[MOBY-dev] data by reference - a request for comments

[José María Fernández González]

IMHO it can be dangerous for the MOBY payload integrity using XInclude at 
mobyContent childs (mobyData) level, but it can be needed in scenarios like 
the one described by Pieter. For security reasons, XInclude / XLink / XPointer 
should be restricted to the contents of mobyData, not to MOBY Data itself. For 
instance, references to Simples or Collections, Collections composed by a 
mixure of Simples and references to Simples, or Secondary parameters copied 
from run to run.

	Best Regards,
		José María

Mark Wilkinson wrote:
> On Wed, 23 Jul 2008 08:06:38 -0700, Pieter Neerincx 
> <pieter.neerincx at gmail.com> wrote:
> 
> 
>> That doesn't sound very appealing to me. I use quite large data 
>> structures and can have tens of thousands of them in a collection 
>> (think of oligos for micro arrays.) If I can only replace the 
>> primitives with references, I would still have to send a BioMoby XML 
>> structure with hundreds of thousands of references replacing the 
>> primitives.
> 
> Hmmm... that's a situation that we had NEVER considered!  Putting xlinks 
> into a component of the Moby message higher than the mobyData block was 
> not a scenario that came up during our discussions in Tokyo.  the xlink 
> was really only intended to carry data, not data + moby message 
> structure...  but I suppose it COULD!
> 
> How do others feel about this?
> 
> M
> 
> 
> 

-- 
"There is no reason why anybody would want a computer in their home" -
	Ken Olson, founder of DEC 1977
"640K ought to be enough for anybody" - Bill Gates, 1981
"Nobody will ever outgrow a 20Mb hard drive." - ???

"Premature optimization is the root of all evil." - Donald Knuth

José María Fernández González
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
Unidad del Instituto Nacional de Bioinformática
Biología Estructural y Biocomputación	Structural Biology and Biocomputing
Centro Nacional de Investigaciones Oncológicas
C.P.: 28029				Zip Code: 28029
C/. Melchor Fernández Almagro, 3	Madrid (Spain)

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.