[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