[Bioperl-l] SwissProt/UniProt GN line format changed

Hilmar Lapp hlapp at gmx.net
Sun Aug 1 06:04:43 EDT 2004

On Saturday, July 31, 2004, at 07:05  PM, Ewan Birney wrote:

>> The problem with writing the new format is that that would require 
>> some
>> additions to the object model, because it would require context for 
>> the
>> individual annotation values ('Name', 'Synonym', 'OrderedLocusName', 
>> or
>> ORFName). Presently, annotation values do not have context in Bioperl.
> Or rather I think we would have to make a new Annotation type, being
> something like 'MultiTaggedValue' which would have tags 'Name', 
> 'Synonym'
> etc and then the 'gene_name' annotation key would give a list of
> 'MultiTaggedValues' --- presumably with some magic to detect "old 
> style"
> simplevalue tags as well.

The thing is that SimpleValue is not the only one that could use 
context. There are dbxrefs with context too. If you made annotation 
objects generally context aware (while it would be left to the 
implementing class to define what to do with the context - much as with 
as_text()), you'd kill all those cases simultaneously.


Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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