[DAS] Info about BioXML

[Schreiber, Mark]

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
> >>
> >>**************************************************************
> >>************
> >>This email (including any attachments) is intended for the 
> >>sole use of the
> >>intended recipient/s and may contain material that is 
> CONFIDENTIAL AND
> >>PRIVATE COMPANY INFORMATION. Any review or reliance by others 
> >>or copying or
> >>distribution or forwarding of any or all of the contents in 
> >>this message is
> >>STRICTLY PROHIBITED. If you are not the intended recipient, 
> >>please contact
> >>the sender by email and delete all copies; your cooperation 
> >>in this regard
> >>is appreciated.
> >>**************************************************************
> >>************
> >>_______________________________________________
> >>DAS mailing list
> >>DAS@biodas.org
> >>http://biodas.org/mailman/listinfo/das
> >>
> > 
> > _______________________________________________
> > DAS mailing list
> > DAS@biodas.org
> > http://biodas.org/mailman/listinfo/das
> > 
> 
> 
> -- 
> BioJava Consulting LTD - Support and training for BioJava 
> http://www.biojava.co.uk
> 
> 
> 
> _______________________________________________
> DAS mailing list
> DAS@biodas.org
> http://biodas.org/mailman/listinfo/das
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================