[Open-bio-l] Agreed name for UniProt XML file format

[Chris Fields]

On Jul 27, 2010, at 11:27 AM, Peter wrote:

> On Tue, Jul 27, 2010 at 5:14 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>> On Jul 27, 2010, at 10:31 AM, Peter wrote:
>> 
>>> Andrea has since pointed out that in the EBI REST services the file
>>> format is referred as "uniprot-xml" which is also less ambiguous
>>> (after all the old "swiss" plain text format might equally be referred
>>> to as the plain text UniProt format).
>>> 
>>> So, what do people feel about standardising on "uniprot" and/or
>>> "uniprot-xml" as the format name in Biopython, BioPerl & EMBOSS?
>> 
>> Agree with hilmar, 'uniprot-xml'.
> 
> That looks like a consensus (so far). Thank you all.
> 
>>> P.S. Chris, am I right in thinking that if BioPerl were to support this
>>> file format under the name "uniprot-xml" this would be equivalent
>>> to accepting format="uniprot" and variant="xml"? And furthermore
>>> and assuming you regard this as the default/only variant, Bio::SeqIO
>>> would also just accept format="uniprot"?
>> 
>> In cases where 'uniprot' is passed, we could handle it either way:
>> delegate to 'swiss' if xml isn't specified (so 'uniprot' is just an alias
>> of 'swiss'), or always use the XML handler for 'uniprot' and ignore
>> the variant argument.  Either way is fine with us.
> 
> Or raise an error as it is ambiguous? But that wouldn't be in the spirit
> of Perl though would it? ;)
> 
> Peter

An error is fine by me as well.  

chrus