[Go] odd characters in term names

[Suzanna Lewis]

So when OBO-Edit becomes ISO compliant (hopefully some time this  
year), what will the ramifications be for the rest of the software?

On Jan 8, 2009, at 11:33 AM, Chris Mungall wrote:

>
> FlyBase used to use SGML in gene names, not any more I believe.
>
> We generally strip errant latin-1 characters from the obo file prior  
> to loading into the main database. It sounds like it may benefit  
> others if this is done further upstream, between copying the editors  
> file to the public area.
>
> And whilst I agree that single apostrophes are fine for  
> computational processing, I think for human purposes they should be  
> avoided in term names, except where usage is either standard English  
> usage or extremely well known across species and part of standard  
> chemical nomenclature (e.g 5', 3').
>
> On Jan 8, 2009, at 10:06 AM, Jim Hu wrote:
>
>> I've run into a bunch of odd characters before when I was  
>> converting the GO obo file and gene associations to XML for loading  
>> GONUTS.  There used to be a bunch of SBML greek letters in some of  
>> the files.  I also used to see curly quotes that were probably from  
>> things pasted in from Word.  Primes aren't so bad... the worst was  
>> a right arrow in a sugar chemical name.
>>
>> Jim
>>
>> On Jan 8, 2009, at 9:58 AM, Benjamin Hitz wrote:
>>
>>> objection withdrawn.
>>>
>>> On Jan 7, 2009, at 1:15 PM, Benjamin Hitz wrote:
>>>
>>>>
>>>> So, we recently had two terms added under "Protein Complexes"
>>>> GO: 32221, Clr6 histone deacetylase complex II'
>>>> and
>>>> GO: 33698, Clr6 histone deacetylase complex I/I'
>>>>
>>>> I understand that the ' is part of the name, but it's sort of an  
>>>> unpleasant character to deal with.  These broke the SGD slim  
>>>> mapper.  Is there a set of characters that are not allowed in  
>>>> term names?  Should there be?  Or should I just man up and make  
>>>> sure to escape them.
>>>>
>>>> Ben
>>>>
>>>> --
>>>> Ben Hitz
>>>> Senior Scientific Programmer ** Saccharomyces Genome Database **  
>>>> GO Consortium
>>>> Stanford University ** hitz at genome.stanford.edu
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>
>>> --
>>> Ben Hitz
>>> Senior Scientific Programmer ** Saccharomyces Genome Database **  
>>> GO Consortium
>>> Stanford University ** hitz at genome.stanford.edu
>>>
>>>
>>>
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>>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
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>> http://fafner.stanford.edu/mailman/listinfo/go
>
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