psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] term proposal

[Salvador M. de B. <sma...@pr...>]

Hi Juanan,
I know that PRIDE XML will "disappear" when you adopt the mzIdentML, but
currently there are several tools generating PRIDE XML files that may want
to clarify that.
However, if the guideline is to include only the "correct" identifications,
that's all.
One question, what are your plans to substitute PRIDE XML by mzIdentML?
Until when are you going to accept PRIDE XML files?
Thanks!

Salvador Martínez de Bartolomé Izquierdo 
Bioinformatics Support - ProteoRed
Lab- B1, National Center for Biotechnology 
C/ Darwin, 3 Universidad Autónoma de Madrid Cantoblanco, 
28049 Madrid Spain
Phone: +34 91 585 4613
Fax: +34 91 585 4506

http://www.proteored.org
http://proteo.cnb.csic.es/trac
https://sites.google.com/site/bioinformaticaproteomica/


-----Mensaje original-----
De: Juan Antonio Vizcaino [mailto:ju...@eb...] 
Enviado el: 09 November 2012 16:48
Para: psi...@li...
CC: psi...@li...; 'Gerhard Mayer'; 'Mass spectrometry
standard development'
Asunto: Re: [Psidev-pi-dev] [Psidev-ms-vocab] term proposal

Hi Salva,

I don't think a CV term is actually needed for this case. PRIDE XML will be
slowly phased out and mzIdentML should be the substitute.

The guideline would be to include in the PRIDE XML file only the
identifications that you consider to be reliable. 

Cheers,

Juan Antonio



On 7 Nov 2012, at 08:51, Salvador Martínez de Bartolomé wrote:

> Well, maybe is more suitable for a PRIDE XML file. What does the PRIDE 
> team think?
> 
> Salvador Martínez de Bartolomé Izquierdo Bioinformatics Support - 
> ProteoRed
> Lab- B1, National Center for Biotechnology C/ Darwin, 3 Universidad 
> Autónoma de Madrid Cantoblanco,
> 28049 Madrid Spain
> Phone: +34 91 585 4613
> Fax: +34 91 585 4506
> 
> http://www.proteored.org
> http://proteo.cnb.csic.es/trac
> https://sites.google.com/site/bioinformaticaproteomica/
> 
> 
> 
> -----Mensaje original-----
> De: Gerhard Mayer [mailto:Ger...@ru...]
> Enviado el: 07 November 2012 09:49
> Para: Salvador Martínez de Bartolomé; 
> psi...@li...;
> psi...@li...; Mass spectrometry standard 
> development
> Asunto: Re: term proposal
> 
> Hi Salvador, hi all,
> 
> I think you mean the attribute passThreshold of the elements 
> SpectrumIdentificationItem and ProteindetectionHypothesis of mzIdentML.
> 
> In general we decided to avoid CV terms for informations which we can 
> describe by attributes of our standard file formats.
> In which ParamGroup do you want to state such a CV term?
> 
> Does anyone of the PRIDE team sees a need for such a CV term?
> 
> Best,
> Gerhard
> 
> 
> Am 07.11.2012 09:30, schrieb Salvador Martínez de Bartolomé:
>> Hi Gerhard:
>> Just a proposal for a new term:
>> A term like "pass threshold" that takes boolean values.
>> In the mzIdentML file there is already an attribute that means 
>> exactly that, but maybe it would be useful to have the possibility of 
>> having this term to state it in some ParamGroup... or to use it in 
>> the a PRIDE XML file using the PSI-MS ontology.
>> It just my opinion...
>> Thanks!
>> 
>> Salvador Martínez de Bartolomé Izquierdo Bioinformatics Support - 
>> ProteoRed
>> Lab- B1, National Center for Biotechnology C/ Darwin, 3 Universidad 
>> Autónoma de Madrid Cantoblanco,
>> 28049 Madrid Spain
>> Phone: +34 91 585 4613
>> Fax: +34 91 585 4506
>> 
>> http://www.proteored.org
>> http://proteo.cnb.csic.es/trac
>> https://sites.google.com/site/bioinformaticaproteomica/
>> 
>> 
> 
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik 
> Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für 
> klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
> 
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
> 
> 
> 
> ----------------------------------------------------------------------
> -------- LogMeIn Central: Instant, anywhere, Remote PC access and 
> management.
> Stay in control, update software, and manage PCs from one command 
> center Diagnose problems and improve visibility into emerging IT 
> issues Automate, monitor and manage. Do more in less time with Central 
> http://p.sf.net/sfu/logmein12331_d2d
> _______________________________________________
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> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab


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Re: [Psidev-ms-dev] [Psidev-ms-vocab] term proposal

[Juan A. V. <ju...@eb...>]

Hi Salva,

I don't think a CV term is actually needed for this case. PRIDE XML will be slowly phased out and mzIdentML should be the substitute.

The guideline would be to include in the PRIDE XML file only the identifications that you consider to be reliable. 

Cheers,

Juan Antonio



On 7 Nov 2012, at 08:51, Salvador Martínez de Bartolomé wrote:

> Well, maybe is more suitable for a PRIDE XML file. What does the PRIDE team
> think?
> 
> Salvador Martínez de Bartolomé Izquierdo 
> Bioinformatics Support - ProteoRed
> Lab- B1, National Center for Biotechnology 
> C/ Darwin, 3 Universidad Autónoma de Madrid Cantoblanco, 
> 28049 Madrid Spain
> Phone: +34 91 585 4613
> Fax: +34 91 585 4506
> 
> http://www.proteored.org
> http://proteo.cnb.csic.es/trac
> https://sites.google.com/site/bioinformaticaproteomica/
> 
> 
> 
> -----Mensaje original-----
> De: Gerhard Mayer [mailto:Ger...@ru...] 
> Enviado el: 07 November 2012 09:49
> Para: Salvador Martínez de Bartolomé; psi...@li...;
> psi...@li...; Mass spectrometry standard development
> Asunto: Re: term proposal
> 
> Hi Salvador, hi all,
> 
> I think you mean the attribute passThreshold of the elements
> SpectrumIdentificationItem and ProteindetectionHypothesis of mzIdentML.
> 
> In general we decided to avoid CV terms for informations which we can
> describe by attributes of our standard file formats.
> In which ParamGroup do you want to state such a CV term?
> 
> Does anyone of the PRIDE team sees a need for such a CV term?
> 
> Best,
> Gerhard
> 
> 
> Am 07.11.2012 09:30, schrieb Salvador Martínez de Bartolomé:
>> Hi Gerhard:
>> Just a proposal for a new term:
>> A term like "pass threshold" that takes boolean values.
>> In the mzIdentML file there is already an attribute that means exactly 
>> that, but maybe it would be useful to have the possibility of having 
>> this term to state it in some ParamGroup... or to use it in the a 
>> PRIDE XML file using the PSI-MS ontology.
>> It just my opinion...
>> Thanks!
>> 
>> Salvador Martínez de Bartolomé Izquierdo Bioinformatics Support - 
>> ProteoRed
>> Lab- B1, National Center for Biotechnology C/ Darwin, 3 Universidad 
>> Autónoma de Madrid Cantoblanco,
>> 28049 Madrid Spain
>> Phone: +34 91 585 4613
>> Fax: +34 91 585 4506
>> 
>> http://www.proteored.org
>> http://proteo.cnb.csic.es/trac
>> https://sites.google.com/site/bioinformaticaproteomica/
>> 
>> 
> 
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik
> Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für
> klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
> 
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
> 
> 
> 
> ------------------------------------------------------------------------------
> LogMeIn Central: Instant, anywhere, Remote PC access and management.
> Stay in control, update software, and manage PCs from one command center
> Diagnose problems and improve visibility into emerging IT issues
> Automate, monitor and manage. Do more in less time with Central
> http://p.sf.net/sfu/logmein12331_d2d
> _______________________________________________
> Psidev-ms-vocab mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.38.0_rc1 of psi-ms.obo

[pierre-alain b. <pie...@is...>]

Hi Gerhard,

send me the list of terms or ID for me to look at in priority.
Thanks
Pierre-Alain


On 09.11.2012 11:13, Jones, Andy wrote:
> Hi Gerhard,
>
> I think there's a minor misinterpretation about the quantification datatype. We did not intend that this would change place in the CV, simply that we would add an extra mapping in the mzq mapping file to "MS:1001405" allowing quantlayers to store peptide or protein scores as well as quantitation data types, in case people want to encode PSM scores etc. Do you think this is the best term in the hierarchy to map to?
>
> Thanks for sending round the listing of terms without a definition, this is something that should be quite easy to sort out if we delegate to the right people. Many of these are related to specific search engines, so:
>
>
> - perhaps David Creasy and Pierre-Alain can provide a pointer to definitions for their terms?
> - Who does ProteinExtractor belong to?
> - Can someone offer to take the Sequest terms - perhaps Martin since I guess these are used in ProDAC?
> - Anyone know of a good definition source for the ion types?
>
>
> Cheers
> Andy
>
>
>
>
>
> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: 09 November 2012 08:47
> To: psi...@li...; psi...@li...; Mass spectrometry standard development
> Subject: [Psidev-ms-vocab] Release candidate 3.38.0_rc1 of psi-ms.obo
>
> Dear proteomics community,
>
> attached there's the release candidate 3.38.0_rc1 of the psi-ms.obo file.
> 'spectrum identification result' details now is_a 'quantification datatype'.
>
> In addition a added a Word file listing all CV terms that have currently no definition defined.
>
> Because I'm not an expert in the technical details of instruments and all search engine parameters and it would be sensible to have meaningful definitions for the terms, it would be nice if everyone can look at this list and can complete the definition for terms where he thinks he has special knowledge and expertise.
> I will then collect all your proposals and try to suggest you later on this mailing list something like a consensus of all the proposals I will receive.
>
>
> Changed CV terms in version 3.38.0_rc1 of psi-ms.obo:
> =====================================================
> ************ Added is_a relation to enable mzQuantML validation through the mapping files
> ************ Remark: protein result details (MS:1001085) is already a child of spectrum identification result details (MS:1001405) [Term]
> id: MS:1001405
> name: spectrum identification result details
> def: "This subsection describes terms which can describe details of spectrum identification results." [PSI:PI]
> relationship: part_of MS:1001000 ! spectrum interpretation
> is_a: MS:1001805 ! quantification datatype
>
>
> New CV terms in version 3.38.0_rc1 of psi-ms.obo:
> =================================================
> No new CV terms
>
> Best Regards,
> Gerhard
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
>    
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_nov
> _______________________________________________
> Psidev-ms-vocab mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.38.0_rc1 of psi-ms.obo

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

Hi Gerhard,

I think there's a minor misinterpretation about the quantification datatype. We did not intend that this would change place in the CV, simply that we would add an extra mapping in the mzq mapping file to "MS:1001405" allowing quantlayers to store peptide or protein scores as well as quantitation data types, in case people want to encode PSM scores etc. Do you think this is the best term in the hierarchy to map to?

Thanks for sending round the listing of terms without a definition, this is something that should be quite easy to sort out if we delegate to the right people. Many of these are related to specific search engines, so:


- perhaps David Creasy and Pierre-Alain can provide a pointer to definitions for their terms? 
- Who does ProteinExtractor belong to?
- Can someone offer to take the Sequest terms - perhaps Martin since I guess these are used in ProDAC? 
- Anyone know of a good definition source for the ion types?


Cheers
Andy 





-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...] 
Sent: 09 November 2012 08:47
To: psi...@li...; psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Release candidate 3.38.0_rc1 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate 3.38.0_rc1 of the psi-ms.obo file.
'spectrum identification result' details now is_a 'quantification datatype'.

In addition a added a Word file listing all CV terms that have currently no definition defined.

Because I'm not an expert in the technical details of instruments and all search engine parameters and it would be sensible to have meaningful definitions for the terms, it would be nice if everyone can look at this list and can complete the definition for terms where he thinks he has special knowledge and expertise.
I will then collect all your proposals and try to suggest you later on this mailing list something like a consensus of all the proposals I will receive.


Changed CV terms in version 3.38.0_rc1 of psi-ms.obo:
=====================================================
************ Added is_a relation to enable mzQuantML validation through the mapping files
************ Remark: protein result details (MS:1001085) is already a child of spectrum identification result details (MS:1001405) [Term]
id: MS:1001405
name: spectrum identification result details
def: "This subsection describes terms which can describe details of spectrum identification results." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation
is_a: MS:1001805 ! quantification datatype


New CV terms in version 3.38.0_rc1 of psi-ms.obo:
=================================================
No new CV terms

Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.38.0_rc1 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.38.0_rc1 of the psi-ms.obo file.
'spectrum identification result' details now is_a 'quantification datatype'.

In addition a added a Word file listing all CV terms that have currently 
no definition defined.

Because I'm not an expert in the technical details of instruments and 
all search engine parameters
and it would be sensible to have meaningful definitions for the terms, 
it would be nice if everyone
can look at this list and can complete the definition for terms where he 
thinks he has special
knowledge and expertise.
I will then collect all your proposals and try to suggest you later on 
this mailing list
something like a consensus of all the proposals I will receive.


Changed CV terms in version 3.38.0_rc1 of psi-ms.obo:
=====================================================
************ Added is_a relation to enable mzQuantML validation through 
the mapping files
************ Remark: protein result details (MS:1001085) is already a 
child of spectrum identification result details (MS:1001405)
[Term]
id: MS:1001405
name: spectrum identification result details
def: "This subsection describes terms which can describe details of 
spectrum identification results." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation
is_a: MS:1001805 ! quantification datatype


New CV terms in version 3.38.0_rc1 of psi-ms.obo:
=================================================
No new CV terms

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] New version 3.37.0 of psi-ms.obo

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

Hi Gerhard, many thanks for your continued efforts. This looks good to me.
Except one question. At the bottom for the terms that you changed to
"Boolean", is there a definition for each term? No definition is shown in
the your email and I wonder if it is truly missing or just not shown in
your email because they are unchanged.

Thanks,
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Thursday, November 08, 2012 1:10 AM
To: psi...@li...;
psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-dev] New version 3.37.0 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate 3.37.0 of the psi-ms.obo file.

It contains definition changes for some terms.


Changed CV terms in version 3.37.0 of psi-ms.obo:
=================================================
************ Changed the definition
[Term]
id: MS:1001829
name: SRM transition ID
def: "Identifier for an SRM transition in an external document describing
additional information about the transition." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001828 ! Feature attribute

************ Changed the definition in the following terms (Removed
"Branch containing ..." resp. "This branch ..." from the definition).
[Term]
id: MS:1001006
name: Sequest:ViewCV
def: "Sequest View Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001041
name: Sequest:sortCV
def: "Sequest View / Sort Input Parameters." [PSI:PI]
is_a: MS:1001006 ! Sequest:ViewCV

[Term]
id: MS:1001087
name: Sequest:ProcessCV
def: "Sequest View / Process Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001101
name: protein group/subset relationship
def: "Protein group/subset relationships." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001110
name: Sequest:modeCV
def: "Sequest Mode Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001128
name: Sequest:selectCV
def: "Sequest Select Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001145
name: Sequest:SelectAdvancedCV
def: "Sequest Select Advanced Input Parameters." [PSI:PI]
is_a: MS:1001128 ! Sequest:selectCV

[Term]
id: MS:1001180
name: Cleavage agent regular expression
def: "Regular expressions for cleavage enzymes." [PSI:PI]
relationship: part_of MS:1001044 ! cleavage agent details


[Term]
id: MS:1002093
name: search engine input parameter
def: "Search engine input parameter." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002094
name: common search engine input parameter
def: "Search engine input parameter that is shared by more than one search
engine." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter

[Term]
id: MS:1001302
name: search engine specific input parameter
def: "Search engine specific input parameters." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter


[Term]
id: MS:1002103
name: software input parameter
def: "Software input parameters." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002104
name: common software input parameter
def: "Software input parameter that is shared by more than one software."
[PSI:PI]
is_a: MS:1002103 ! software input parameter

[Term]
id: MS:1002105
name: software specific input parameter
def: "Software specific input parameter." [PSI:PI]
is_a: MS:1002103 ! software input parameter

************ Changed the xref value-type from xsd\:bool to xsd\:boolean in
the following three terms to be consistent
************ with the official types defined in the documentation
http://www.w3.org/TR/xmlschema-2/#built-in-datatypes
************ of the W3C, which specifies only the type boolean.
[Term]
id: MS:1001111
name: Sequest:Full
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! Sequest:modeCV

[Term]
id: MS:1001120
name: Sequest:FormatAndLinks
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! Sequest:modeCV

[Term]
id: MS:1001126
name: Sequest:Fast
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! Sequest:modeCV


New CV terms in version 3.37.0 of psi-ms.obo:
=============================================
No new CV terms

Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik
Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für
klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.37.0 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.37.0 of the psi-ms.obo file.

It contains definition changes for some terms.


Changed CV terms in version 3.37.0 of psi-ms.obo:
=================================================
************ Changed the definition
[Term]
id: MS:1001829
name: SRM transition ID
def: "Identifier for an SRM transition in an external document 
describing additional information about the transition." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001828 ! Feature attribute

************ Changed the definition in the following terms (Removed 
"Branch containing ..." resp. "This branch ..." from the definition).
[Term]
id: MS:1001006
name: Sequest:ViewCV
def: "Sequest View Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001041
name: Sequest:sortCV
def: "Sequest View / Sort Input Parameters." [PSI:PI]
is_a: MS:1001006 ! Sequest:ViewCV

[Term]
id: MS:1001087
name: Sequest:ProcessCV
def: "Sequest View / Process Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001101
name: protein group/subset relationship
def: "Protein group/subset relationships." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001110
name: Sequest:modeCV
def: "Sequest Mode Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001128
name: Sequest:selectCV
def: "Sequest Select Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001145
name: Sequest:SelectAdvancedCV
def: "Sequest Select Advanced Input Parameters." [PSI:PI]
is_a: MS:1001128 ! Sequest:selectCV

[Term]
id: MS:1001180
name: Cleavage agent regular expression
def: "Regular expressions for cleavage enzymes." [PSI:PI]
relationship: part_of MS:1001044 ! cleavage agent details


[Term]
id: MS:1002093
name: search engine input parameter
def: "Search engine input parameter." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002094
name: common search engine input parameter
def: "Search engine input parameter that is shared by more than one 
search engine." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter

[Term]
id: MS:1001302
name: search engine specific input parameter
def: "Search engine specific input parameters." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter


[Term]
id: MS:1002103
name: software input parameter
def: "Software input parameters." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002104
name: common software input parameter
def: "Software input parameter that is shared by more than one 
software." [PSI:PI]
is_a: MS:1002103 ! software input parameter

[Term]
id: MS:1002105
name: software specific input parameter
def: "Software specific input parameter." [PSI:PI]
is_a: MS:1002103 ! software input parameter

************ Changed the xref value-type from xsd\:bool to xsd\:boolean 
in the following three terms to be consistent
************ with the official types defined in the documentation 
http://www.w3.org/TR/xmlschema-2/#built-in-datatypes
************ of the W3C, which specifies only the type boolean.
[Term]
id: MS:1001111
name: Sequest:Full
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! Sequest:modeCV

[Term]
id: MS:1001120
name: Sequest:FormatAndLinks
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! Sequest:modeCV

[Term]
id: MS:1001126
name: Sequest:Fast
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! Sequest:modeCV


New CV terms in version 3.37.0 of psi-ms.obo:
=============================================
No new CV terms

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] term proposal

[Salvador M. de B. <sma...@pr...>]

Well, maybe is more suitable for a PRIDE XML file. What does the PRIDE team
think?

Salvador Martínez de Bartolomé Izquierdo 
Bioinformatics Support - ProteoRed
Lab- B1, National Center for Biotechnology 
C/ Darwin, 3 Universidad Autónoma de Madrid Cantoblanco, 
28049 Madrid Spain
Phone: +34 91 585 4613
Fax: +34 91 585 4506

http://www.proteored.org
http://proteo.cnb.csic.es/trac
https://sites.google.com/site/bioinformaticaproteomica/



-----Mensaje original-----
De: Gerhard Mayer [mailto:Ger...@ru...] 
Enviado el: 07 November 2012 09:49
Para: Salvador Martínez de Bartolomé; psi...@li...;
psi...@li...; Mass spectrometry standard development
Asunto: Re: term proposal

Hi Salvador, hi all,

I think you mean the attribute passThreshold of the elements
SpectrumIdentificationItem and ProteindetectionHypothesis of mzIdentML.

In general we decided to avoid CV terms for informations which we can
describe by attributes of our standard file formats.
In which ParamGroup do you want to state such a CV term?

Does anyone of the PRIDE team sees a need for such a CV term?

Best,
Gerhard


Am 07.11.2012 09:30, schrieb Salvador Martínez de Bartolomé:
> Hi Gerhard:
> Just a proposal for a new term:
> A term like "pass threshold" that takes boolean values.
> In the mzIdentML file there is already an attribute that means exactly 
> that, but maybe it would be useful to have the possibility of having 
> this term to state it in some ParamGroup... or to use it in the a 
> PRIDE XML file using the PSI-MS ontology.
> It just my opinion...
> Thanks!
>
> Salvador Martínez de Bartolomé Izquierdo Bioinformatics Support - 
> ProteoRed
> Lab- B1, National Center for Biotechnology C/ Darwin, 3 Universidad 
> Autónoma de Madrid Cantoblanco,
> 28049 Madrid Spain
> Phone: +34 91 585 4613
> Fax: +34 91 585 4506
>
> http://www.proteored.org
> http://proteo.cnb.csic.es/trac
> https://sites.google.com/site/bioinformaticaproteomica/
>
>

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik
Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für
klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] term proposal

[Gerhard M. <Ger...@ru...>]

Hi Salvador, hi all,

I think you mean the attribute passThreshold of the elements 
SpectrumIdentificationItem and ProteindetectionHypothesis of mzIdentML.

In general we decided to avoid CV terms for informations which we can 
describe by attributes of our standard file formats.
In which ParamGroup do you want to state such a CV term?

Does anyone of the PRIDE team sees a need for such a CV term?

Best,
Gerhard


Am 07.11.2012 09:30, schrieb Salvador Martínez de Bartolomé:
> Hi Gerhard:
> Just a proposal for a new term:
> A term like "pass threshold" that takes boolean values.
> In the mzIdentML file there is already an attribute that means exactly that,
> but maybe it would be useful to have the possibility of having this term to
> state it in some ParamGroup... or to use it in the a PRIDE XML file using
> the PSI-MS ontology.
> It just my opinion...
> Thanks!
>
> Salvador Martínez de Bartolomé Izquierdo
> Bioinformatics Support - ProteoRed
> Lab- B1, National Center for Biotechnology
> C/ Darwin, 3 Universidad Autónoma de Madrid Cantoblanco,
> 28049 Madrid Spain
> Phone: +34 91 585 4613
> Fax: +34 91 585 4506
>
> http://www.proteored.org
> http://proteo.cnb.csic.es/trac
> https://sites.google.com/site/bioinformaticaproteomica/
>
>

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.37.0_rc1 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.37.0_rc1 of the psi-ms.obo file.

It contains definition changes for some terms.


Changed CV terms in version 3.37.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the definition
[Term]
id: MS:1001829
name: SRM transition ID
def: "Identifier for an SRM transition in an external document 
describing additional information about the transition." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001828 ! Feature attribute

************ Changed the definition in the following terms (Removed 
"Branch containing ..." resp. "This branch ..." from the definition).
[Term]
id: MS:1001006
name: Sequest:ViewCV
def: "Sequest View Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001041
name: Sequest:sortCV
def: "Sequest View / Sort Input Parameters." [PSI:PI]
is_a: MS:1001006 ! Sequest:ViewCV

[Term]
id: MS:1001087
name: Sequest:ProcessCV
def: "Sequest View / Process Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001101
name: protein group/subset relationship
def: "Protein group/subset relationships." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001110
name: Sequest:modeCV
def: "Sequest Mode Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001128
name: Sequest:selectCV
def: "Sequest Select Input Parameters." [PSI:PI]
is_a: MS:1002096 ! Sequest input parameter

[Term]
id: MS:1001145
name: Sequest:SelectAdvancedCV
def: "Sequest Select Advanced Input Parameters." [PSI:PI]
is_a: MS:1001128 ! Sequest:selectCV

[Term]
id: MS:1001180
name: Cleavage agent regular expression
def: "Regular expressions for cleavage enzymes." [PSI:PI]
relationship: part_of MS:1001044 ! cleavage agent details


[Term]
id: MS:1002093
name: search engine input parameter
def: "Search engine input parameter." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002094
name: common search engine input parameter
def: "Search engine input parameter that is shared by more than one 
search engine." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter

[Term]
id: MS:1001302
name: search engine specific input parameter
def: "Search engine specific input parameters." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter


[Term]
id: MS:1002103
name: software input parameter
def: "Software input parameters." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002104
name: common software input parameter
def: "Software input parameter that is shared by more than one 
software." [PSI:PI]
is_a: MS:1002103 ! software input parameter

[Term]
id: MS:1002105
name: software specific input parameter
def: "Software specific input parameter." [PSI:PI]
is_a: MS:1002103 ! software input parameter


New CV terms in version 3.37.0_rc1 of psi-ms.obo:
=================================================
No new CV terms


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] New version 3.36.0 of psi-ms.obo

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

Hi Gerhard, many thanks for continuing to update the CV!

I have two suggestions for improving this a little:

I suggest expanding this definition a bit:

id: MS:1001829
name: SRM transition ID
def: "SRM transition ID." [PSI:MS]
to:
def: "Identifier for an SRM transition in an external document describing
additional information about the transition." [PSI:MS]

And then my second quibble is that I don't think it is proper to mention
"branches" in a term definition. Each term and its definition should stand
on their own, and the structure of the CV itself designates information
about branches. So rather than:

id: MS:1002094
name: common search engine input parameter
def: "This branch contains search engine input parameters that are shared
by more than one search engine." [PSI:PI]
I suggest:
def: "Search engine input parameter that is shared by more than one search
engine." [PSI:PI]

Any children of this term are therefore assumed to also fit this
definition via the is_a relationship. There are several terms in this
group that should have this adjustment.

If there is disagreement on this, let's discuss.

Thanks,
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Tuesday, October 30, 2012 3:49 AM
To: psi...@li...;
psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-dev] New version 3.36.0 of psi-ms.obo

Dear proteomics community,

attached there's the new version 3.36.0 of the psi-ms.obo file.

It contains changes to some CV terms used in mzQuantML and a restructuring
of the tree for the search engine input parameters, which has a little bit
more structure now:
- search engine input parameter (MS:1002093)
   - common search engine input parameter (MS:1002094)
     - ... (terms shared by more than one search engine)
   - search engine specific input parameter (MS:1001302)
     - Mascot input parameter
       - ...
     - Sequest input parameter
       - ...
     - ...

- software input parameter (MS:1002103)
   - common software input parameter (MS:1002104)
     - ... (terms shared by more than one software)
   - software specific input parameter (MS:1002105)
     - Percolator input parameter
       - ...
     - Scaffold input parameter
       - ...


Changed CV terms in version 3.36.0 of psi-ms.obo:
=================================================
************ The term 'Peptide raw area' is now obsolete.
[Term]
id: MS:1001130
name: peptide raw area
def: "OBSOLETE Peptide raw area." [PSI:PI]
comment: This term was made obsolete because it is replaced by 'MS1
feature area' (MS:1001844).
is_a: MS:1001805 ! quantification datatype
is_obsolete: true

************ The term 'p-value (protein diff from 1 randomly)' is now
obsolete.
[Term]
id: MS:1001136
name: p-value (protein diff from 1 randomly)
def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI]
comment: This term was made obsolete because it is replaced by 't-test
p-value' (MS:1001855).
is_a: MS:1001805 ! quantification datatype
is_obsolete: true

************ Added String datatype to the term 'SRM transition ID'.
[Term]
id: MS:1001829
name: SRM transition ID
def: "SRM transition ID." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001828 ! Feature attribute



New CV terms in version 3.36.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002093
name: search engine input parameter
def: "This branch contains search engine input parameters." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002094
name: common search engine input parameter
def: "This branch contains search engine input parameters that are shared
by more than one search engine." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter

[Term]
id: MS:1002095
name: Mascot input parameter
def: "Search engine input parameters specific to Mascot." [PSI:PI,
source:http://www.matrixscience.com/help/search_field_help.html]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002096
name: Sequest input parameter
def: "Search engine input parameters specific to Sequest." [PSI:PI,
source:http://fields.scripps.edu/sequest/parameters.html]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002097
name: Phenyx input parameter
def: "Search engine input parameters specific to Phenyx." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002098
name: ProteinExtractor input parameter
def: "Search engine input parameters specific to ProteinExtractor."
[PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002099
name: OMSSA input parameter
def: "Search engine input parameters specific to OMSSA." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002100
name: ProteinScape input parameter
def: "Search engine input parameters specific to ProteinScape." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002101
name: ProteomeDiscoverer input parameter
def: "Search engine input parameters specific to ProteomeDiscoverer."
[PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002103
name: software input parameter
def: "This branch contains software input parameters." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002104
name: common software input parameter
def: "This branch contains software input parameters that are shared by
more than one software." [PSI:PI]
is_a: MS:1002103 ! software input parameter

[Term]
id: MS:1002105
name: software specific input parameter
def: "This branch contains software input parameters that are shared by
more than one software." [PSI:PI]
is_a: MS:1002103 ! software input parameter

[Term]
id: MS:1002106
name: Scaffold input parameter
def: "Search engine input parameters specific to Scaffold." [PSI:PI]
is_a: MS:1002105 ! software specific input parameter

[Term]
id: MS:1002107
name: Percolator input parameter
def: "Search engine input parameters specific to Percolator." [PSI:PI]
is_a: MS:1002105 ! software specific input parameter


Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik
Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für
klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.36.0 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the new version 3.36.0 of the psi-ms.obo file.

It contains changes to some CV terms used in mzQuantML
and a restructuring of the tree for the search engine input parameters,
which has a little bit more structure now:
- search engine input parameter (MS:1002093)
   - common search engine input parameter (MS:1002094)
     - ... (terms shared by more than one search engine)
   - search engine specific input parameter (MS:1001302)
     - Mascot input parameter
       - ...
     - Sequest input parameter
       - ...
     - ...

- software input parameter (MS:1002103)
   - common software input parameter (MS:1002104)
     - ... (terms shared by more than one software)
   - software specific input parameter (MS:1002105)
     - Percolator input parameter
       - ...
     - Scaffold input parameter
       - ...


Changed CV terms in version 3.36.0 of psi-ms.obo:
=================================================
************ The term 'Peptide raw area' is now obsolete.
[Term]
id: MS:1001130
name: peptide raw area
def: "OBSOLETE Peptide raw area." [PSI:PI]
comment: This term was made obsolete because it is replaced by 'MS1 
feature area' (MS:1001844).
is_a: MS:1001805 ! quantification datatype
is_obsolete: true

************ The term 'p-value (protein diff from 1 randomly)' is now 
obsolete.
[Term]
id: MS:1001136
name: p-value (protein diff from 1 randomly)
def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI]
comment: This term was made obsolete because it is replaced by 't-test 
p-value' (MS:1001855).
is_a: MS:1001805 ! quantification datatype
is_obsolete: true

************ Added String datatype to the term 'SRM transition ID'.
[Term]
id: MS:1001829
name: SRM transition ID
def: "SRM transition ID." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001828 ! Feature attribute



New CV terms in version 3.36.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002093
name: search engine input parameter
def: "This branch contains search engine input parameters." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002094
name: common search engine input parameter
def: "This branch contains search engine input parameters that are 
shared by more than one search engine." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter

[Term]
id: MS:1002095
name: Mascot input parameter
def: "Search engine input parameters specific to Mascot." [PSI:PI, 
source:http://www.matrixscience.com/help/search_field_help.html]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002096
name: Sequest input parameter
def: "Search engine input parameters specific to Sequest." [PSI:PI, 
source:http://fields.scripps.edu/sequest/parameters.html]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002097
name: Phenyx input parameter
def: "Search engine input parameters specific to Phenyx." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002098
name: ProteinExtractor input parameter
def: "Search engine input parameters specific to ProteinExtractor." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002099
name: OMSSA input parameter
def: "Search engine input parameters specific to OMSSA." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002100
name: ProteinScape input parameter
def: "Search engine input parameters specific to ProteinScape." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002101
name: ProteomeDiscoverer input parameter
def: "Search engine input parameters specific to ProteomeDiscoverer." 
[PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002103
name: software input parameter
def: "This branch contains software input parameters." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002104
name: common software input parameter
def: "This branch contains software input parameters that are shared by 
more than one software." [PSI:PI]
is_a: MS:1002103 ! software input parameter

[Term]
id: MS:1002105
name: software specific input parameter
def: "This branch contains software input parameters that are shared by 
more than one software." [PSI:PI]
is_a: MS:1002103 ! software input parameter

[Term]
id: MS:1002106
name: Scaffold input parameter
def: "Search engine input parameters specific to Scaffold." [PSI:PI]
is_a: MS:1002105 ! software specific input parameter

[Term]
id: MS:1002107
name: Percolator input parameter
def: "Search engine input parameters specific to Percolator." [PSI:PI]
is_a: MS:1002105 ! software specific input parameter


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Final version of MIAPE-Quant successfully through PSI document process

[Martin E. <mar...@ru...>]

  Dear all,
 
  this is to announce that the "MIAPE-Quant" went successfully
  through the PSI document process and the document type changed
  to "Final".
 
  The final version 1.0 can be found here:
  http://psidev.info/groups/miape 
 
 
    Best regards
      Martin Eisenacher (PSI Editor)
 
 
  --
  Dr. Martin Eisenacher
  Group Leader Bioinformatics / Biostatistics
  Medizinisches Proteom-Center (MPC)
  Ruhr-Universität Bochum
 
  phone: +49 / 234 / 32 - 29288
  fax: +49 / 234 / 32 - 14554
  http://www.medizinisches-proteom-center.de/

Re: [Psidev-ms-dev] [Psidev-pi-dev] FW: [Psi-announce] Call for Papers, Biocuration 2013, Cambridge UK, April 7-10, 2013

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

Yes, this sounds great. Maybe it would be a good idea to circulate a
manuscript outline that lists all the concepts we want to cover in the
paper before the writing begins.

Regards,
Eric


> -----Original Message-----
> From: pierre-alain binz [mailto:pie...@is...]
> Sent: Monday, October 22, 2012 4:52 AM
> To: Jones, Andy
> Cc: 'psi...@li...'; 'Mass spectrometry standard
> development'
> Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] FW: [Psi-announce] Call
> for Papers, Biocuration 2013, Cambridge UK, April 7-10, 2013
>
> Hi Andy, all,
>
> I'm strongly supportive of having a publication to describe and explain
> the PSI MS-CV. This great resource is the result of a strong and long
> term effort that has contributions from many people and institutions in
> proteomics (hardware vendors, software vendors, open source developers,
> experimentalists and MS experts). It has been positively evaluated by
> other fields. It is also a central piece in the PSI standards (is the
> main CV for mzML, mzIdentML, mzQuantML, mzTAB, TraML and PEFF).
>
> And yes, it is of interest to present this work at the conference.
>
> Gerhard, ready to start writing a forst draft?
>
> Cheers,
> Pierre-Alain
>
>
>
> On 22.10.2012 12:25, Jones, Andy wrote:
> > Hi all,
> >
> > As I mentioned before, I think it would be great if there was a PSI-
> MS CV paper, to recognize the work of particular people in curating
> this, to provide us with a single paper we can all reference and to
> show how the different workgroups have all collaborated to create what
> is now a pretty big and useful CV.
> >
> > I wonder if Gerhard perhaps or someone else would like to get
> together a paper on this. This call might be appropriate although this
> conference is the week preceding the PSI meeting in Liverpool, so might
> not be the ideal time for someone to travel and present it.
> Alternatively, we could pull together a paper and submit to Database or
> to one of the proteomics journals.
> >
> > Any opinions?
> > Cheers
> > Andy
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: psi...@eb... [mailto:psi-announce-
> bo...@eb...] On Behalf Of Sandra Orchard
> > Sent: 19 October 2012 21:10
> > To: psi...@eb...
> > Subject: [Psi-announce] Call for Papers, Biocuration 2013, Cambridge
> UK, April 7-10, 2013
> >
> > Dear Colleagues,
> >
> > The International Biocuration Conference is a unique event for
> curators and developers of biological databases to discuss their work,
> promote collaborations, and foster a sense of community in this very
> active and growing area of research. For the 6th International
> Biocuration Conference in Cambridge UK you are invited to submit your
> work for publication. This call for papers is done in collaboration
> with DATABASE: The Journal of Biological Databases and Curation. The
> DATABASE journal will publish an online Virtual Issue of the accepted
> papers. This is a great occasion to enhance the recognition of your
> work and of our profession by the greater biological research
> communities.
> >
> > This year there are five topic sessions from which submitters are
> invited to select:
> >
> > 1. Community annotation
> > 2. Functional annotation, tools and pipelines 3. Data mining and
> automated prediction 4. Ontologies and Standards 5. Data integration:
> Interactions, pathways and networks
> >
> > An additional session, "Lightning talks/hot topics", will include
> presentations outside the above topics.
> >
> > The manuscript review process will be expedited for these papers and
> we will thus need to be firm on the submission deadline:
> >
> > - Submission deadline: November 30, 2012
> > - First decisions: January 7, 2013
> > - Deadline for revisions: January 28, 2013
> > - Final decisions: February 18, 2013
> > - Conference: April 7-10, 2013
> >
> > Authors wishing to submit to DATABASE for the 2013 Biocuration
> Virtual issue should go to the DATABASE home page
> (http://database.oxfordjournals.org/) and click on the "submit now"
> after having read the "Instructions to Authors". Authors should CLEARLY
> state that they are submitting this manuscript for consideration for
> the Biocuration 2013 conference so that the DATABASE staff will ensure
> appropriate fast-track for inclusion in this meeting's proceedings. In
> addition, in the database submission form, they should also select
> "Biocuration Conference Paper" as a manuscript type. We look forward to
> your participation at Biocuration 2013 the 6th International
> Biocuration Conference.
> >
> > To be considered for a Biocuration 2013 presentation you MUST
> register and SUBMIT an abstract for the
> meeting<http://www.ebi.ac.uk/biocuration2013/>. On the abstract
> submission form, note that you will submit a manuscript for
> consideration by DATABASE for the Biocuration 2013 Virtual Issue.
> >
> > The proceedings of the 2012 meeting, the Biocuration 2012 Virtual
> Issue, are online
> <http://www.oxfordjournals.org/our_journals/databa/biocuration_virtual_
> issue.html>
> >
> > Kind regards,
> > -Biocuration 2013 Organizing Committee
> >
> > _______________________________________________
> > Psi-announce mailing list
> > Psi...@eb...
> > http://listserver.ebi.ac.uk/mailman/listinfo/psi-announce
> >
> > ---------------------------------------------------------------------
> ---------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> > http://p.sf.net/sfu/appdyn_sfd2d_oct
> > _______________________________________________
> > Psidev-pi-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>
> -----------------------------------------------------------------------
> -------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] [Psidev-pi-dev] FW: [Psi-announce] Call for Papers, Biocuration 2013, Cambridge UK, April 7-10, 2013

[pierre-alain b. <pie...@is...>]

Hi Andy, all,

I'm strongly supportive of having a publication to describe and explain 
the PSI MS-CV. This great resource is the result of a strong and long 
term effort that has contributions from many people and institutions in 
proteomics (hardware vendors, software vendors, open source developers, 
experimentalists and MS experts). It has been positively evaluated by 
other fields. It is also a central piece in the PSI standards (is the 
main CV for mzML, mzIdentML, mzQuantML, mzTAB, TraML and PEFF).

And yes, it is of interest to present this work at the conference.

Gerhard, ready to start writing a forst draft?

Cheers,
Pierre-Alain



On 22.10.2012 12:25, Jones, Andy wrote:
> Hi all,
>
> As I mentioned before, I think it would be great if there was a PSI-MS CV paper, to recognize the work of particular people in curating this, to provide us with a single paper we can all reference and to show how the different workgroups have all collaborated to create what is now a pretty big and useful CV.
>
> I wonder if Gerhard perhaps or someone else would like to get together a paper on this. This call might be appropriate although this conference is the week preceding the PSI meeting in Liverpool, so might not be the ideal time for someone to travel and present it. Alternatively, we could pull together a paper and submit to Database or to one of the proteomics journals.
>
> Any opinions?
> Cheers
> Andy
>
>
>
>
>
> -----Original Message-----
> From: psi...@eb... [mailto:psi...@eb...] On Behalf Of Sandra Orchard
> Sent: 19 October 2012 21:10
> To: psi...@eb...
> Subject: [Psi-announce] Call for Papers, Biocuration 2013, Cambridge UK, April 7-10, 2013
>
> Dear Colleagues,
>
> The International Biocuration Conference is a unique event for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research. For the 6th International Biocuration Conference in Cambridge UK you are invited to submit your work for publication. This call for papers is done in collaboration with DATABASE: The Journal of Biological Databases and Curation. The DATABASE journal will publish an online Virtual Issue of the accepted papers. This is a great occasion to enhance the recognition of your work and of our profession by the greater biological research communities.
>
> This year there are five topic sessions from which submitters are invited to select:
>
> 1. Community annotation
> 2. Functional annotation, tools and pipelines 3. Data mining and automated prediction 4. Ontologies and Standards 5. Data integration: Interactions, pathways and networks
>
> An additional session, “Lightning talks/hot topics”, will include presentations outside the above topics.
>
> The manuscript review process will be expedited for these papers and we will thus need to be firm on the submission deadline:
>
> - Submission deadline: November 30, 2012
> - First decisions: January 7, 2013
> - Deadline for revisions: January 28, 2013
> - Final decisions: February 18, 2013
> - Conference: April 7-10, 2013
>
> Authors wishing to submit to DATABASE for the 2013 Biocuration Virtual issue should go to the DATABASE home page (http://database.oxfordjournals.org/) and click on the "submit now" after having read the "Instructions to Authors". Authors should CLEARLY state that they are submitting this manuscript for consideration for the Biocuration 2013 conference so that the DATABASE staff will ensure appropriate fast-track for inclusion in this meeting's proceedings. In addition, in the database submission form, they should also select "Biocuration Conference Paper" as a manuscript type. We look forward to your participation at Biocuration 2013 the 6th International Biocuration Conference.
>
> To be considered for a Biocuration 2013 presentation you MUST register and SUBMIT an abstract for the meeting<http://www.ebi.ac.uk/biocuration2013/>. On the abstract submission form, note that you will submit a manuscript for consideration by DATABASE for the Biocuration 2013 Virtual Issue.
>
> The proceedings of the 2012 meeting, the Biocuration 2012 Virtual Issue, are online <http://www.oxfordjournals.org/our_journals/databa/biocuration_virtual_issue.html>
>
> Kind regards,
> -Biocuration 2013 Organizing Committee
>
> _______________________________________________
> Psi-announce mailing list
> Psi...@eb...
> http://listserver.ebi.ac.uk/mailman/listinfo/psi-announce
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

[Psidev-ms-dev] FW: [Psi-announce] Call for Papers, Biocuration 2013, Cambridge UK, April 7-10, 2013

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

Hi all,

As I mentioned before, I think it would be great if there was a PSI-MS CV paper, to recognize the work of particular people in curating this, to provide us with a single paper we can all reference and to show how the different workgroups have all collaborated to create what is now a pretty big and useful CV.

I wonder if Gerhard perhaps or someone else would like to get together a paper on this. This call might be appropriate although this conference is the week preceding the PSI meeting in Liverpool, so might not be the ideal time for someone to travel and present it. Alternatively, we could pull together a paper and submit to Database or to one of the proteomics journals.

Any opinions?
Cheers
Andy





-----Original Message-----
From: psi...@eb... [mailto:psi...@eb...] On Behalf Of Sandra Orchard
Sent: 19 October 2012 21:10
To: psi...@eb...
Subject: [Psi-announce] Call for Papers, Biocuration 2013, Cambridge UK, April 7-10, 2013

Dear Colleagues,

The International Biocuration Conference is a unique event for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research. For the 6th International Biocuration Conference in Cambridge UK you are invited to submit your work for publication. This call for papers is done in collaboration with DATABASE: The Journal of Biological Databases and Curation. The DATABASE journal will publish an online Virtual Issue of the accepted papers. This is a great occasion to enhance the recognition of your work and of our profession by the greater biological research communities.

This year there are five topic sessions from which submitters are invited to select:

1. Community annotation
2. Functional annotation, tools and pipelines 3. Data mining and automated prediction 4. Ontologies and Standards 5. Data integration: Interactions, pathways and networks

An additional session, “Lightning talks/hot topics”, will include presentations outside the above topics.

The manuscript review process will be expedited for these papers and we will thus need to be firm on the submission deadline:

- Submission deadline: November 30, 2012
- First decisions: January 7, 2013
- Deadline for revisions: January 28, 2013
- Final decisions: February 18, 2013
- Conference: April 7-10, 2013

Authors wishing to submit to DATABASE for the 2013 Biocuration Virtual issue should go to the DATABASE home page (http://database.oxfordjournals.org/) and click on the "submit now" after having read the "Instructions to Authors". Authors should CLEARLY state that they are submitting this manuscript for consideration for the Biocuration 2013 conference so that the DATABASE staff will ensure appropriate fast-track for inclusion in this meeting's proceedings. In addition, in the database submission form, they should also select "Biocuration Conference Paper" as a manuscript type. We look forward to your participation at Biocuration 2013 the 6th International Biocuration Conference.

To be considered for a Biocuration 2013 presentation you MUST register and SUBMIT an abstract for the meeting<http://www.ebi.ac.uk/biocuration2013/>. On the abstract submission form, note that you will submit a manuscript for consideration by DATABASE for the Biocuration 2013 Virtual Issue.

The proceedings of the 2012 meeting, the Biocuration 2012 Virtual Issue, are online <http://www.oxfordjournals.org/our_journals/databa/biocuration_virtual_issue.html>

Kind regards,
-Biocuration 2013 Organizing Committee

_______________________________________________
Psi-announce mailing list
Psi...@eb...
http://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

[Psidev-ms-dev] multidimensional chromatography

[Robles, S. <Ste...@le...>]

<?xml version="1.0" encoding="utf-8"?>
<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" version="1.1.0">
  <cvList count="1">
    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.35.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" />
  </cvList>
  <fileDescription>
    <fileContent>
      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
      <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
    </fileContent>
  </fileDescription>
  <referenceableParamGroupList count="1">
    <referenceableParamGroup id="SpectrumParamsPositive">
      <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
      <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
    </referenceableParamGroup>
  </referenceableParamGroupList>
  <softwareList count="1">
    <software id="ChromaTOF_HRT" version="Version: 1.80.0.0.0">
      <cvParam cvRef="MS" accession="MS:1001868" name="ChromaTOF HRT software" />
    </software>
  </softwareList>
  <instrumentConfigurationList count="1">
    <instrumentConfiguration id="IC1">
      <cvParam cvRef="MS" accession="MS:1001801" name="Pegasus HRT" />
      <componentList count="3">
        <source order="1">
          <cvParam cvRef="MS" accession="MS:1000389" name="electron ionization" />
        </source>
        <analyzer order="2">
          <cvParam cvRef="MS" accession="MS:1000084" name="time-of-flight" />
        </analyzer>
        <detector order="3">
          <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" />
        </detector>
      </componentList>
    </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="1">
    <dataProcessing id="DP1">
      <processingMethod order="1" softwareRef="ChromaTOF_HRT">
        <cvParam cvRef="MS" accession="MS:1001485" name="m/z calibration" />
        <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" />
      </processingMethod>
    </dataProcessing>
  </dataProcessingList>
  <run defaultInstrumentConfigurationRef="IC1" id="Run1">
    <cvParam cvRef="MS" accession="MS:1002086" name="two-dimensional gas chromatography with discrete modulation time steps" />
    <spectrumList count="3" defaultDataProcessingRef="DP1">
      <spectrum index="0" id="scan=0" defaultArrayLength="2">
        <referenceableParamGroupRef ref="SpectrumParamsPositive" />
        <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="99.995546" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
        <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1376.172119" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1419.234619" />
        <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
          <scan instrumentConfigurationRef="IC1">
            <cvParam cvRef="MS" accession="MS:1000826" name="elution time" value="80.738617" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
            <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.738617" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
            <cvParam cvRef="MS" accession="MS:1002082" name="first column elution time" value="80.000000" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
            <cvParam cvRef="MS" accession="MS:1002083" name="second column elution time" value="0.738617" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
          </scan>
        </scanList>
        <binaryDataArrayList count="2">
          <binaryDataArray encodedLength="24">
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
            <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
            <binary>OzY0Brf/WEBrDC8U7D9ZQA==</binary>
          </binaryDataArray>
          <binaryDataArray encodedLength="24">
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
            <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
            <binary>AAAAQLCAlUAAAAAAAIhFQA==</binary>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum index="1" id="scan=1" defaultArrayLength="2">
        <referenceableParamGroupRef ref="SpectrumParamsPositive" />
        <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="118.994240" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
        <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1303.666748" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1364.666748" />
        <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
          <scan instrumentConfigurationRef="IC1">
            <cvParam cvRef="MS" accession="MS:1000826" name="elution time" value="80.792529" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
            <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.792529" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
            <cvParam cvRef="MS" accession="MS:1002082" name="first column elution time" value="80.000000" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
            <cvParam cvRef="MS" accession="MS:1002083" name="second column elution time" value="0.792529" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
          </scan>
        </scanList>
        <binaryDataArrayList count="2">
          <binaryDataArray encodedLength="24">
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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            <binary>Ds0oWuM/WUDmdw2fob9dQA==</binary>
          </binaryDataArray>
          <binaryDataArray encodedLength="24">
            <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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            <binary>AAAAAACATkAAAADAql6UQA==</binary>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
      <spectrum index="2" id="scan=2" defaultArrayLength="2">
        <referenceableParamGroupRef ref="SpectrumParamsPositive" />
        <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="99.995546" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
        <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1198.498413" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1262.873413" />
        <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
          <scan instrumentConfigurationRef="IC1">
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            <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.999867" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
            <cvParam cvRef="MS" accession="MS:1002082" name="first column elution time" value="80.000000" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
            <cvParam cvRef="MS" accession="MS:1002083" name="second column elution time" value="0.999867" unitCvRef="MS" unitAccession="UO:0000010" unitName="second" />
          </scan>
        </scanList>
        <binaryDataArrayList count="2">
          <binaryDataArray encodedLength="24">
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            <binary>OzY0Brf/WEA8ToKo6j9ZQA==</binary>
          </binaryDataArray>
          <binaryDataArray encodedLength="24">
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            <binary>AAAAYP65kkAAAAAAABhQQA==</binary>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>
    </spectrumList>
  </run>
</mzML>

[Psidev-ms-dev] PROLONGED: submission of PSI recommendation document (mzTab): now open for Public Comment

[Martin E. <mar...@ru...>]

Dear colleague,
dear member of the Proteomics community,

as it was and IS not easy to receive comments from invited reviewers, the
deadline
for the mzTab Public and External Comment phase is prolonged (until 26th
October 2012).

Please make use of this participation mechanism to improve the standard
format!

Even small / short comments are helpful, please motivate colleagues and
co-workers 
to have a look at specification and / or examples!

  Best regards
    Martin Eisenacher (PSI Editor) 


> -----Ursprüngliche Nachricht-----
> Von: Martin Eisenacher [mailto:mar...@ru...]
> Gesendet: Montag, 13. August 2012 20:45
> An: psi...@li...; psidev-pi-
> de...@li...; 'psi...@eb...'
> Cc: 'Andy Jones'
> Betreff: submission of PSI recommendation document (mzTab): now open
> for Public Comment
> 
> Dear colleague,
> dear member of the Proteomics community,
> 
> please forward this message to potentially interested colleagues!
> 
> The HUPO Proteomics Standards Initiative (PSI) develops standards
> for documentation and storage of Proteomics data
> (see http://www.psidev.info for an overview of activities).
> 
> 
> A recommendation document specifying the mzTab file format has been
> submitted to the PSI document process.
> The submission can be found here: http://www.psidev.info/node/83
> 
> After having passed a 30-day review of the PSI steering commitee with
> minor formal changes, the proposed document version 1.0 release
> candidate
> now goes through 60-days public comments and external review phase
> (end: 12th October 2012).
> 
> "mzTab is intended as a lightweight supplement to the already existing
> standard file formats mzIdentML and mzQuantML, providing a summary
> of the final results of a MS-based proteomics experiment. mzTab
> files can contain protein, peptide, and small molecule identifications
> together with basic quantitative information and supports different
> levels
> of metadata reporting." (see also Cover Letter submitted)
> 
> It is important to highlight again that mzTab is not intended to store
> an experiment’s complete data / evidence but only its final reported
> results.
> 
> The public comment period enables the wider community to provide
> feedback
> on a proposed standard before it is formally accepted, and thus is an
> important
> step in the standardisation process.
> 
> 
> PLEASE ADD COMMENTS to the submission page
> (http://www.psidev.info/node/83)
> (or send them directly to martin.eisenacher: at : rub.de) for example
> regarding the following criteria:
> 
> - That it is well formed – that is, it is presented in accordance with
> the
>   templates and is clearly written.
> - That it is sufficiently detailed and clearly contains and
> comprehensively
>   describes the necessary and sufficient explanation of the format.
> - That the examples are in accordance with the specification.
> 
> This message is to encourage you to contribute to the standards
> development
> activity by commenting on the material that is available online. We
> invite
> both positive and negative comments. If negative comments are being
> made, these
> could be on the relevance, clarity, correctness, appropriateness, etc,
> of
> the proposal as a whole or of specific parts of the proposal.
> 
>    Many thanks for your valuable time and participation
>      Martin Eisenacher (PSI Editor)
> 
> 
> --
> Dr. Martin Eisenacher
> Group Leader Bioinformatics / Biostatistics
> Medizinisches Proteom-Center (MPC)
> Ruhr-Universität Bochum
> 
> phone: +49 / 234 / 32 - 29288
> fax: +49 / 234 / 32 - 14554
> http://www.medizinisches-proteom-center.de/

[Psidev-ms-dev] Release candidate 3.36.0_rc1 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.36.0_rc1 of the psi-ms.obo file.

Following a proposal of Eric from May 24th last year, it contains a 
restructuring
of the tree for the search engine input parameters, which has a little 
bit more structure now:
- search engine input parameter
   - common search engine input parameter
     - ... (terms shared by more than one search engine)
   - engine specific search engine input parameter
     - Mascot input parameter
       - ...
     - Sequest input parameter
       - ...
     - ...


Changed CV terms in version 3.36.0_rc1 of psi-ms.obo:
=====================================================
************ made obsolete
[Term]
id: MS:1001302
name: search engine specific input parameter
def: "OBSOLETE This branch contains search engine specific input 
parameters (e.g. Mascot Sig Threshold)." [PSI:PI]
is_a: MS:1001249 ! search input details
comment: This term was made obsolete because it was replaced by search 
engine input parameter (MS:1002093) and child terms thereof.
is_obsolete: true

In addition all is_a references to this term are replaced by references 
to the newly introduced terms.


New CV terms in version 3.36.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002093
name: search engine input parameter
def: "This branch contains search engine input parameters." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002094
name: common search engine input parameter
def: "This branch contains search engine input parameters that are 
shared by more than one search engine." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter

[Term]
id: MS:1002095
name: engine specific search engine input parameter
def: "This branch contains search engine input parameters that are 
specific to a search engine." [PSI:PI]
is_a: MS:1002093 ! search engine input parameter

[Term]
id: MS:1002096
name: Mascot input parameter
def: "Search engine input parameters specific to Mascot." [PSI:PI, 
source:http://www.matrixscience.com/help/search_field_help.html]
is_a: MS:1002095 ! engine specific search engine input parameter

[Term]
id: MS:1002097
name: Sequest input parameter
def: "Search engine input parameters specific to Sequest." [PSI:PI, 
source:http://fields.scripps.edu/sequest/parameters.html]
is_a: MS:1002095 ! engine specific search engine input parameter

[Term]
id: MS:1002098
name: Phenyx input parameter
def: "Search engine input parameters specific to Phenyx." [PSI:PI]
is_a: MS:1002095 ! engine specific search engine input parameter

[Term]
id: MS:1002099
name: ProteinExtractor input parameter
def: "Search engine input parameters specific to ProteinExtractor." [PSI:PI]
is_a: MS:1002095 ! engine specific search engine input parameter

[Term]
id: MS:1002100
name: OMSSA input parameter
def: "Search engine input parameters specific to OMSSA." [PSI:PI]
is_a: MS:1002095 ! engine specific search engine input parameter

[Term]
id: MS:1002101
name: Scaffold input parameter
def: "Search engine input parameters specific to Scaffold." [PSI:PI]
is_a: MS:1002095 ! engine specific search engine input parameter

[Term]
id: MS:1002102
name: Percolator input parameter
def: "Search engine input parameters specific to Percolator." [PSI:PI]
is_a: MS:1002095 ! engine specific search engine input parameter

[Term]
id: MS:1002103
name: ProteinScape input parameter
def: "Search engine input parameters specific to ProteinScape." [PSI:PI]
is_a: MS:1002095 ! engine specific search engine input parameter

[Term]
id: MS:1002104
name: ProteomeDiscoverer input parameter
def: "Search engine input parameters specific to ProteomeDiscoverer." 
[PSI:PI]
is_a: MS:1002095 ! engine specific search engine input parameter


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.35.0 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the new version 3.35.0 of the psi-ms.obo.

It contains new terms for first and second column elution times, the
terms for the multidimensional chromatography modulation description
and 4 new terms for ProteomeDiscoverer input parameters.
In addition the missing def items to some terms were added.


Changed CV terms in version 3.35.0 of psi-ms.obo:
=================================================
************ Changed the definition from
************ The time of elution from a chromatographic column, relative 
to the start of the chromatography. -->
************ The time of elution from all used chromatographic columns 
(one or more) in the chromatographic separation step, relative to the 
start of the chromatography.
[Term]
id: MS:1000826
name: elution time
def: "The time of elution from all used chromatographic columns (one or 
more) in the chromatographic separation step, relative to the start of 
the chromatography." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

************ Added the def: item
[Term]
id: MS:1001007
name: Sequest:OutputLines
def: "Number of peptide results to show." [PSI:MS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001009
name: Sequest:DescriptionLines
def: "Number of full protein descriptions to show for top N peptides." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001028
name: Sequest:SequenceHeaderFilter
def: "String in the header of a sequence entry for that entry to be 
searched." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001037
name: Sequest:ShowFragmentIons
def: "Flag indicating that fragment ions should be shown" [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001062
name: Mascot MGF file
def: "Mascot MGF file." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

************ Added the def: item
[Term]
id: MS:1001513
name: DB sequence filter pattern
def: "DB sequence filter pattern." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters

************ Added the def: item
[Term]
id: MS:1001514
name: DB accession filter string
def: "DB accession filter string." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters



New CV terms in version 3.35.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002082
name: first column elution time
def: "The time of elution from the first chromatographic column in the 
chromatographic separation step, relative to the start of chromatography 
on the first column."[PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1002083
name: second column elution time
def: "The time of elution from the second chromatographic column in the 
chromatographic separation step, relative to the start of the 
chromatography on the second column." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1002084
name: multidimensional chromatography modulation description
def: "Multidimensional chromatography modulation description." [PSI:MS]
is_a: MS:1000857 ! run attribute

[Term]
id: MS:1002085
name: two-dimensional gas chromatography with fixed modulation time
def: "Two-dimensional gas chromatography where a single modulation time 
is used throughout the acquisition." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002086
name: two-dimensional gas chromatography with discrete modulation time steps
def: "Two-dimensional gas chromatography where the acquisition is 
divided into steps, each with a different modulation time." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002087
name: two-dimensional liquid chromatography with fixed modulation time
def: "Two-dimensional liquid chromatography where a single modulation 
time is used throughout the acquisition." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002088
name: two-dimensional liquid chromatography with discrete modulation 
time steps
def: "Two-dimensional liquid chromatography where the acquisition is 
divided into steps, each with a different modulation time." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002089
name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold
def: "XCorr threshold for storing peptides that do not belong to a 
protein." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002090
name: Calculate Probability Scores
def: "Flag indicating that a probability score for the assessment that a 
reported peptide match is a random occurence is calculated." [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002091
name: ProteomeDiscoverer:Maximum Delta Cn
def: "Delta Cn threshold for filtering out PSM's." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002092
name: Percolator:Validation based on
def: "Algorithm (e.g. q-value or PEP) used for calculation of the 
validation score using Percolator." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] mzML for GCxGC/MS

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

Further to this – Henning and I have recently applied to BBSRC for on-going PSI funding, and one of the work package items involves promoting re-use / re-design of PSI standards for metabolomics, particularly mzML, mzQuantML and mzTab. Even if the grant isn’t awarded, we should certainly work towards this goal.

Not sure about the benefits of re-activating MIAPE-CC guidelines at the moment, I would think that getting things right in mzML is more important in the short term. Perhaps we could relevant people to join a PSI-MS conference call one week to float a few ideas?







From: Chris Taylor [mailto:chr...@eb...]
Sent: 05 October 2012 14:41
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS

Hi,

Christophe Steinbeck should get to comment too, or Jules Griffin (i.e. the rump of the Metabolomics Standards Initiative). Just to be careful about treading on toes...

Chris.

- Sent from my HTC on 3 -

----- Reply message -----
From: "pierre-alain binz" <pie...@is...<mailto:pie...@is...>>
To: <psi...@li...<mailto:psi...@li...>>
Subject: [Psidev-ms-dev] mzML for GCxGC/MS
Date: Fri, Oct 5, 2012 14:18


Hi Steffen,

you are absolutely right, we should not duplicate efforts.
Here we talk about two separate, however partly interdependant things:

on one side there is a need to revisit MIAPE CC and see what can be done
to incorporate, if possible, the comprehensive 2D chromatography usecases
on a parallel side, there is a need to have appropriate CV terms to
describe what should be stored in a supporting format mzML (we do not
have and CCML or an equivalent)

For the CV terms, let see if adding the requested terms fullfil the
needs in mzML.

About MIAPE CC, if someone is willing to reactivate and update the
guidelines and better match the requirements for complex chromatography,
this is more that welcome. Volunteers?

Formally, MIAPE CC is under the auspices of the protein separation
group, while mzML is under the responsibility of the MS group. But I'm
sure we can coordinate this in a seemless manner.

Pierre-Alain


On 05.10.2012 13:41, Steffen Neumann wrote:
> Hi,
>
> After the redesign of http://www.psidev.info
> I stumbled upon MIAPE CC (Column Chromatography) at
> http://www.psidev.info/protein-separation.
>
> At a first glance this does not really cover the use cases
> of complex GCxGC (or LCxLC), but we should not duplicate efforts
> if we can avoid it.
>
> Yours,
> Steffen
>
>
>
> On Fri, 2012-09-28 at 13:30 +0000, Robles, Steve wrote:
>> Hi Pierre-Alain,
>>
>>
>>
>> I think a term describing the function would be necessary if we
>> provided the multiple modulation times and had the importing program
>> calculate the 1st and 2nd elution times instead of providing all the
>> elution times. But such a term could be useful to provide some kind of
>> description that can account for the observed elution times of the
>> spectra.
>>
>>
>>
>> How about a parent term like:
>>
>> Multidimensional chromatography modulation description
>>
>>
>>
>> And starting with child terms:
>>
>> Two-dimensional gas chromatography with fixed modulation time
>> “Two-dimensional gas chromatography where a single modulation time is
>> used throughout the acquisition”
>>
>> Two-dimensional gas chromatography with discrete modulation time steps
>> “Two-dimensional gas chromatography where the acquisition is divided
>> into steps, each with a different modulation time”
>>
>> Two-dimensional liquid chromatography with fixed modulation time
>> “Two-dimensional liquid chromatography where a single modulation time
>> is used throughout the acquisition”
>>
>> Two-dimensional liquid chromatography with discrete modulation time
>> steps “Two-dimensional liquid chromatography where the acquisition is
>> divided into steps, each with a different modulation time”
>>
>>
>>
>> I would avoid including formulas because they would take up a lot of
>> space, be difficult to read without formatting, and aren’t necessary.
>> If we provided the table of modulation times, then the formula could
>> be used to validate the data but I can also imagine them being
>> misinterpreted.
>>
>>
>>
>> These are just some thoughts and suggestions. I’d leave the final
>> decision up to you and the rest of the group. I’d be satisfied with
>> 1st and 2nd column elution time but a descriptive term seems
>> beneficial.
>>
>> Best Regards,
>>
>>
>>
>> Steven Robles| Software design engineer
>> ste...@le...<mailto:ste...@le...>
>>
>> Description: LECOLOGO3.png
>> Delivering the Right Results | 3000 Lakeview Ave. | St. Joseph | MI
>> | 49085
>>
>> Visit us online at  www.leco.com|Register<http://www.leco.com|Register> to receive e-news & updates
>>
>>
>>
>>
>> From: pierre-alain binz [mailto:pie...@is...]
>> Sent: Friday, September 28, 2012 3:15 AM
>> To: Mass spectrometry standard development
>> Cc: Robles, Steve; mat...@gm...<mailto:mat...@gm...>
>> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS
>>
>>
>>
>>
>> Hi Steven,
>>
>> On 27.09.2012 21:58, Robles, Steve wrote:
>>
>>
>>          Hi Nils, Pierre-Alain, Matt and all,
>>
>>
>>
>>          Thanks for the feedback. It seems like everyone agrees that
>>          there should be an elution time for each column.
>>
>>
>>
>>          Pierre-Alain’s suggestion for MS:100826 definition change
>>          to"The time of elution from all used chromatographic columns
>>          (one or more) in the chromatographic separation step, relative
>>          to the start of the chromatography." sounds good to me. But
>>          I’m not sure what the third global term for the function would
>>          be. Are you suggesting a term for the run element that
>>          indicates if it GCxGC, LCxLC ? Or something about the
>>          modulation period?
>>
>>
>>
>> I'm referring to a term describing the function that implements the
>> relationship between elution time and modulation time (you have given
>> two examples below). This might be useful or not. mzML describes MS
>> acquisition parameters, and we could as well describe this as part of
>> the run gobal params. If this sounds a useful term, I let you propose
>> what is the most appropriate.
>>
>> Cheers
>> Pierre-Alain
>>
>>
>>
>>
>>
>>
>> Thanks again,
>>
>>
>>
>> Steven Robles| Software design engineer
>> ste...@le...<mailto:ste...@le...>
>>
>> Description: LECOLOGO3.png
>> Delivering the Right Results | 3000 Lakeview Ave. | St. Joseph | MI
>> | 49085
>>
>> Visit us online at  www.leco.com|Register<http://www.leco.com|Register> to receive e-news & updates
>>
>>
>>
>> From: Nils Hoffmann [mailto:nil...@ce...]
>> Sent: Thursday, September 27, 2012 2:32 PM
>> To: Robles, Steve
>> Cc: psi...@li...<mailto:psi...@li...>
>> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS
>>
>>
>>
>> Hi Steve,
>> as one of the original requestors of the modulation_time term, I
>> totally agree with your option nr. 2 to handle more possible
>> use-cases. We simply opted for the simpler option first since we did
>> not have reference data available for other modulation regimes. Fyi,
>> there was a thread started by Steve Reichenbach recently on 2D LC-MS
>> that circled around non-uniform modulation schemes and which might
>> also be of interest here.
>>
>> Nils Hoffmann
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Got visibility?
>> Most devs has no idea what their production app looks like.
>> Find out how fast your code is with AppDynamics Lite.
>> http://ad.doubleclick.net/clk;262219671;13503038;y?
>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...<mailto:Psi...@li...>
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


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[Psidev-ms-dev] Release candidate 3.35.0_rc1 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.35.0_rc1 of the psi-ms.obo.

It contains new terms for first and second column elution times, the
terms for the multidimensional chromatography modulation description
and 4 new terms for ProteomeDiscoverer input parameters.
In addition the missing def items to some terms were added.

@Steve Robles: please check, if the new terms are appropriate for your need.


Changed CV terms in version 3.35.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the definition from
************ The time of elution from a chromatographic column, relative 
to the start of the chromatography. -->
************ The time of elution from all used chromatographic columns 
(one or more) in the chromatographic separation step, relative to the 
start of the chromatography.
[Term]
id: MS:1000826
name: elution time
def: "The time of elution from all used chromatographic columns (one or 
more) in the chromatographic separation step, relative to the start of 
the chromatography." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

************ Added the def: item
[Term]
id: MS:1001007
name: Sequest:OutputLines
def: "Number of peptide results to show." [PSI:MS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001009
name: Sequest:DescriptionLines
def: "Number of full protein descriptions to show for top N peptides." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001028
name: Sequest:SequenceHeaderFilter
def: "String in the header of a sequence entry for that entry to be 
searched." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001037
name: Sequest:ShowFragmentIons
def: "Flag indicating that fragment ions should be shown" [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001062
name: Mascot MGF file
def: "Mascot MGF file." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

************ Added the def: item
[Term]
id: MS:1001513
name: DB sequence filter pattern
def: "DB sequence filter pattern." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters

************ Added the def: item
[Term]
id: MS:1001514
name: DB accession filter string
def: "DB accession filter string." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters


New CV terms in version 3.35.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002082
name: first column elution time
def: "The time of elution from the first chromatographic column in the 
chromatographic separation step, relative to the start of the 
chromatography." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1002083
name: second column elution time
def: "The time of elution from the second chromatographic column in the 
chromatographic separation step, relative to the start of the 
chromatography." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1002084
name: multidimensional chromatography modulation description
def: "Multidimensional chromatography modulation description." [PSI:MS]
is_a: MS:1000857 ! run attribute

[Term]
id: MS:1002085
name: two-dimensional gas chromatography with fixed modulation time
def: "Two-dimensional gas chromatography where a single modulation time 
is used throughout the acquisition." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002086
name: two-dimensional gas chromatography with discrete modulation time steps
def: "Two-dimensional gas chromatography where the acquisition is 
divided into steps, each with a different modulation time." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002087
name: two-dimensional liquid chromatography with fixed modulation time
def: "Two-dimensional liquid chromatography where a single modulation 
time is used throughout the acquisition." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002088
name: two-dimensional liquid chromatography with discrete modulation 
time steps
def: "Two-dimensional liquid chromatography where the acquisition is 
divided into steps, each with a different modulation time." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002089
name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold
def: "XCorr threshold for storing peptides that do not belong to a 
protein." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002090
name: Calculate Probability Scores
def: "Flag indicating that a probability score for the assessment that a 
reported peptide match is a random occurence is calculated." [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002091
name: ProteomeDiscoverer:Maximum Delta Cn
def: "Delta Cn threshold for filtering out PSM's." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002092
name: Percolator:Validation based on
def: "Algorithm (e.g. q-value or PEP) used for calculation of the 
validation score using Percolator." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum
  
Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] mzML for GCxGC/MS

[C. T. <chr...@eb...>]

Hi,

Christophe Steinbeck should get to comment too, or Jules Griffin (i.e. the rump of the Metabolomics Standards Initiative). Just to be careful about treading on toes...

Chris.

- Sent from my HTC on 3 -

----- Reply message -----
From: "pierre-alain binz" <pie...@is...>
To: <psi...@li...>
Subject: [Psidev-ms-dev] mzML for GCxGC/MS
Date: Fri, Oct 5, 2012 14:18


Hi Steffen,

you are absolutely right, we should not duplicate efforts.
Here we talk about two separate, however partly interdependant things:

on one side there is a need to revisit MIAPE CC and see what can be done 
to incorporate, if possible, the comprehensive 2D chromatography usecases
on a parallel side, there is a need to have appropriate CV terms to 
describe what should be stored in a supporting format mzML (we do not 
have and CCML or an equivalent)

For the CV terms, let see if adding the requested terms fullfil the 
needs in mzML.

About MIAPE CC, if someone is willing to reactivate and update the 
guidelines and better match the requirements for complex chromatography, 
this is more that welcome. Volunteers?

Formally, MIAPE CC is under the auspices of the protein separation 
group, while mzML is under the responsibility of the MS group. But I'm 
sure we can coordinate this in a seemless manner.

Pierre-Alain


On 05.10.2012 13:41, Steffen Neumann wrote:
> Hi,
>
> After the redesign of http://www.psidev.info
> I stumbled upon MIAPE CC (Column Chromatography) at
> http://www.psidev.info/protein-separation.
>
> At a first glance this does not really cover the use cases
> of complex GCxGC (or LCxLC), but we should not duplicate efforts
> if we can avoid it.
>
> Yours,
> Steffen
>
>
>
> On Fri, 2012-09-28 at 13:30 +0000, Robles, Steve wrote:
>> Hi Pierre-Alain,
>>
>>   
>>
>> I think a term describing the function would be necessary if we
>> provided the multiple modulation times and had the importing program
>> calculate the 1st and 2nd elution times instead of providing all the
>> elution times. But such a term could be useful to provide some kind of
>> description that can account for the observed elution times of the
>> spectra.
>>
>>   
>>
>> How about a parent term like:
>>
>> Multidimensional chromatography modulation description
>>
>>   
>>
>> And starting with child terms:
>>
>> Two-dimensional gas chromatography with fixed modulation time
>> “Two-dimensional gas chromatography where a single modulation time is
>> used throughout the acquisition”
>>
>> Two-dimensional gas chromatography with discrete modulation time steps
>> “Two-dimensional gas chromatography where the acquisition is divided
>> into steps, each with a different modulation time”
>>
>> Two-dimensional liquid chromatography with fixed modulation time
>> “Two-dimensional liquid chromatography where a single modulation time
>> is used throughout the acquisition”
>>
>> Two-dimensional liquid chromatography with discrete modulation time
>> steps “Two-dimensional liquid chromatography where the acquisition is
>> divided into steps, each with a different modulation time”
>>
>>   
>>
>> I would avoid including formulas because they would take up a lot of
>> space, be difficult to read without formatting, and aren’t necessary.
>> If we provided the table of modulation times, then the formula could
>> be used to validate the data but I can also imagine them being
>> misinterpreted.
>>
>>   
>>
>> These are just some thoughts and suggestions. I’d leave the final
>> decision up to you and the rest of the group. I’d be satisfied with
>> 1st and 2nd column elution time but a descriptive term seems
>> beneficial.
>>
>> Best Regards,
>>
>>   
>>
>> Steven Robles| Software design engineer
>> ste...@le...
>>
>> Description: LECOLOGO3.png
>> Delivering the Right Results | 3000 Lakeview Ave. | St. Joseph | MI
>> | 49085
>>
>> Visit us online at  www.leco.com|Register to receive e-news & updates
>>
>>
>>   
>>
>> From: pierre-alain binz [mailto:pie...@is...]
>> Sent: Friday, September 28, 2012 3:15 AM
>> To: Mass spectrometry standard development
>> Cc: Robles, Steve; mat...@gm...
>> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS
>>
>>
>>   
>>
>> Hi Steven,
>>
>> On 27.09.2012 21:58, Robles, Steve wrote:
>>
>>
>>          Hi Nils, Pierre-Alain, Matt and all,
>>          
>>           
>>          
>>          Thanks for the feedback. It seems like everyone agrees that
>>          there should be an elution time for each column.
>>          
>>           
>>          
>>          Pierre-Alain’s suggestion for MS:100826 definition change
>>          to"The time of elution from all used chromatographic columns
>>          (one or more) in the chromatographic separation step, relative
>>          to the start of the chromatography." sounds good to me. But
>>          I’m not sure what the third global term for the function would
>>          be. Are you suggesting a term for the run element that
>>          indicates if it GCxGC, LCxLC ? Or something about the
>>          modulation period?
>>          
>>          
>>
>> I'm referring to a term describing the function that implements the
>> relationship between elution time and modulation time (you have given
>> two examples below). This might be useful or not. mzML describes MS
>> acquisition parameters, and we could as well describe this as part of
>> the run gobal params. If this sounds a useful term, I let you propose
>> what is the most appropriate.
>>
>> Cheers
>> Pierre-Alain
>>
>>
>>
>>
>>   
>>
>> Thanks again,
>>
>>   
>>
>> Steven Robles| Software design engineer
>> ste...@le...
>>
>> Description: LECOLOGO3.png
>> Delivering the Right Results | 3000 Lakeview Ave. | St. Joseph | MI
>> | 49085
>>
>> Visit us online at  www.leco.com|Register to receive e-news & updates
>>
>>   
>>
>> From: Nils Hoffmann [mailto:nil...@ce...]
>> Sent: Thursday, September 27, 2012 2:32 PM
>> To: Robles, Steve
>> Cc: psi...@li...
>> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS
>>
>>   
>>
>> Hi Steve,
>> as one of the original requestors of the modulation_time term, I
>> totally agree with your option nr. 2 to handle more possible
>> use-cases. We simply opted for the simpler option first since we did
>> not have reference data available for other modulation regimes. Fyi,
>> there was a thread started by Steve Reichenbach recently on 2D LC-MS
>> that circled around non-uniform modulation schemes and which might
>> also be of interest here.
>>
>> Nils Hoffmann
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Got visibility?
>> Most devs has no idea what their production app looks like.
>> Find out how fast your code is with AppDynamics Lite.
>> http://ad.doubleclick.net/clk;262219671;13503038;y?
>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


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Re: [Psidev-ms-dev] mzML for GCxGC/MS

[pierre-alain b. <pie...@is...>]

Hi Steffen,

you are absolutely right, we should not duplicate efforts.
Here we talk about two separate, however partly interdependant things:

on one side there is a need to revisit MIAPE CC and see what can be done 
to incorporate, if possible, the comprehensive 2D chromatography usecases
on a parallel side, there is a need to have appropriate CV terms to 
describe what should be stored in a supporting format mzML (we do not 
have and CCML or an equivalent)

For the CV terms, let see if adding the requested terms fullfil the 
needs in mzML.

About MIAPE CC, if someone is willing to reactivate and update the 
guidelines and better match the requirements for complex chromatography, 
this is more that welcome. Volunteers?

Formally, MIAPE CC is under the auspices of the protein separation 
group, while mzML is under the responsibility of the MS group. But I'm 
sure we can coordinate this in a seemless manner.

Pierre-Alain


On 05.10.2012 13:41, Steffen Neumann wrote:
> Hi,
>
> After the redesign of http://www.psidev.info
> I stumbled upon MIAPE CC (Column Chromatography) at
> http://www.psidev.info/protein-separation.
>
> At a first glance this does not really cover the use cases
> of complex GCxGC (or LCxLC), but we should not duplicate efforts
> if we can avoid it.
>
> Yours,
> Steffen
>
>
>
> On Fri, 2012-09-28 at 13:30 +0000, Robles, Steve wrote:
>> Hi Pierre-Alain,
>>
>>   
>>
>> I think a term describing the function would be necessary if we
>> provided the multiple modulation times and had the importing program
>> calculate the 1st and 2nd elution times instead of providing all the
>> elution times. But such a term could be useful to provide some kind of
>> description that can account for the observed elution times of the
>> spectra.
>>
>>   
>>
>> How about a parent term like:
>>
>> Multidimensional chromatography modulation description
>>
>>   
>>
>> And starting with child terms:
>>
>> Two-dimensional gas chromatography with fixed modulation time
>> “Two-dimensional gas chromatography where a single modulation time is
>> used throughout the acquisition”
>>
>> Two-dimensional gas chromatography with discrete modulation time steps
>> “Two-dimensional gas chromatography where the acquisition is divided
>> into steps, each with a different modulation time”
>>
>> Two-dimensional liquid chromatography with fixed modulation time
>> “Two-dimensional liquid chromatography where a single modulation time
>> is used throughout the acquisition”
>>
>> Two-dimensional liquid chromatography with discrete modulation time
>> steps “Two-dimensional liquid chromatography where the acquisition is
>> divided into steps, each with a different modulation time”
>>
>>   
>>
>> I would avoid including formulas because they would take up a lot of
>> space, be difficult to read without formatting, and aren’t necessary.
>> If we provided the table of modulation times, then the formula could
>> be used to validate the data but I can also imagine them being
>> misinterpreted.
>>
>>   
>>
>> These are just some thoughts and suggestions. I’d leave the final
>> decision up to you and the rest of the group. I’d be satisfied with
>> 1st and 2nd column elution time but a descriptive term seems
>> beneficial.
>>
>> Best Regards,
>>
>>   
>>
>> Steven Robles| Software design engineer
>> ste...@le...
>>
>> Description: LECOLOGO3.png
>> Delivering the Right Results | 3000 Lakeview Ave. | St. Joseph | MI
>> | 49085
>>
>> Visit us online at  www.leco.com|Register to receive e-news & updates
>>
>>
>>   
>>
>> From: pierre-alain binz [mailto:pie...@is...]
>> Sent: Friday, September 28, 2012 3:15 AM
>> To: Mass spectrometry standard development
>> Cc: Robles, Steve; mat...@gm...
>> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS
>>
>>
>>   
>>
>> Hi Steven,
>>
>> On 27.09.2012 21:58, Robles, Steve wrote:
>>
>>
>>          Hi Nils, Pierre-Alain, Matt and all,
>>          
>>           
>>          
>>          Thanks for the feedback. It seems like everyone agrees that
>>          there should be an elution time for each column.
>>          
>>           
>>          
>>          Pierre-Alain’s suggestion for MS:100826 definition change
>>          to"The time of elution from all used chromatographic columns
>>          (one or more) in the chromatographic separation step, relative
>>          to the start of the chromatography." sounds good to me. But
>>          I’m not sure what the third global term for the function would
>>          be. Are you suggesting a term for the run element that
>>          indicates if it GCxGC, LCxLC ? Or something about the
>>          modulation period?
>>          
>>          
>>
>> I'm referring to a term describing the function that implements the
>> relationship between elution time and modulation time (you have given
>> two examples below). This might be useful or not. mzML describes MS
>> acquisition parameters, and we could as well describe this as part of
>> the run gobal params. If this sounds a useful term, I let you propose
>> what is the most appropriate.
>>
>> Cheers
>> Pierre-Alain
>>
>>
>>
>>
>>   
>>
>> Thanks again,
>>
>>   
>>
>> Steven Robles| Software design engineer
>> ste...@le...
>>
>> Description: LECOLOGO3.png
>> Delivering the Right Results | 3000 Lakeview Ave. | St. Joseph | MI
>> | 49085
>>
>> Visit us online at  www.leco.com|Register to receive e-news & updates
>>
>>   
>>
>> From: Nils Hoffmann [mailto:nil...@ce...]
>> Sent: Thursday, September 27, 2012 2:32 PM
>> To: Robles, Steve
>> Cc: psi...@li...
>> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS
>>
>>   
>>
>> Hi Steve,
>> as one of the original requestors of the modulation_time term, I
>> totally agree with your option nr. 2 to handle more possible
>> use-cases. We simply opted for the simpler option first since we did
>> not have reference data available for other modulation regimes. Fyi,
>> there was a thread started by Steve Reichenbach recently on 2D LC-MS
>> that circled around non-uniform modulation schemes and which might
>> also be of interest here.
>>
>> Nils Hoffmann
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Got visibility?
>> Most devs has no idea what their production app looks like.
>> Find out how fast your code is with AppDynamics Lite.
>> http://ad.doubleclick.net/clk;262219671;13503038;y?
>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] mzML for GCxGC/MS

[Steffen N. <sne...@ip...>]

Hi,

After the redesign of http://www.psidev.info
I stumbled upon MIAPE CC (Column Chromatography) at
http://www.psidev.info/protein-separation.

At a first glance this does not really cover the use cases
of complex GCxGC (or LCxLC), but we should not duplicate efforts 
if we can avoid it.

Yours,
Steffen



On Fri, 2012-09-28 at 13:30 +0000, Robles, Steve wrote:
> Hi Pierre-Alain,
> 
>  
> 
> I think a term describing the function would be necessary if we
> provided the multiple modulation times and had the importing program
> calculate the 1st and 2nd elution times instead of providing all the
> elution times. But such a term could be useful to provide some kind of
> description that can account for the observed elution times of the
> spectra.
> 
>  
> 
> How about a parent term like:
> 
> Multidimensional chromatography modulation description
> 
>  
> 
> And starting with child terms:
> 
> Two-dimensional gas chromatography with fixed modulation time
> “Two-dimensional gas chromatography where a single modulation time is
> used throughout the acquisition”
> 
> Two-dimensional gas chromatography with discrete modulation time steps
> “Two-dimensional gas chromatography where the acquisition is divided
> into steps, each with a different modulation time”
> 
> Two-dimensional liquid chromatography with fixed modulation time
> “Two-dimensional liquid chromatography where a single modulation time
> is used throughout the acquisition”
> 
> Two-dimensional liquid chromatography with discrete modulation time
> steps “Two-dimensional liquid chromatography where the acquisition is
> divided into steps, each with a different modulation time”
> 
>  
> 
> I would avoid including formulas because they would take up a lot of
> space, be difficult to read without formatting, and aren’t necessary.
> If we provided the table of modulation times, then the formula could
> be used to validate the data but I can also imagine them being
> misinterpreted.
> 
>  
> 
> These are just some thoughts and suggestions. I’d leave the final
> decision up to you and the rest of the group. I’d be satisfied with
> 1st and 2nd column elution time but a descriptive term seems
> beneficial.
> 
> Best Regards,
> 
>  
> 
> Steven Robles| Software design engineer
> ste...@le...
> 
> Description: LECOLOGO3.png
> Delivering the Right Results | 3000 Lakeview Ave. | St. Joseph | MI
> | 49085
> 
> Visit us online at  www.leco.com|Register to receive e-news & updates
> 
> 
>  
> 
> From: pierre-alain binz [mailto:pie...@is...] 
> Sent: Friday, September 28, 2012 3:15 AM
> To: Mass spectrometry standard development
> Cc: Robles, Steve; mat...@gm...
> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS
> 
> 
>  
> 
> Hi Steven,
> 
> On 27.09.2012 21:58, Robles, Steve wrote:
> 
> 
>         Hi Nils, Pierre-Alain, Matt and all,
>         
>          
>         
>         Thanks for the feedback. It seems like everyone agrees that
>         there should be an elution time for each column.
>         
>          
>         
>         Pierre-Alain’s suggestion for MS:100826 definition change
>         to"The time of elution from all used chromatographic columns
>         (one or more) in the chromatographic separation step, relative
>         to the start of the chromatography." sounds good to me. But
>         I’m not sure what the third global term for the function would
>         be. Are you suggesting a term for the run element that
>         indicates if it GCxGC, LCxLC ? Or something about the
>         modulation period?
>         
>         
> 
> I'm referring to a term describing the function that implements the
> relationship between elution time and modulation time (you have given
> two examples below). This might be useful or not. mzML describes MS
> acquisition parameters, and we could as well describe this as part of
> the run gobal params. If this sounds a useful term, I let you propose
> what is the most appropriate.
> 
> Cheers
> Pierre-Alain
> 
> 
> 
> 
>  
> 
> Thanks again,
> 
>  
> 
> Steven Robles| Software design engineer
> ste...@le...
> 
> Description: LECOLOGO3.png
> Delivering the Right Results | 3000 Lakeview Ave. | St. Joseph | MI
> | 49085
> 
> Visit us online at  www.leco.com|Register to receive e-news & updates
> 
>  
> 
> From: Nils Hoffmann [mailto:nil...@ce...] 
> Sent: Thursday, September 27, 2012 2:32 PM
> To: Robles, Steve
> Cc: psi...@li...
> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS
> 
>  
> 
> Hi Steve, 
> as one of the original requestors of the modulation_time term, I
> totally agree with your option nr. 2 to handle more possible
> use-cases. We simply opted for the simpler option first since we did
> not have reference data available for other modulation regimes. Fyi,
> there was a thread started by Steve Reichenbach recently on 2D LC-MS
> that circled around non-uniform modulation schemes and which might
> also be of interest here.
> 
> Nils Hoffmann
> 
> 
> 
> ------------------------------------------------------------------------------
> Got visibility?
> Most devs has no idea what their production app looks like.
> Find out how fast your code is with AppDynamics Lite.
> http://ad.doubleclick.net/clk;262219671;13503038;y?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409