psidev-ms-dev

[Psidev-ms-dev] dataXML 0.9 ready for first feedbacks

[Pierre-Alain B. <pie...@is...>]

Dear mzdata implementers and psi-ms-dev mailing list registrants,

1) *dataXML*
dataXML (as being the merge between mzData and mzXML, and becoming the 
PSI MS data standard replacing mzData) is ready for a first feedback 
from you, implementers and PSI MS active members. We target to finalise 
version 1.0 right after the next PSI Spring Workshop (see below)

The related documents and information can be obtained on the new PSI 
website http://psidev.info, and more precisely at 
http://psidev.info/index.php?q=node/257

The page has a restriction to MS group registrants. If you cannot access 
the page, you can register to the website and ask to view the MS group 
information

Please look at the documents and feedback to psidev-ms-dev mailing list 
or to Eric Deutsch directly.


2) *PSI Spring Meeting 2007*
I would also like to inform you about the PSI spring meeting 
http://psidev.info/index.php?q=node/113. It is organized in Lyon, 
France, April 23-25th, 2007. A preliminary agenda is available. We 
target to get a version 1.0 of dataXML right after the workshop. The 
registration is not formally open, but you can already book the dates. 
Information on hotels will also appear soon.

With my best regards
Pierre-Alain


-- 
--
 Dr. Pierre-Alain Binz
 Swiss Institute of Bioinformatics
 Proteome Informatics Group
 1, Rue Michel Servet
 CH-1211 Geneve 4
 Switzerland
 - - - - - - - - - - - - - - - - -
 Tel: +41-22-379 50 50
 Fax: +41-22-379 58 58
 Pie...@is...
 http://www.expasy.org/people/Pierre-Alain.Binz.html

Re: [Psidev-ms-dev] dataXML 0.9 ready for first feedbacks

[Mike C. <tu...@gm...>]

On 2/6/07, Pierre-Alain Binz <pie...@is...> wrote:
>  dataXML (as being the merge between mzData and mzXML, and becoming the PSI
> MS data standard replacing mzData) is ready for a first feedback from you,
> implementers and PSI MS active members. We target to finalise version 1.0
> right after the next PSI Spring Workshop (see below)

Looking on this page, the only normative material I'm seeing are the
two XML schema.  Is there other material that I'm missing?  I would
have expected to see detailed normative prose describing the meaning
and proper usage of the various elements.  Without this, implementers
will probably use this schema in incompatible ways, leading to future
headaches.

Here are a couple of examples of what seems to be missing.  I think I
know that the X axis for spectrum data represents M/Z values, where M
is mass in amu's and Z is the integer charge.  This ought to be
specified explicitly.

As a more detailed example, I think I know that spectrum data is
represented as the base64-encoded form of IEEE float values.  (This
also needs to be specified.)   IEEE floats can take on several special
values like "positive infinity" and error values.  Is it legal to
place these values in a dataXML file?  Whether or not this is so, what
is a receiver expected to do if it encounters such values?

As an example of the kind of normative prose I'm thinking of, here is
a link to a working copy of an ANSI C standard

    http://www.open-std.org/jtc1/sc22/wg14/www/docs/n1124.pdf

(Obviously, the dataXML prose would be much shorter.)

Another nice thing that the ANSI C committee produces is a rationale
document, which explains the reasoning behind many of the major
decisions taken, correlated to the specification.  It would be nice to
have an mzData rationale document as well, to explain the thinking
behind its design decisions (e.g., base64/binary representation of
floats).

    http://www.open-std.org/jtc1/sc22/wg14/www/C99RationaleV5.10.pdf

Regards,
Mike Coleman

Re: [Psidev-ms-dev] dataXML 0.9 ready for first feedbacks

[Eric D. <ede...@sy...>]

Hi Mike, thank you for your comments. In response, I would say:

1) The detailed prose describing the schema is still something that
needs to be done, either before or during the April workshop.

2) Your example of the meaning of m/z should probably be handled in the
ontology, because the axis is defined by an ontology keyword. The
ontology also needs significant work before or during the workshop.

3) Regarding your question about the type and use of float values, this
should indeed be defined.  I don't think this was quite so explicitly
defined in either of the original specifications, but in any case, we
should be as precise as possible for dataXML.

Thank you for these comments. Feel free to respond and/or send more.  I
will assemble a list of open issues to be discussed on the list or in
Lyon and resolved before release.

Regards,
Eric


> -----Original Message-----
> From: Mike Coleman [mailto:tu...@gm...]
> Sent: Tuesday, February 06, 2007 7:53 AM
> To: Pierre-Alain Binz; Eric Deutsch
> Cc: PSI MS Dev
> Subject: Re: [Psidev-ms-dev] dataXML 0.9 ready for first feedbacks
>=20
> On 2/6/07, Pierre-Alain Binz <pie...@is...> wrote:
> >  dataXML (as being the merge between mzData and mzXML, and becoming
the
> PSI
> > MS data standard replacing mzData) is ready for a first feedback
from
> you,
> > implementers and PSI MS active members. We target to finalise
version
> 1.0
> > right after the next PSI Spring Workshop (see below)
>=20
> Looking on this page, the only normative material I'm seeing are the
> two XML schema.  Is there other material that I'm missing?  I would
> have expected to see detailed normative prose describing the meaning
> and proper usage of the various elements.  Without this, implementers
> will probably use this schema in incompatible ways, leading to future
> headaches.
>=20
> Here are a couple of examples of what seems to be missing.  I think I
> know that the X axis for spectrum data represents M/Z values, where M
> is mass in amu's and Z is the integer charge.  This ought to be
> specified explicitly.
>=20
> As a more detailed example, I think I know that spectrum data is
> represented as the base64-encoded form of IEEE float values.  (This
> also needs to be specified.)   IEEE floats can take on several special
> values like "positive infinity" and error values.  Is it legal to
> place these values in a dataXML file?  Whether or not this is so, what
> is a receiver expected to do if it encounters such values?
>=20
> As an example of the kind of normative prose I'm thinking of, here is
> a link to a working copy of an ANSI C standard
>=20
>     http://www.open-std.org/jtc1/sc22/wg14/www/docs/n1124.pdf
>=20
> (Obviously, the dataXML prose would be much shorter.)
>=20
> Another nice thing that the ANSI C committee produces is a rationale
> document, which explains the reasoning behind many of the major
> decisions taken, correlated to the specification.  It would be nice to
> have an mzData rationale document as well, to explain the thinking
> behind its design decisions (e.g., base64/binary representation of
> floats).
>=20
>     http://www.open-std.org/jtc1/sc22/wg14/www/C99RationaleV5.10.pdf
>=20
> Regards,
> Mike Coleman