[Go] odd characters in term names

[Chris Mungall]

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 objection withdrawn.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
>>>
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
>> Consortium
>> Stanford University ** hitz at genome.stanford.edu
>>
>>
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> 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
>
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go