[DAS] categorize

[Lincoln Stein]

I think the "categorize" functionality is obsolete.

Lincoln

On Tue, Aug 31, 2010 at 2:32 PM, Thomas Down <thomas.a.down at gmail.com>wrote:

> FYI, Dazzle does respect categorize=(yes|no):
>
>          view-source:
>
> http://www.derkholm.net:8080/das/hsa_54_36p/features?segment=22:30000000,30010000;type=transcript;type=translation
>
>          view-source:
>
> http://www.derkholm.net:8080/das/hsa_54_36p/features?segment=22:30000000,30010000;type=transcript;type=translation;categorize=yes
>
> ...but it's always struck me as fairly useless -- one "optional" field in a
> fairly verbose XML schema, and I certainly won't mourn it if you feel like
> deprecating.
>
>                   Thomas.
>
> On Tue, Aug 31, 2010 at 5:15 PM, Andy Jenkinson <andy.jenkinson at ebi.ac.uk
> >wrote:
>
> > Hi list,
> >
> > One of the (hopefully final) questions over the 1.6 specification
> concerns
> > the "categorize" parameter in the features request. In DAS 1.53, this
> > parameter is optional and may be either "yes" or "no". The default value
> is
> > "no". The purpose is to instruct the server as to whether it must include
> in
> > its response the optional "category" attribute of the <TYPE> element.
> > However in practice, I believe most servers actually ignore this
> parameter
> > and always include category information if it is available. If it is not
> > available, servers cannot satisfactorily comply with a "categorize=yes"
> > request and generally always provide an empty category attribute.
> >
> > In current drafts of 1.6, the category attribute remains optional but the
> > categorize parameter has its default reversed (that is, it matches what
> > servers currently do, and a request to specifically remove the category
> from
> > the response can more easily be honoured by core server software.
> However,
> > it is apparent that the functionality offered by the categorize parameter
> is
> > really rather limited. Its only real purpose in this form is to reduce
> the
> > volume of the response. In addition, given the introduction of the
> ontology
> > and expansion of DAS to more diverse domains, the category itself is
> > becoming less important. If, for example, the ontology cvIds become
> > mandatory in the next version of the specification, we could feasibly
> > deprecate it.
> >
> > So, it has been proposed that the categorize parameter be deprecated in
> > 1.6, with a view to also deprecating the category attribute if and when
> > ontology support becomes mandatory. Does anyone have any objections?
> >
> > Cheers,
> > Andy
> > _______________________________________________
> > DAS mailing list
> > DAS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das
> >
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>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>