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

[Peter]

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