wrote:
>
>  
>
>>J Clark wrote:
>>
>>    
>>
>>>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?
>>>      
>>>
>>We have synonym types in OBO-Edit... just hang on! A beta-version will
>>be out soon (of course, you won't be able to save your changes to the
>>repository for a while after that, because everyone else will still be
>>using DAG-Edit).
>>
>>For now, I suggest you add a synonym dbxref to the OBO synonyms (like
>>"syntype:obol"). Once we move to full-fledged synonym types, we can do a
>>quick search-and-replace to change those dbxrefs into synonym category
>>identifiers.
>>
>>    -John
>>
>>
>>    
>>