[DAS] Info about BioXML

[James Freeman]

Hi Folks,

A good start to this exists and is at:

http://www.visualgenomics.ca/gordonp/xml/

The I3C has its sights on either AGAVE or BSML, BSML is a valid output 
in bioperl, so that is also a good start, at least a fast one.

Warmest Regards,

Jim

Schreiber, Mark wrote:

>I would agree with the desire to have several small schemas (schemata if
>you had a classical education).
>
>I particularly like the way GenBank uses three weights of XML. One
>represents everything in a GB file in ridiculous detail down to the most
>light weight which is pretty much the name and the sequence. The use of
>mod files is a good way to let you plug and play to make a include
>everything schema out of several small schemas.
>
>And finally, um, shouldn't we move this discussion to something like
>Open Bio as its not really DAS (just a thought)
>
>- Mark
>
>
>>-----Original Message-----
>>From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
>>Sent: Wednesday, 25 September 2002 12:16 a.m.
>>To: Wiepert, Mathieu
>>Cc: 'Suraj_Meiyur'; 'das@biodas.org'
>>Subject: Re: [DAS] Info about BioXML
>>
>>
>>Hi,
>>
>>BioXML would be a good thing to resurrect. I would be happy to help 
>>manage it. My vision would be to publish several (perhaps many) small 
>>xml-schema deffinitions for common biological data types & 
>>encoders/decoders for each project. This should help us avoid getting 
>>bogged down in the eternal data-model for everything quagmire.
>>
>>There is also the issue of SOAP services & interfaces - we 
>>should realy 
>>be doing something in this area, but java seems to be becomming the 
>>standard webservices language, so I don't know if the other projects 
>>would be interested.
>>
>>
>>
>>Wiepert, Mathieu wrote:
>>
>>>Hi,
>>>
>>>I can only point you to some posts from the archive, such 
>>>
>>as this one, 
>>
>>>from April...
>>>
>>><post>
>>>There are a number of standards; none has swept the others yet, 
>>>although this
>>>will probably happen in time:
>>>
>>>	GAME	- berkeley annotation format
>>>	BSML	- from visual genomics
>>>	AGAVE	- from doubletwist, now defunct
>>>	DAS	- for simple annotations
>>>
>>>The departure of BioXML is lamentable.  We really need to bring it 
>>>back!  Any
>>>volunteers?
>>></post>
>>>
>>>http://bioperl.org/pipermail/bioperl-l/2002-April/007720.html
>>>
>>>-Mat
>>>
>>>
>>>>-----Original Message-----
>>>>From: Suraj_Meiyur [mailto:Suraj_Meiyur@satyam.com]
>>>>Sent: Monday, September 23, 2002 5:16 AM
>>>>To: 'das@biodas.org'
>>>>Subject: [DAS] Info about BioXML
>>>>
>>>>
>>>>Hi,
>>>>	I am a Bioinformatician and would like to know more
>>>>about bioxml.
>>>>The site www.bioxml.org doesn't seem to work. Does that mean 
>>>>an end to the
>>>>initiative or a temporary hitch in services that are being 
>>>>rendered by the
>>>>bioxml community.
>>>>
>>>>Regards,
>>>>Suraj
>>>>
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>>
>>-- 
>>BioJava Consulting LTD - Support and training for BioJava 
>>http://www.biojava.co.uk
>>
>>
>>
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