psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] Update from the PSI meeting

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

Hi Matt, the examples we need are mainly the off-the-beaten track things. So, a standard LTQ run we've got covered.  Here's some of what we need:

- Workin examples that include compressed spectra
- Get an example 4700 file. How to encode the sourceFile for that?
- MS^E example (I think Rune sent one out. Is it great?)
- We need to develop a good MALDI example file with spot id refs
- We need to develop a good example of a file created from individual dtas including examples to multiple possible charge states
- We need to develop a good example of a file that contains summed scans and acquisitionList
- Create an example of encoding a transient in an mzML file
- Get example than includes both PDA and MSn spectra in one file

As far as the Excel sheets, Luisa is preparing Excel sheets for each vendor with:

Accession     Model Name      Model Definition

To send to each vendor for updating/filling in so that by June 1, we have a pretty decent encoding of the current instruments in the CV.

Thanks!
Eric



> From: psi...@li... [mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Matt Chambers
> Sent: Monday, April 28, 2008 6:33 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Update from the PSI meeting
> 
> Hi Eric,
> 
> When you say you want example files, do you want the native file(s), the
> converted file, or both? Or do you mean a manually constructed example?
> I can probably get permission to release to the public some native files
> for some blank or QC runs from several different Thermo instruments
> (LTQ, LTQ/Orbitrap, Quantum). The corresponding output from pwiz's
> msconvert is trivial from that point.
> 
> What are the Excel sheets going to the vendors supposed to be for?
> 
> -Matt
> 
> 
> Eric Deutsch wrote:
> >
> > Hi everyone, we had a productive track at the PSI spring meeting. The
> > highlights are:
> >
> >
> >
> > - All suggested and needed schema revisions were completed and schema
> > version 0.99.9 is available
> >
> > - Most documentation updates were written. Revised full spec doc and
> > html doc still to be released.
> >
> > - MIAPE-MS example document almost completed
> >
> > - ASMS poster features planned
> >
> > - Journal article plans discussed
> >
> > - Some CV updates and future update procedure planned. Still much to do
> >
> > - Additional example documents are needed
> >
> > - Web site updated with completed work
> >
> >
> >
> > Many thanks to those who did the work at the workshop: Lennart Martens
> > (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl
> > (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI),
> > Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid),
> > Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina
> > (Madrid)
> >
> >
> >
> > Moving forward, we have an aggressive schedule to release mzML 1.0.0
> > one month from now. Your participation is needed!
> >
> >
> >
> > We will have weekly teleconferences for the next month to try to keep
> > the focus strong. The next teleconference will be this Tuesday at 9am
> > PDT at the usual place.
> >
> >
> >
> > We have the following list of action items set at the end of the
> meeting:
> >
> >
> >
> > - Eric will finish documentation items (incl reviewer reply)
> >
> > - Pierre-Alain will finish MIAPE-MS example
> >
> > - Eric will do the CV to do items
> >
> > - Lennart will get validator finished and working
> >
> > - Eric will put together poster with various assistance
> >
> > - Lennart will write draft of manuscript
> >
> > - Darren and Matt and Jim will work on example files
> >
> > - Luisa will create the Excel sheets, one for each vendor. Eric will
> > send. Luisa will reintegrate.
> >
> >
> >
> > If you have an interest in mzML, we need your help to get it finished.
> > One of the important things we still need is more example files. If
> > you are willing to create from example files, especially by parts of
> > the schema that have not been well tested, please help. Create an
> > example file and post it. Or contact me for ideas.
> >
> >
> >
> > Thank you!
> >
> > Eric
> >
> >
> >
> >
> >
> >
> 
> 
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Re: [Psidev-ms-dev] New help in the CV group solicited

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

Hi Liming and Darren, thank you for volunteering to help us out, it is
much appreciated. Why don't you start off by looking through the current
CV with OBO-Edit. Go to our dev page:

 

http://psidev.info/index.php?q=node/257

 

and download the latest CV and OBO-Edit itself and get that installed on
your computer (See the very bottom of the above web page). Let me know
if you have trouble.

 

Once you have gotten a little familiar with the CV and the tool, let's
discuss how to proceed with tackling the to do list and maintaining the
CV. Randy is editing the CV at the moment, so don't make any changes to
the file yet. We have to be a little careful to avoid accession
numbering collisions and other little problems with using OBO-Edit.

 

Thank you for stepping up!

Eric

 

 

> -----Original Message-----

> From: psi...@li...
[mailto:psidev-ms-dev-

> bo...@li...] On Behalf Of Darren Kessner

> Sent: Monday, April 28, 2008 8:38 AM

> To: Mass spectrometry standard development

> Subject: Re: [Psidev-ms-dev] New help in the CV group solicited

> 

> Hi Eric,

> 

> I meant to volunteer when you were discussing this on the last day,
but

> I had my head in my code.

> 

> Anyway, I'm happy to help maintain the CV going forward.

> 

> 

> Darren

 

 

________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of Yang,
Liming (NIH/NCI) [E]
Sent: Monday, April 28, 2008 6:13 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] New help in the CV group solicited

 

Eric,

 

I would like to help you in the CV group.  I have some experience with
mass spec instrumentation and I am working with CPTAC informatics
support at National Cancer Institute.

 

Please let me know if you need more information.

 

Best,

Liming

 

Liming Yang, PhD

National Cancer Institute

 

________________________________

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Monday, April 28, 2008 2:16 AM
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: [Psidev-ms-dev] New help in the CV group solicited

 

Hi everyone, as I mentioned at the workshop, we could really use some
fresh help with the controlled vocabulary in the mass spectrometry
standards working group. Our CV is actually in pretty good shape, but
there is a long list of little items that need attention and it would be
use if some more eyes looked for trouble spots (and helped us fix them!)

 

An ontology coordinator helps the working group by addressing new CV
term and change requests, editing the CV with OBO-Edit, and maintaining
it in CVS. Some familiarity with mass spec instrumentation is necessary.

 

Anyone who is willing to serve as one of our ontology coordinators,
please contact me!

 

Thanks,

Eric

 

 

 

[Psidev-ms-dev] userParam attributes (was: Update from the PSI meeting)

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

Hi everyone, my own summary and thoughts on the userParam issue:

 

My first question is: what are these userParams supposed to look like anyway? There don't seem to be any good examples of use of this (except for something about cats, which I don't understand). We should definitely fix that and get some example userParams in the example docs. I always thought userParam was supposed to look like this:

 

<userParam name="ReAdW quality score" value="0.94" type="xs:float">

 

What would be a good example of a userParam without a value?

 

<userParam name="rejected">

 

? I kind of like the idea of requiring a value and a type. Seems like we'd get more useful userParams. We argued for quite a while about whether to include a "category" like thing in cvParam, and concluded "no" because it is implicit in the CV. For a userParam, there is no CV, and so it seems natural to use the name attribute as a kind of category, which is then qualified by the value. Instead of the above, I'd rather see:

 

<userParam name="MSFilter spectrum inclusion flag" value="rejected" type="xs:string">

 

 

Regarding adding optional units, I like the idea. We want something like:

 

<userParam name="LTQ cycle delay time" value="0.00012" type="xs:float" unitAccession="MS:1000038" unitName="minute"/>

 

? (adjusted by the impending change to the unit ontology)

 

 

Maybe I'm confused because type doesn't mean datatype, but rather category?

 

We need quality examples!

 

Thanks,

Eric

 

 

 

________________________________

From: psi...@li... [mailto:psi...@li...] On Behalf Of Darren Kessner
Sent: Monday, April 28, 2008 8:47 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

I think it's a good idea to add a units attribute to CVParam -- actually, I just noticed it was missing on Sunday when I was working on the latest example file.  I agree that everything other than "name" should be optional.

 

Regarding data type -- I believe Lennart was finalizing how it will be encoded in the terms in the OBO file, but there wasn't much discussion about how it will be validated.  It seems that data types could be validated during semantic validation though.  

 

In pwiz I'm planning to use the type info to validate casts at compile time.

 

 

Darren

 

 

 

On Apr 28, 2008, at 8:05 AM, Randy Julian wrote:





Good catch Andy,

 

I don't see why the value is a required attribute.  The idea of userParam is that it is just like cvParam, expect the names and values are uncontrolled.

 

I think we need the units in the userParam too.  This raises the question of data type in both elements.

 

In userParam we have a data type field explicitly:

 

<xs:complexType name="UserParamType">

            <xs:attribute name="name" type="xs:string" use="required"/>

            <xs:attribute name="type" type="xs:string" />

            <xs:attribute name="value" type="xs:string" />

            <xs:attribute name="unitName" type="xs:string" />

</xs:complexType>

 

Is everyone OK with adding unitName to the userParam as an optional attribute, and changing the other attributes (except name) to optional?

 

Also, I must have missed the data type discussion - are we adding something somewhere for data type validation?

 

Thanks,

Randy

 

From: psi...@li... [mailto:psi...@li...]On Behalf Of Jones, Andy
Sent: Monday, April 28, 2008 10:01 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Y it is this one that I have a problem with...

 

                <xs:complexType name="UserParamType">

                                <xs:annotation>

                                                <xs:documentation>Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead</xs:documentation>

                                </xs:annotation>

                                <xs:attribute name="name" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The name for the parameter.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                                <xs:attribute name="type" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The type of the parameter, where appropriate.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                                <xs:attribute name="value" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The value for the parameter, where appropriate.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                </xs:complexType>

 

 

 

From: psi...@li... [mailto:psi...@li...]On Behalf Of Randy Julian
Sent: 28 April 2008 14:54
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Andy,

 

In the schema I have, the element looks like this:

 

<xs:complexType name="CVParamType">

                <xs:attribute name="cvRef" type="xs:IDREF" use="required"/>

                <xs:attribute name="accession" type="xs:string" use="required"/>

                <xs:attribute name="value" type="xs:string" use="optional"/>

                <xs:attribute name="name" type="xs:string" use="required"/>

                <xs:attribute name="unitAccession" type="xs:string" use="optional"/>

                <xs:attribute name="unitName" type="xs:string" use="optional"/>

</xs:complexType>

 

This is version 0.99.9 (attached).  Let me know if this makes sense.

 

Thanks,

Randy

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Jones, Andy
Sent: Monday, April 28, 2008 9:14 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Hi all,

 

I'm incorporating the mzML cvParam part (working from 0.99.9) into the analysisXML draft, to see how this works with the current schema.

 

I noticed that userParam has attributes name, value and type, and all are required attributes. I would have expected value and type to be optional (as suggested by the documentation) - is this an error?

Cheers

Andy

 

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Eric Deutsch
Sent: 28 April 2008 07:16
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: [Psidev-ms-dev] Update from the PSI meeting

 

Hi everyone, we had a productive track at the PSI spring meeting. The highlights are:

 

- All suggested and needed schema revisions were completed and schema version 0.99.9 is available

- Most documentation updates were written. Revised full spec doc and html doc still to be released.

- MIAPE-MS example document almost completed

- ASMS poster features planned

- Journal article plans discussed

- Some CV updates and future update procedure planned. Still much to do

- Additional example documents are needed

- Web site updated with completed work

 

Many thanks to those who did the work at the workshop: Lennart Martens (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina (Madrid)

 

Moving forward, we have an aggressive schedule to release mzML 1.0.0 one month from now. Your participation is needed!

 

We will have weekly teleconferences for the next month to try to keep the focus strong. The next teleconference will be this Tuesday at 9am PDT at the usual place.

 

We have the following list of action items set at the end of the meeting:

 

- Eric will finish documentation items (incl reviewer reply)

- Pierre-Alain will finish MIAPE-MS example

- Eric will do the CV to do items

- Lennart will get validator finished and working

- Eric will put together poster with various assistance

- Lennart will write draft of manuscript

- Darren and Matt and Jim will work on example files

- Luisa will create the Excel sheets, one for each vendor. Eric will send. Luisa will reintegrate.

 

If you have an interest in mzML, we need your help to get it finished. One of the important things we still need is more example files. If you are willing to create from example files, especially by parts of the schema that have not been well tested, please help. Create an example file and post it. Or contact me for ideas.

 

Thank you!

Eric

 

 

 

 

 

 

 

 

 

 

 

 

 

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[Psidev-ms-dev] Recursive referenceableParamGroups (was: CV param question)

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

Hi everyone, it seems like there are reasonable ideas for keeping and
removing the possibility of recursive referenceableParamGroups. Let's
make this a topic for the call.  Seems like:

Pros:
- would allow inheritance structure for similar referenceableParamGroups
- Darren has already implemented it this way
- Not a problem for the validator

Cons:
- More complicated for other implementations
- More complicated to understand

We'll decide Tuesday.

Thanks,
Eric




> From: psi...@li...
[mailto:psidev-ms-dev-
> 
> Hi all,
> 
> Just an FYI -- when writing the pwiz CVParam handling, I had assumed
> that recursive references were legal.  Internally we store the
reference
> structure (i.e. we don't resolve fully) and parameter searches are
done
> recursively on demand.  So I imagine it wouldn't be too difficult to
> handle this recursion in the validator if we want to keep this
> flexibility.
> 
> On the other hand, I won't cry if recursive param groups are removed.
> 
> 
> Darren
> 
> 
> -----Original Message-----
> From: psi...@li...
> [mailto:psi...@li...] On Behalf Of
> Lennart Martens
> Sent: Monday, April 28, 2008 9:39 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] CV param question
> 
> Hi Andy,
> 
> 
> > Another query about the cvParam structure (apologies for only
looking
> at
> > this so late in the process)...
> >
> > As I understand it, the current schema draft contains several places
> > where ParamGroup is used, which is an option to have cv terms (or
> > userParams) either inline and/or by reference to a pre-defined
> > ReferenceableParamGroup.
> >
> > The ReferenceableParamGroup inherits from ParamGroup, and so can
also
> > contain cvParam, userParam or a reference to a
> ReferenceableParamGroup.
> >
> > So... I have two questions:
> >
> > 1) Is it intended that a ParamGroup could contain inline CV/user
> > parameters  _/and/_ a reference to a pre-defined set of parameters
> (i.e.
> > this is not an explicit OR)?
> 
> The current schema does allow recursive referencing. So you could make
a
> 
> ReferenceableParamGroup with one or two params, and then derive two
> other ones from this one, which would extend the original one with
some
> more params. I'm not sure whether we really want this actually, I
think
> we just missed this.
> 
> So my proposal is to revise this. I'll bring it up in the phone con
> tomorrow, and if no one feels strongly that it should stay, it'll be
> removed.
> 
> 
> > 2) Is it intended that a ReferenceableParamGroup could contain a
> > reference to another ReferenceableParamGroup and if so what is the
> > meaning of the reference?
> 
> It would be a recursive reference.
> 
> 
> > I'm just trying to envisage how the validator works with this
> structure,
> > is it possible to map explicitly to allowed CV terms if they are
used
> in
> > the referenceableParamGroup?
> 
> In the validator code, we simply hold the referenceableParamGroups in
a
> lookup table. When one of these is referenced, we simply substitute
all
> params into the ParamGroup that is referencing, while removing the
> reference (we essentially fully resolve the soft link). So there's no
> problem with this way of working from the validators point of view.
> 
> 
> Cheers,
> 
> lnnrt.
> 
>
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[Psidev-ms-dev] PSI-MSS WG call tomorrow

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

Hi everyone, as previously mentioned, the PSI Mass Spectrometry
Standards Working Group call is tomorrow at 9am PDT:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=29&month=4&year
=2008&hour=17&min=0&sec=0&p1=136

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

 

access code: 297427

 

The agenda will be to quickly review and discuss what remains to be done
after the workshop in the next month, and discuss some of the flurry of
emails since the workshop already.

 

Please attend!

 

Thanks,

Eric

 

 

 

Re: [Psidev-ms-dev] CV param question

[Kessner, D. E. <Dar...@cs...>]

Hi all,

Just an FYI -- when writing the pwiz CVParam handling, I had assumed
that recursive references were legal.  Internally we store the reference
structure (i.e. we don't resolve fully) and parameter searches are done
recursively on demand.  So I imagine it wouldn't be too difficult to
handle this recursion in the validator if we want to keep this
flexibility.

On the other hand, I won't cry if recursive param groups are removed.  


Darren


-----Original Message-----
From: psi...@li...
[mailto:psi...@li...] On Behalf Of
Lennart Martens
Sent: Monday, April 28, 2008 9:39 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] CV param question

Hi Andy,


> Another query about the cvParam structure (apologies for only looking
at 
> this so late in the process)...
> 
> As I understand it, the current schema draft contains several places 
> where ParamGroup is used, which is an option to have cv terms (or 
> userParams) either inline and/or by reference to a pre-defined 
> ReferenceableParamGroup.
> 
> The ReferenceableParamGroup inherits from ParamGroup, and so can also 
> contain cvParam, userParam or a reference to a
ReferenceableParamGroup.
> 
> So... I have two questions:
> 
> 1) Is it intended that a ParamGroup could contain inline CV/user 
> parameters  _/and/_ a reference to a pre-defined set of parameters
(i.e. 
> this is not an explicit OR)?

The current schema does allow recursive referencing. So you could make a

ReferenceableParamGroup with one or two params, and then derive two 
other ones from this one, which would extend the original one with some 
more params. I'm not sure whether we really want this actually, I think 
we just missed this.

So my proposal is to revise this. I'll bring it up in the phone con 
tomorrow, and if no one feels strongly that it should stay, it'll be 
removed.


> 2) Is it intended that a ReferenceableParamGroup could contain a 
> reference to another ReferenceableParamGroup and if so what is the 
> meaning of the reference?

It would be a recursive reference.


> I'm just trying to envisage how the validator works with this
structure, 
> is it possible to map explicitly to allowed CV terms if they are used
in 
> the referenceableParamGroup?

In the validator code, we simply hold the referenceableParamGroups in a 
lookup table. When one of these is referenced, we simply substitute all 
params into the ParamGroup that is referencing, while removing the 
reference (we essentially fully resolve the soft link). So there's no 
problem with this way of working from the validators point of view.


Cheers,

lnnrt.

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IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by
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Re: [Psidev-ms-dev] Update from the PSI meeting

[Lennart M. <len...@eb...>]

Hi Andy,


Jones, Andy wrote:
> It is this one that I have a problem with...
> 
>                 <xs:complexType name="UserParamType">
>                                 <xs:attribute name="name" 
> type="xs:string" use="required">
>                                 </xs:attribute>
>                                 <xs:attribute name="type" 
> type="xs:string" use="required">
>                                 </xs:attribute>
>                                 <xs:attribute name="value" 
> type="xs:string" use="required">
>                                 </xs:attribute>
>                 </xs:complexType>

I would imagine this is a silly mistake we simply forgot to take out. So 
thanks for spotting this.

We'll probably discuss the comments by Randy (to allow units in these 
userparams) on the phonecon, and I'll update the schema accordingly 
afterwards.


Cheers,

lnnrt.

Re: [Psidev-ms-dev] CV param question

[Lennart M. <len...@eb...>]

Hi Andy,


> Another query about the cvParam structure (apologies for only looking at 
> this so late in the process)...
> 
> As I understand it, the current schema draft contains several places 
> where ParamGroup is used, which is an option to have cv terms (or 
> userParams) either inline and/or by reference to a pre-defined 
> ReferenceableParamGroup.
> 
> The ReferenceableParamGroup inherits from ParamGroup, and so can also 
> contain cvParam, userParam or a reference to a ReferenceableParamGroup.
> 
> So... I have two questions:
> 
> 1) Is it intended that a ParamGroup could contain inline CV/user 
> parameters  _/and/_ a reference to a pre-defined set of parameters (i.e. 
> this is not an explicit OR)?

The current schema does allow recursive referencing. So you could make a 
ReferenceableParamGroup with one or two params, and then derive two 
other ones from this one, which would extend the original one with some 
more params. I'm not sure whether we really want this actually, I think 
we just missed this.

So my proposal is to revise this. I'll bring it up in the phone con 
tomorrow, and if no one feels strongly that it should stay, it'll be 
removed.


> 2) Is it intended that a ReferenceableParamGroup could contain a 
> reference to another ReferenceableParamGroup and if so what is the 
> meaning of the reference?

It would be a recursive reference.


> I’m just trying to envisage how the validator works with this structure, 
> is it possible to map explicitly to allowed CV terms if they are used in 
> the referenceableParamGroup?

In the validator code, we simply hold the referenceableParamGroups in a 
lookup table. When one of these is referenced, we simply substitute all 
params into the ParamGroup that is referencing, while removing the 
reference (we essentially fully resolve the soft link). So there's no 
problem with this way of working from the validators point of view.


Cheers,

lnnrt.

Re: [Psidev-ms-dev] Update from the PSI meeting

[Henning H. <hen...@go...>]

Just to add an additional thought, and the potential for even more 
harmony between PSI work groups: The Molecular interactions schema has

term 	
	required 			
documentation 	

The kind of parameter, e.g. "dissociation constant".

termAc 	
	optional 			
documentation 	

Accession number of the term in the associated controlled vocabulary.

unit 	
	optional 			
documentation 	

The unit of the term, e.g. "kiloDalton".

unitAc 	
	optional 			
documentation 	

Accession number of the unit in the associated controlled vocabulary.

base 	xs:short 	optional 	10 		
documentation 	

Base of the parameter expression. Defaults to 10.

exponent 	xs:short 	optional 	0 		
documentation 	

Exponent of the value.

factor 	xs:decimal 	required 			
documentation 	

The "main" value of the parameter.


see
http://psidev.sourceforge.net/mi/rel25/doc/#complexType_parameterType_Link03B1FB80

Best regards,

Henning

Randy Julian wrote:
>
> Good catch Andy,
>
> I don’t see why the value is a required attribute. The idea of 
> userParam is that it is just like cvParam, expect the names and values 
> are uncontrolled.
>
> I think we need the units in the userParam too. This raises the 
> question of data type in both elements.
>
> In userParam we have a data type field explicitly:
>
> <xs:complexType name="UserParamType">
>
> <xs:attribute name="name" type="xs:string" use="required"/>
>
> <xs:attribute name="type" type="xs:string" />
>
> <xs:attribute name="value" type="xs:string" />
>
> <xs:attribute name="unitName" type="xs:string" />
>
> </xs:complexType>
>
> Is everyone OK with adding unitName to the userParam as an optional 
> attribute, and changing the other attributes (except name) to optional?
>
> Also, I must have missed the data type discussion – are we adding 
> something somewhere for data type validation?
>
> Thanks,
>
> Randy
>
> *From:* psi...@li... 
> [mailto:psi...@li...] *On Behalf Of 
> *Jones, Andy
> *Sent:* Monday, April 28, 2008 10:01 AM
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Y it is this one that I have a problem with...
>
> <xs:complexType name="UserParamType">
>
> <xs:annotation>
>
> <xs:documentation>Uncontrolled user parameters (essentially allowing 
> free text). Before using these, one should verify whether there is an 
> appropriate CV term available, and if so, use the CV term 
> instead</xs:documentation>
>
> </xs:annotation>
>
> <xs:attribute name="name" type="xs:string" use="required">
>
> <xs:annotation>
>
> <xs:documentation>The name for the parameter.</xs:documentation>
>
> </xs:annotation>
>
> </xs:attribute>
>
> <xs:attribute name="type" type="xs:string" use="required">
>
> <xs:annotation>
>
> <xs:documentation>The type of the parameter, where 
> appropriate.</xs:documentation>
>
> </xs:annotation>
>
> </xs:attribute>
>
> <xs:attribute name="value" type="xs:string" use="required">
>
> <xs:annotation>
>
> <xs:documentation>The value for the parameter, where 
> appropriate.</xs:documentation>
>
> </xs:annotation>
>
> </xs:attribute>
>
> </xs:complexType>
>
> *From:* psi...@li... 
> [mailto:psi...@li...] *On Behalf Of 
> *Randy Julian
> *Sent:* 28 April 2008 14:54
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Andy,
>
> In the schema I have, the element looks like this:
>
> <xs:complexType name="CVParamType">
>
> <xs:attribute name="cvRef" type="xs:IDREF" use="required"/>
>
> <xs:attribute name="accession" type="xs:string" use="required"/>
>
> <xs:attribute name="value" type="xs:string" use="optional"/>
>
> <xs:attribute name="name" type="xs:string" use="required"/>
>
> <xs:attribute name="unitAccession" type="xs:string" use="optional"/>
>
> <xs:attribute name="unitName" type="xs:string" use="optional"/>
>
> </xs:complexType>
>
> This is version 0.99.9 (attached). Let me know if this makes sense.
>
> Thanks,
>
> Randy
>
> *From:* psi...@li... 
> [mailto:psi...@li...] *On Behalf Of 
> *Jones, Andy
> *Sent:* Monday, April 28, 2008 9:14 AM
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Hi all,
>
> I’m incorporating the mzML cvParam part (working from 0.99.9) into the 
> analysisXML draft, to see how this works with the current schema.
>
> I noticed that userParam has attributes name, value and type, and all 
> are required attributes. I would have expected value and type to be 
> optional (as suggested by the documentation) – is this an error?
>
> Cheers
>
> Andy
>
> *From:* psi...@li... 
> [mailto:psi...@li...] *On Behalf Of 
> *Eric Deutsch
> *Sent:* 28 April 2008 07:16
> *To:* Mass spectrometry standard development
> *Cc:* Eric Deutsch
> *Subject:* [Psidev-ms-dev] Update from the PSI meeting
>
> Hi everyone, we had a productive track at the PSI spring meeting. The 
> highlights are:
>
> - All suggested and needed schema revisions were completed and schema 
> version 0.99.9 is available
>
> - Most documentation updates were written. Revised full spec doc and 
> html doc still to be released.
>
> - MIAPE-MS example document almost completed
>
> - ASMS poster features planned
>
> - Journal article plans discussed
>
> - Some CV updates and future update procedure planned. Still much to do
>
> - Additional example documents are needed
>
> - Web site updated with completed work
>
> Many thanks to those who did the work at the workshop: Lennart Martens 
> (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl 
> (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), 
> Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), 
> Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina 
> (Madrid)
>
> Moving forward, we have an aggressive schedule to release mzML 1.0.0 
> one month from now. Your participation is needed!
>
> We will have weekly teleconferences for the next month to try to keep 
> the focus strong. The next teleconference will be this Tuesday at 9am 
> PDT at the usual place.
>
> We have the following list of action items set at the end of the meeting:
>
> - Eric will finish documentation items (incl reviewer reply)
>
> - Pierre-Alain will finish MIAPE-MS example
>
> - Eric will do the CV to do items
>
> - Lennart will get validator finished and working
>
> - Eric will put together poster with various assistance
>
> - Lennart will write draft of manuscript
>
> - Darren and Matt and Jim will work on example files
>
> - Luisa will create the Excel sheets, one for each vendor. Eric will 
> send. Luisa will reintegrate.
>
> If you have an interest in mzML, we need your help to get it finished. 
> One of the important things we still need is more example files. If 
> you are willing to create from example files, especially by parts of 
> the schema that have not been well tested, please help. Create an 
> example file and post it. Or contact me for ideas.
>
> Thank you!
>
> Eric
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> Don't miss this year's exciting event. There's still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> ------------------------------------------------------------------------
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>   

Re: [Psidev-ms-dev] Update from the PSI meeting

[Darren K. <Dar...@cs...>]

I think it's a good idea to add a units attribute to CVParam --  
actually, I just noticed it was missing on Sunday when I was working  
on the latest example file.  I agree that everything other than "name"  
should be optional.

Regarding data type -- I believe Lennart was finalizing how it will be  
encoded in the terms in the OBO file, but there wasn't much discussion  
about how it will be validated.  It seems that data types could be  
validated during semantic validation though.

In pwiz I'm planning to use the type info to validate casts at compile  
time.


Darren



On Apr 28, 2008, at 8:05 AM, Randy Julian wrote:

> Good catch Andy,
>
> I don’t see why the value is a required attribute.  The idea of  
> userParam is that it is just like cvParam, expect the names and  
> values are uncontrolled.
>
> I think we need the units in the userParam too.  This raises the  
> question of data type in both elements.
>
> In userParam we have a data type field explicitly:
>
> <xs:complexType name="UserParamType">
>             <xs:attribute name="name" type="xs:string"  
> use="required"/>
>             <xs:attribute name="type" type="xs:string" />
>             <xs:attribute name="value" type="xs:string" />
>             <xs:attribute name="unitName" type="xs:string" />
> </xs:complexType>
>
> Is everyone OK with adding unitName to the userParam as an optional  
> attribute, and changing the other attributes (except name) to  
> optional?
>
> Also, I must have missed the data type discussion – are we adding  
> something somewhere for data type validation?
>
> Thanks,
> Randy
>
> From: psi...@li... [mailto:psi...@li... 
> ]On Behalf Of Jones, Andy
> Sent: Monday, April 28, 2008 10:01 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Y it is this one that I have a problem with...
>
>                 <xs:complexType name="UserParamType">
>                                 <xs:annotation>
>                                                  
> <xs:documentation>Uncontrolled user parameters (essentially allowing  
> free text). Before using these, one should verify whether there is  
> an appropriate CV term available, and if so, use the CV term  
> instead</xs:documentation>
>                                 </xs:annotation>
>                                 <xs:attribute name="name"  
> type="xs:string" use="required">
>                                                 <xs:annotation>
>                                                                  
> <xs:documentation>The name for the parameter.</xs:documentation>
>                                                 </xs:annotation>
>                                 </xs:attribute>
>                                 <xs:attribute name="type"  
> type="xs:string" use="required">
>                                                 <xs:annotation>
>                                                                  
> <xs:documentation>The type of the parameter, where appropriate.</ 
> xs:documentation>
>                                                 </xs:annotation>
>                                 </xs:attribute>
>                                 <xs:attribute name="value"  
> type="xs:string" use="required">
>                                                 <xs:annotation>
>                                                                  
> <xs:documentation>The value for the parameter, where appropriate.</ 
> xs:documentation>
>                                                 </xs:annotation>
>                                 </xs:attribute>
>                 </xs:complexType>
>
>
>
> From: psi...@li... [mailto:psi...@li... 
> ]On Behalf Of Randy Julian
> Sent: 28 April 2008 14:54
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Andy,
>
> In the schema I have, the element looks like this:
>
> <xs:complexType name="CVParamType">
>                 <xs:attribute name="cvRef" type="xs:IDREF"  
> use="required"/>
>                 <xs:attribute name="accession" type="xs:string"  
> use="required"/>
>                 <xs:attribute name="value" type="xs:string"  
> use="optional"/>
>                 <xs:attribute name="name" type="xs:string"  
> use="required"/>
>                 <xs:attribute name="unitAccession" type="xs:string"  
> use="optional"/>
>                 <xs:attribute name="unitName" type="xs:string"  
> use="optional"/>
> </xs:complexType>
>
> This is version 0.99.9 (attached).  Let me know if this makes sense.
>
> Thanks,
> Randy
>
> From: psi...@li... [mailto:psi...@li... 
> ] On Behalf Of Jones, Andy
> Sent: Monday, April 28, 2008 9:14 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Update from the PSI meeting
>
> Hi all,
>
> I’m incorporating the mzML cvParam part (working from 0.99.9) into  
> the analysisXML draft, to see how this works with the current schema.
>
> I noticed that userParam has attributes name, value and type, and  
> all are required attributes. I would have expected value and type to  
> be optional (as suggested by the documentation) – is this an error?
> Cheers
> Andy
>
>
> From: psi...@li... [mailto:psi...@li... 
> ] On Behalf Of Eric Deutsch
> Sent: 28 April 2008 07:16
> To: Mass spectrometry standard development
> Cc: Eric Deutsch
> Subject: [Psidev-ms-dev] Update from the PSI meeting
>
> Hi everyone, we had a productive track at the PSI spring meeting.  
> The highlights are:
>
> - All suggested and needed schema revisions were completed and  
> schema version 0.99.9 is available
> - Most documentation updates were written. Revised full spec doc and  
> html doc still to be released.
> - MIAPE-MS example document almost completed
> - ASMS poster features planned
> - Journal article plans discussed
> - Some CV updates and future update procedure planned. Still much to  
> do
> - Additional example documents are needed
> - Web site updated with completed work
>
> Many thanks to those who did the work at the workshop: Lennart  
> Martens (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim  
> Shofstahl (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi- 
> Palazzi (EBI), Randy Julian (Indigo), Lars Nilse (Manchester),  
> Benito Cañas (Madrid), Lola Gutierrez (Madrid), Matt Chambers  
> (Vanderbilt), Alberto Medina (Madrid)
>
> Moving forward, we have an aggressive schedule to release mzML 1.0.0  
> one month from now. Your participation is needed!
>
> We will have weekly teleconferences for the next month to try to  
> keep the focus strong. The next teleconference will be this Tuesday  
> at 9am PDT at the usual place.
>
> We have the following list of action items set at the end of the  
> meeting:
>
> - Eric will finish documentation items (incl reviewer reply)
> - Pierre-Alain will finish MIAPE-MS example
> - Eric will do the CV to do items
> - Lennart will get validator finished and working
> - Eric will put together poster with various assistance
> - Lennart will write draft of manuscript
> - Darren and Matt and Jim will work on example files
> - Luisa will create the Excel sheets, one for each vendor. Eric will  
> send. Luisa will reintegrate.
>
> If you have an interest in mzML, we need your help to get it  
> finished. One of the important things we still need is more example  
> files. If you are willing to create from example files, especially  
> by parts of the schema that have not been well tested, please help.  
> Create an example file and post it. Or contact me for ideas.
>
> Thank you!
> Eric
>
>
>
>
>
>
>
>
>
>
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> Don't miss this year's exciting event. There's still time to save  
> $100.
> Use priority code J8TL2D2.
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone 
> <mime-attachment.txt>

Re: [Psidev-ms-dev] New help in the CV group solicited

[Darren K. <dke...@ya...>]

Hi Eric,

I meant to volunteer when you were discussing this on the last day, but 
I had my head in my code.

Anyway, I'm happy to help maintain the CV going forward.


Darren


On Sun, 27 Apr 2008 11:15 pm, Eric Deutsch wrote:
> Hi everyone, as I mentioned at the workshop, we could really use some 
> fresh help with the controlled vocabulary in the mass spectrometry 
> standards working group. Our CV is actually in pretty good shape, but 
> there is a long list of little items that need attention and it would 
> be use if some more eyes looked for trouble spots (and helped us fix 
> them!)
>
> An ontology coordinator helps the working group by addressing new CV 
> term and change requests, editing the CV with OBO-Edit, and maintaining 
> it in CVS. Some familiarity with mass spec instrumentation is 
> necessary.
>
> Anyone who is willing to serve as one of our ontology coordinators, 
> please contact me!
>
> Thanks,
>
> Eric
>


Darren

Re: [Psidev-ms-dev] Update from the PSI meeting

[Randy J. <rkj...@in...>]

Good catch Andy,

 

I don't see why the value is a required attribute.  The idea of userParam is that it is just like cvParam, expect the names and values are uncontrolled.

 

I think we need the units in the userParam too.  This raises the question of data type in both elements.

 

In userParam we have a data type field explicitly:

 

<xs:complexType name="UserParamType">

            <xs:attribute name="name" type="xs:string" use="required"/>

            <xs:attribute name="type" type="xs:string" />

            <xs:attribute name="value" type="xs:string" />

            <xs:attribute name="unitName" type="xs:string" />

</xs:complexType>

 

Is everyone OK with adding unitName to the userParam as an optional attribute, and changing the other attributes (except name) to optional?

 

Also, I must have missed the data type discussion - are we adding something somewhere for data type validation?

 

Thanks,

Randy

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Jones, Andy
Sent: Monday, April 28, 2008 10:01 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Y it is this one that I have a problem with...

 

                <xs:complexType name="UserParamType">

                                <xs:annotation>

                                                <xs:documentation>Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead</xs:documentation>

                                </xs:annotation>

                                <xs:attribute name="name" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The name for the parameter.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                                <xs:attribute name="type" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The type of the parameter, where appropriate.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                                <xs:attribute name="value" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The value for the parameter, where appropriate.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                </xs:complexType>

 

 

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Randy Julian
Sent: 28 April 2008 14:54
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Andy,

 

In the schema I have, the element looks like this:

 

<xs:complexType name="CVParamType">

                <xs:attribute name="cvRef" type="xs:IDREF" use="required"/>

                <xs:attribute name="accession" type="xs:string" use="required"/>

                <xs:attribute name="value" type="xs:string" use="optional"/>

                <xs:attribute name="name" type="xs:string" use="required"/>

                <xs:attribute name="unitAccession" type="xs:string" use="optional"/>

                <xs:attribute name="unitName" type="xs:string" use="optional"/>

</xs:complexType>

 

This is version 0.99.9 (attached).  Let me know if this makes sense.

 

Thanks,

Randy

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Jones, Andy
Sent: Monday, April 28, 2008 9:14 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Hi all,

 

I'm incorporating the mzML cvParam part (working from 0.99.9) into the analysisXML draft, to see how this works with the current schema. 

 

I noticed that userParam has attributes name, value and type, and all are required attributes. I would have expected value and type to be optional (as suggested by the documentation) - is this an error?

Cheers

Andy

 

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Eric Deutsch
Sent: 28 April 2008 07:16
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: [Psidev-ms-dev] Update from the PSI meeting

 

Hi everyone, we had a productive track at the PSI spring meeting. The highlights are:

 

- All suggested and needed schema revisions were completed and schema version 0.99.9 is available

- Most documentation updates were written. Revised full spec doc and html doc still to be released.

- MIAPE-MS example document almost completed

- ASMS poster features planned

- Journal article plans discussed

- Some CV updates and future update procedure planned. Still much to do

- Additional example documents are needed

- Web site updated with completed work

 

Many thanks to those who did the work at the workshop: Lennart Martens (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina (Madrid)

 

Moving forward, we have an aggressive schedule to release mzML 1.0.0 one month from now. Your participation is needed!

 

We will have weekly teleconferences for the next month to try to keep the focus strong. The next teleconference will be this Tuesday at 9am PDT at the usual place.

 

We have the following list of action items set at the end of the meeting:

 

- Eric will finish documentation items (incl reviewer reply)

- Pierre-Alain will finish MIAPE-MS example

- Eric will do the CV to do items

- Lennart will get validator finished and working

- Eric will put together poster with various assistance

- Lennart will write draft of manuscript

- Darren and Matt and Jim will work on example files

- Luisa will create the Excel sheets, one for each vendor. Eric will send. Luisa will reintegrate.

 

If you have an interest in mzML, we need your help to get it finished. One of the important things we still need is more example files. If you are willing to create from example files, especially by parts of the schema that have not been well tested, please help. Create an example file and post it. Or contact me for ideas.

 

Thank you!

Eric

 

 

 

 

 

 

 

 

 

 

 

 

 

[Psidev-ms-dev] CV param question

[Jones, A. <And...@li...>]

Another query about the cvParam structure (apologies for only looking at this so late in the process)...

 

As I understand it, the current schema draft contains several places where ParamGroup is used, which is an option to have cv terms (or userParams) either inline and/or by reference to a pre-defined ReferenceableParamGroup.

 

The ReferenceableParamGroup inherits from ParamGroup, and so can also contain cvParam, userParam or a reference to a ReferenceableParamGroup.

 

So... I have two questions:

 

1) Is it intended that a ParamGroup could contain inline CV/user parameters  _and_ a reference to a pre-defined set of parameters (i.e. this is not an explicit OR)?

 

<dx:sample id="">

                <dx:referenceableParamGroupRef ref="Some_reference_to_another_group"/>

                <dx:cvParam accession="" name="" cvRef="A_cv_term"/>

                <dx:userParam type="" value="" name="A_user_term"/>

</dx:sample>

 

2) Is it intended that a ReferenceableParamGroup could contain a reference to another ReferenceableParamGroup and if so what is the meaning of the reference?

 

<dx:referenceableParamGroup id="">

                <dx:referenceableParamGroupRef ref=" Some_reference_to_another_group "/>

                <dx:cvParam accession="" name="" cvRef="A_cv_term "/>

                <dx:userParam type="" value="" name=" A_user_term "/>

</dx:referenceableParamGroup>

 

I’m just trying to envisage how the validator works with this structure, is it possible to map explicitly to allowed CV terms if they are used in the referenceableParamGroup?

 

Cheers

Andy

 

 

 

 

 

 

 

 

 

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Jones, Andy
Sent: 28 April 2008 14:14
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Hi all,

 

I’m incorporating the mzML cvParam part (working from 0.99.9) into the analysisXML draft, to see how this works with the current schema. 

 

I noticed that userParam has attributes name, value and type, and all are required attributes. I would have expected value and type to be optional (as suggested by the documentation) – is this an error?

Cheers

Andy

 

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Eric Deutsch
Sent: 28 April 2008 07:16
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: [Psidev-ms-dev] Update from the PSI meeting

 

Hi everyone, we had a productive track at the PSI spring meeting. The highlights are:

 

- All suggested and needed schema revisions were completed and schema version 0.99.9 is available

- Most documentation updates were written. Revised full spec doc and html doc still to be released.

- MIAPE-MS example document almost completed

- ASMS poster features planned

- Journal article plans discussed

- Some CV updates and future update procedure planned. Still much to do

- Additional example documents are needed

- Web site updated with completed work

 

Many thanks to those who did the work at the workshop: Lennart Martens (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina (Madrid)

 

Moving forward, we have an aggressive schedule to release mzML 1.0.0 one month from now. Your participation is needed!

 

We will have weekly teleconferences for the next month to try to keep the focus strong. The next teleconference will be this Tuesday at 9am PDT at the usual place.

 

We have the following list of action items set at the end of the meeting:

 

- Eric will finish documentation items (incl reviewer reply)

- Pierre-Alain will finish MIAPE-MS example

- Eric will do the CV to do items

- Lennart will get validator finished and working

- Eric will put together poster with various assistance

- Lennart will write draft of manuscript

- Darren and Matt and Jim will work on example files

- Luisa will create the Excel sheets, one for each vendor. Eric will send. Luisa will reintegrate.

 

If you have an interest in mzML, we need your help to get it finished. One of the important things we still need is more example files. If you are willing to create from example files, especially by parts of the schema that have not been well tested, please help. Create an example file and post it. Or contact me for ideas.

 

Thank you!

Eric

 

 

 

 

 

 

 

 

 

 

 

 

 

Re: [Psidev-ms-dev] Update from the PSI meeting

[Jones, A. <And...@li...>]

Y it is this one that I have a problem with...

 

                <xs:complexType name="UserParamType">

                                <xs:annotation>

                                                <xs:documentation>Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead</xs:documentation>

                                </xs:annotation>

                                <xs:attribute name="name" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The name for the parameter.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                                <xs:attribute name="type" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The type of the parameter, where appropriate.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                                <xs:attribute name="value" type="xs:string" use="required">

                                                <xs:annotation>

                                                                <xs:documentation>The value for the parameter, where appropriate.</xs:documentation>

                                                </xs:annotation>

                                </xs:attribute>

                </xs:complexType>

 

 

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Randy Julian
Sent: 28 April 2008 14:54
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Andy,

 

In the schema I have, the element looks like this:

 

<xs:complexType name="CVParamType">

                <xs:attribute name="cvRef" type="xs:IDREF" use="required"/>

                <xs:attribute name="accession" type="xs:string" use="required"/>

                <xs:attribute name="value" type="xs:string" use="optional"/>

                <xs:attribute name="name" type="xs:string" use="required"/>

                <xs:attribute name="unitAccession" type="xs:string" use="optional"/>

                <xs:attribute name="unitName" type="xs:string" use="optional"/>

</xs:complexType>

 

This is version 0.99.9 (attached).  Let me know if this makes sense.

 

Thanks,

Randy

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Jones, Andy
Sent: Monday, April 28, 2008 9:14 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] Update from the PSI meeting

 

Hi all,

 

I’m incorporating the mzML cvParam part (working from 0.99.9) into the analysisXML draft, to see how this works with the current schema. 

 

I noticed that userParam has attributes name, value and type, and all are required attributes. I would have expected value and type to be optional (as suggested by the documentation) – is this an error?

Cheers

Andy

 

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Eric Deutsch
Sent: 28 April 2008 07:16
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: [Psidev-ms-dev] Update from the PSI meeting

 

Hi everyone, we had a productive track at the PSI spring meeting. The highlights are:

 

- All suggested and needed schema revisions were completed and schema version 0.99.9 is available

- Most documentation updates were written. Revised full spec doc and html doc still to be released.

- MIAPE-MS example document almost completed

- ASMS poster features planned

- Journal article plans discussed

- Some CV updates and future update procedure planned. Still much to do

- Additional example documents are needed

- Web site updated with completed work

 

Many thanks to those who did the work at the workshop: Lennart Martens (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina (Madrid)

 

Moving forward, we have an aggressive schedule to release mzML 1.0.0 one month from now. Your participation is needed!

 

We will have weekly teleconferences for the next month to try to keep the focus strong. The next teleconference will be this Tuesday at 9am PDT at the usual place.

 

We have the following list of action items set at the end of the meeting:

 

- Eric will finish documentation items (incl reviewer reply)

- Pierre-Alain will finish MIAPE-MS example

- Eric will do the CV to do items

- Lennart will get validator finished and working

- Eric will put together poster with various assistance

- Lennart will write draft of manuscript

- Darren and Matt and Jim will work on example files

- Luisa will create the Excel sheets, one for each vendor. Eric will send. Luisa will reintegrate.

 

If you have an interest in mzML, we need your help to get it finished. One of the important things we still need is more example files. If you are willing to create from example files, especially by parts of the schema that have not been well tested, please help. Create an example file and post it. Or contact me for ideas.

 

Thank you!

Eric

 

 

 

 

 

 

 

 

 

 

 

 

 

Re: [Psidev-ms-dev] Update from the PSI meeting

[Matt C. <mat...@va...>]

Hi Eric,

When you say you want example files, do you want the native file(s), the 
converted file, or both? Or do you mean a manually constructed example? 
I can probably get permission to release to the public some native files 
for some blank or QC runs from several different Thermo instruments 
(LTQ, LTQ/Orbitrap, Quantum). The corresponding output from pwiz's 
msconvert is trivial from that point.

What are the Excel sheets going to the vendors supposed to be for?

-Matt


Eric Deutsch wrote:
>
> Hi everyone, we had a productive track at the PSI spring meeting. The 
> highlights are:
>
>  
>
> - All suggested and needed schema revisions were completed and schema 
> version 0.99.9 is available
>
> - Most documentation updates were written. Revised full spec doc and 
> html doc still to be released.
>
> - MIAPE-MS example document almost completed
>
> - ASMS poster features planned
>
> - Journal article plans discussed
>
> - Some CV updates and future update procedure planned. Still much to do
>
> - Additional example documents are needed
>
> - Web site updated with completed work
>
>  
>
> Many thanks to those who did the work at the workshop: Lennart Martens 
> (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl 
> (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), 
> Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), 
> Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina 
> (Madrid)
>
>  
>
> Moving forward, we have an aggressive schedule to release mzML 1.0.0 
> one month from now. Your participation is needed!
>
>  
>
> We will have weekly teleconferences for the next month to try to keep 
> the focus strong. The next teleconference will be this Tuesday at 9am 
> PDT at the usual place.
>
>  
>
> We have the following list of action items set at the end of the meeting:
>
>  
>
> - Eric will finish documentation items (incl reviewer reply)
>
> - Pierre-Alain will finish MIAPE-MS example
>
> - Eric will do the CV to do items
>
> - Lennart will get validator finished and working
>
> - Eric will put together poster with various assistance
>
> - Lennart will write draft of manuscript
>
> - Darren and Matt and Jim will work on example files
>
> - Luisa will create the Excel sheets, one for each vendor. Eric will 
> send. Luisa will reintegrate.
>
>  
>
> If you have an interest in mzML, we need your help to get it finished. 
> One of the important things we still need is more example files. If 
> you are willing to create from example files, especially by parts of 
> the schema that have not been well tested, please help. Create an 
> example file and post it. Or contact me for ideas.
>
>  
>
> Thank you!
>
> Eric
>
>  
>
>  
>
>

Re: [Psidev-ms-dev] Update from the PSI meeting

[Jones, A. <And...@li...>]

Hi all,

 

I’m incorporating the mzML cvParam part (working from 0.99.9) into the analysisXML draft, to see how this works with the current schema. 

 

I noticed that userParam has attributes name, value and type, and all are required attributes. I would have expected value and type to be optional (as suggested by the documentation) – is this an error?

Cheers

Andy

 

 

From: psi...@li... [mailto:psi...@li...] On Behalf Of Eric Deutsch
Sent: 28 April 2008 07:16
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: [Psidev-ms-dev] Update from the PSI meeting

 

Hi everyone, we had a productive track at the PSI spring meeting. The highlights are:

 

- All suggested and needed schema revisions were completed and schema version 0.99.9 is available

- Most documentation updates were written. Revised full spec doc and html doc still to be released.

- MIAPE-MS example document almost completed

- ASMS poster features planned

- Journal article plans discussed

- Some CV updates and future update procedure planned. Still much to do

- Additional example documents are needed

- Web site updated with completed work

 

Many thanks to those who did the work at the workshop: Lennart Martens (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina (Madrid)

 

Moving forward, we have an aggressive schedule to release mzML 1.0.0 one month from now. Your participation is needed!

 

We will have weekly teleconferences for the next month to try to keep the focus strong. The next teleconference will be this Tuesday at 9am PDT at the usual place.

 

We have the following list of action items set at the end of the meeting:

 

- Eric will finish documentation items (incl reviewer reply)

- Pierre-Alain will finish MIAPE-MS example

- Eric will do the CV to do items

- Lennart will get validator finished and working

- Eric will put together poster with various assistance

- Lennart will write draft of manuscript

- Darren and Matt and Jim will work on example files

- Luisa will create the Excel sheets, one for each vendor. Eric will send. Luisa will reintegrate.

 

If you have an interest in mzML, we need your help to get it finished. One of the important things we still need is more example files. If you are willing to create from example files, especially by parts of the schema that have not been well tested, please help. Create an example file and post it. Or contact me for ideas.

 

Thank you!

Eric

 

 

 

 

 

 

 

 

 

 

 

 

 

Re: [Psidev-ms-dev] New help in the CV group solicited

[Yang, L. (NIH/N. [E] <ly...@ma...>]

Eric,

 

I would like to help you in the CV group.  I have some experience with
mass spec instrumentation and I am working with CPTAC informatics
support at National Cancer Institute.

 

Please let me know if you need more information.

 

Best,

Liming

 

Liming Yang, PhD

National Cancer Institute

 

________________________________

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Monday, April 28, 2008 2:16 AM
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: [Psidev-ms-dev] New help in the CV group solicited

 

Hi everyone, as I mentioned at the workshop, we could really use some
fresh help with the controlled vocabulary in the mass spectrometry
standards working group. Our CV is actually in pretty good shape, but
there is a long list of little items that need attention and it would be
use if some more eyes looked for trouble spots (and helped us fix them!)

 

An ontology coordinator helps the working group by addressing new CV
term and change requests, editing the CV with OBO-Edit, and maintaining
it in CVS. Some familiarity with mass spec instrumentation is necessary.

 

Anyone who is willing to serve as one of our ontology coordinators,
please contact me!

 

Thanks,

Eric

 

 

 

[Psidev-ms-dev] New help in the CV group solicited

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

Hi everyone, as I mentioned at the workshop, we could really use some
fresh help with the controlled vocabulary in the mass spectrometry
standards working group. Our CV is actually in pretty good shape, but
there is a long list of little items that need attention and it would be
use if some more eyes looked for trouble spots (and helped us fix them!)

 

An ontology coordinator helps the working group by addressing new CV
term and change requests, editing the CV with OBO-Edit, and maintaining
it in CVS. Some familiarity with mass spec instrumentation is necessary.

 

Anyone who is willing to serve as one of our ontology coordinators,
please contact me!

 

Thanks,

Eric

 

 

 

[Psidev-ms-dev] Update from the PSI meeting

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

Hi everyone, we had a productive track at the PSI spring meeting. The highlights are:

 

- All suggested and needed schema revisions were completed and schema version 0.99.9 is available

- Most documentation updates were written. Revised full spec doc and html doc still to be released.

- MIAPE-MS example document almost completed

- ASMS poster features planned

- Journal article plans discussed

- Some CV updates and future update procedure planned. Still much to do

- Additional example documents are needed

- Web site updated with completed work

 

Many thanks to those who did the work at the workshop: Lennart Martens (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI), Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid), Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina (Madrid)

 

Moving forward, we have an aggressive schedule to release mzML 1.0.0 one month from now. Your participation is needed!

 

We will have weekly teleconferences for the next month to try to keep the focus strong. The next teleconference will be this Tuesday at 9am PDT at the usual place.

 

We have the following list of action items set at the end of the meeting:

 

- Eric will finish documentation items (incl reviewer reply)

- Pierre-Alain will finish MIAPE-MS example

- Eric will do the CV to do items

- Lennart will get validator finished and working

- Eric will put together poster with various assistance

- Lennart will write draft of manuscript

- Darren and Matt and Jim will work on example files

- Luisa will create the Excel sheets, one for each vendor. Eric will send. Luisa will reintegrate.

 

If you have an interest in mzML, we need your help to get it finished. One of the important things we still need is more example files. If you are willing to create from example files, especially by parts of the schema that have not been well tested, please help. Create an example file and post it. Or contact me for ideas.

 

Thank you!

Eric

 

 

 

 

 

 

 

 

 

 

 

 

 

[Psidev-ms-dev] Sean L Seymour/FOS/PEC is out of the office.

[Sean L S. <Sey...@ap...>]

I will be out of the office starting Tue 04/22/2008 and will not return
until Mon 04/28/2008.

I will have limited access to email.

Re: [Psidev-ms-dev] mzML dev. page.

[Matthew C. <mat...@va...>]

Hi Eric, let me clarify. The CVS hadn't been updated for 6 months even 
though the last schema snapshot was a little over a month ago. It's 
updated now with .99.9, but the snapshots would be nice for reference. 
The snapshots are on a different repository, so we should have a link to 
it. The SVN repository seems to only have the semantic validator (which 
otherwise has no link on the development page?). So it might as well say 
"SVN for semantic validator project" instead of just "SVN". :)

-Matt


Eric Deutsch wrote:
> Hi everyone, it has been a productive time at the PSI workshop. We have
> completed many of the items on the to do list, although there remain
> many things to do yet. We are still aiming for a June 1 release of
> 1.0.0.
>
> The web site has just been updated for what we have right now. This
> includes the new 0.99.9 schemas and some of the example files, but note
> that many of the example files still need to be updated. Additional
> updates will occur over the next week.
>
> I don't understand what is meant by updating the links to the CVS and
> SVN repository.. those seem to be fine to me...?
>
> Regards,
> Eric
>
>
>   
>> -----Original Message-----
>> From: psi...@li...
>>     
> [mailto:psidev-ms-dev-
>   
>> bo...@li...] On Behalf Of Matthew Chambers
>> Sent: Wednesday, April 23, 2008 12:50 PM
>> To: Mass spectrometry standard development
>> Subject: Re: [Psidev-ms-dev] mzML dev. page.
>>
>> Agreed. And links to the CVS schema snapshot repository and the SVN
>> semantic validator repository.
>>
>> -Matt
>>
>> Rune Schjellerup Philosof wrote:
>>     
>>> Maybe release schedule on the mzML dev. homepage should be updated?
>>>
>>>
>>>     mzML Release Schedule
>>>
>>> (updated 2007-11-11)
>>>
>>>     * 2007-10-02 Submitted to PSI Document Process, begin 30-day
>>>       internal review
>>>     * 2007-11-15 Begin 60-day official community review period
>>>    *
>>>
>>>
>>>       
>>     
> ------------------------------------------------------------------------
> -
>   
>> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
>> Don't miss this year's exciting event. There's still time to save
>>     
> $100.
>   
>> Use priority code J8TL2D2.
>>
>>     
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/j
> av
>   
>> aone
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>     
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
> Don't miss this year's exciting event. There's still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
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> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>   

Re: [Psidev-ms-dev] mzML dev. page.

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

Hi everyone, it has been a productive time at the PSI workshop. We have
completed many of the items on the to do list, although there remain
many things to do yet. We are still aiming for a June 1 release of
1.0.0.

The web site has just been updated for what we have right now. This
includes the new 0.99.9 schemas and some of the example files, but note
that many of the example files still need to be updated. Additional
updates will occur over the next week.

I don't understand what is meant by updating the links to the CVS and
SVN repository.. those seem to be fine to me...?

Regards,
Eric


> -----Original Message-----
> From: psi...@li...
[mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Matthew Chambers
> Sent: Wednesday, April 23, 2008 12:50 PM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] mzML dev. page.
> 
> Agreed. And links to the CVS schema snapshot repository and the SVN
> semantic validator repository.
> 
> -Matt
> 
> Rune Schjellerup Philosof wrote:
> > Maybe release schedule on the mzML dev. homepage should be updated?
> >
> >
> >     mzML Release Schedule
> >
> > (updated 2007-11-11)
> >
> >     * 2007-10-02 Submitted to PSI Document Process, begin 30-day
> >       internal review
> >     * 2007-11-15 Begin 60-day official community review period
> >    *
> >
> >
> 
>
------------------------------------------------------------------------
-
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> Don't miss this year's exciting event. There's still time to save
$100.
> Use priority code J8TL2D2.
>
http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/j
av
> aone
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] CV term Proteinlynx

[shivram <shi...@re...>]

  
Dear Sir

I worked on Q-ToF micro waters recently. can you please help me in analysing the data through proteinlynx as im finding it difficult 


thanks and regards
Sheev

On Thu, 24 Apr 2008 Rune Schjellerup Philosof wrote :
>As I understand the Waters software, we have several things named
>proteinlynx.
>- There's a module for MassLynx called ProteinLynx.
>- ProteinLynx Global Server: The search engine used by ProteinLynx Browser.
>- ProteinLynx Browser: Waters software for data analysis.
>
>--
>Regards
>Rune
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
>Don't miss this year's exciting event. There's still time to save $100.
>Use priority code J8TL2D2.
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>_______________________________________________
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RESEARCH SCHOLAR
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Mobile : 91-9829077959  
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Re: [Psidev-ms-dev] mzML dev. page.

[Matthew C. <mat...@va...>]

Agreed. And links to the CVS schema snapshot repository and the SVN 
semantic validator repository.

-Matt

Rune Schjellerup Philosof wrote:
> Maybe release schedule on the mzML dev. homepage should be updated?
>
>
>     mzML Release Schedule
>
> (updated 2007-11-11)
>
>     * 2007-10-02 Submitted to PSI Document Process, begin 30-day
>       internal review
>     * 2007-11-15 Begin 60-day official community review period
>    *
>
>   

[Psidev-ms-dev] mzML dev. page.

[Rune S. P. <ru...@ph...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
</head>
<body bgcolor="#ffffff" text="#000000">
Maybe release schedule on the mzML dev. homepage should be updated?<br>
<br>
<h2>mzML Release Schedule<br>
</h2>
<p>(updated 2007-11-11) </p>
<ul>
  <li>2007-10-02 Submitted to PSI Document Process, begin 30-day
internal review</li>
  <li>2007-11-15 Begin 60-day official community review period</li>
  <li><br>
  </li>
</ul>
</body>
</html>