psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.43.0 of psi-ms.obo

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

Hi everyone, I strongly support Andy's suggestion!

Regards,
Eric


> -----Original Message-----
> From: Jones, Andy [mailto:And...@li...]
> Sent: Tuesday, December 11, 2012 9:10 AM
> To: 'psi...@li...'; 'psidev-pi-
> de...@li...'; 'Mass spectrometry standard development'
> Cc: 'Seymour, Sean L'; 'Gorka Prieto'; 'Terry Farrah'
> Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.43.0 of
> psi-ms.obo
>
> Hi all,
>
> For info, Sean Seymour, Terry Farrah and myself have (on and off) been
> working on the protein inference terminology for some time and we've
> made some proposals to improve terms, which haven't yet made it to
> finalisation. Rather than adding Gorka's terms just yet, I would prefer
> to resurrect our work (say in early January with some conference calls)
> and get agreed a set of consistent terms to be used across all mzid
> files - does this sound okay? Gorka, are you happy to join this effort
> rather than getting these terms in just now?
>
> Best wishes
> Andy
>
> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: 11 December 2012 16:10
> To: psi...@li...; psidev-pi-
> de...@li...; Mass spectrometry standard development
> Subject: [Psidev-ms-vocab] New version 3.43.0 of psi-ms.obo
>
> Dear proteomics community,
>
> the psi-ms.obo file is updated to the new version 3.43.0.
>
> It contains some terms for peptide grouping categories in PAnalyzer,
> requested by Gorka Prieto.
> In addition, following Matt's proposal, the names of terms like
> "Sequest:sort_by_*" are changed to "Sequest:sort by *"
>
>
> Changed CV terms in version 3.43.0 of psi-ms.obo:
> =================================================
> ************ Changed the is_a relationship from
> ************ is_a: MS:1001198 ! protein identification confidence
> metric
> ************ --> is_a: MS:1001101 ! protein group or subset
> relationship [Term]
> id: MS:1001600
> name: protein inference confidence category
> def: "Confidence category of inferred protein (conclusive, non
> conclusive, ambiguous group or indistinguishable)." [PSI:MS]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001101 ! protein group or subset relationship
>
>
> ************ Changed the names for the following terms following Matt's
> proposal from "sort_by_*" to "sort by *"
> [Term]
> id: MS:1001046
> name: Sequest:sort by dCn
> def: "Sort order of Sequest search results by the delta of the
> normalized correlation score." [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001047
> name: Sequest:sort by dM
> def: "Sort order of Sequest search results by the difference between a
> theoretically calculated and the corresponding experimentally measured
> molecular mass M." [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001048
> name: Sequest:sort by Ions
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001049
> name: Sequest:sort by MH+
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001050
> name: Sequest:sort by P
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001052
> name: Sequest:sort by PreviousAminoAcid
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001053
> name: Sequest:sort by Ref
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001059
> name: Sequest:sort by RSp
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001068
> name: Sequest:sort by Sp
> def: "Sort order of Sequest search results by the Sp score." [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001069
> name: Sequest:sort by TIC
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001070
> name: Sequest:sort by Scan
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001071
> name: Sequest:sort by Sequence
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001072
> name: Sequest:sort by Sf
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001086
> name: Sequest:sort by XCorr
> def: "Sort order of Sequest search results by the correlation score."
> [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
> [Term]
> id: MS:1001094
> name: Sequest:sort by z
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001041 ! Sequest:sortCV
>
>
> New CV terms in version 3.43.0 of psi-ms.obo:
> =============================================
> [Term]
> id: MS:1002213
> name: conclusive protein
> def: "A protein identified by at least one unique (distinct, discrete)
> peptide (peptides are considered different only if they can be
> distinguished by evidence in mass spectrum)." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001600 ! protein inference confidence category
>
> [Term]
> id: MS:1002214
> name: indistinguishable protein
> def: "A member of a group of proteins sharing all peptides that are
> exclusive to the group (peptides are considered different only if they
> can be distinguished by evidence in mass spectrum)." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001600 ! protein inference confidence category
>
> [Term]
> id: MS:1002215
> name: non-conclusive protein
> def: "A protein sharing all its matched peptides with either conclusive
> or indistinguishable proteins (peptides are considered different only
> if
> they can be distinguished by evidence in mass spectrum)." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001600 ! protein inference confidence category
>
> [Term]
> id: MS:1002216
> name: ambiguous group member
> def: "A protein sharing at least one peptide not matched to either
> conclusive or indistinguishable proteins (peptides are considered
> different only if they can be distinguished by evidence in mass
> spectrum)." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001600 ! protein inference confidence category
>
> 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
>
>
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Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.43.0 of psi-ms.obo

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

Hi all,

For info, Sean Seymour, Terry Farrah and myself have (on and off) been working on the protein inference terminology for some time and we've made some proposals to improve terms, which haven't yet made it to finalisation. Rather than adding Gorka's terms just yet, I would prefer to resurrect our work (say in early January with some conference calls) and get agreed a set of consistent terms to be used across all mzid files - does this sound okay? Gorka, are you happy to join this effort rather than getting these terms in just now?

Best wishes
Andy 

-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...] 
Sent: 11 December 2012 16:10
To: psi...@li...; psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] New version 3.43.0 of psi-ms.obo

Dear proteomics community,

the psi-ms.obo file is updated to the new version 3.43.0.

It contains some terms for peptide grouping categories in PAnalyzer, requested by Gorka Prieto.
In addition, following Matt's proposal, the names of terms like "Sequest:sort_by_*" are changed to "Sequest:sort by *"


Changed CV terms in version 3.43.0 of psi-ms.obo:
=================================================
************ Changed the is_a relationship from
************ is_a: MS:1001198 ! protein identification confidence metric
************ --> is_a: MS:1001101 ! protein group or subset relationship [Term]
id: MS:1001600
name: protein inference confidence category
def: "Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable)." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship


************ Changed the names for the following terms following Matt's 
proposal from "sort_by_*" to "sort by *"
[Term]
id: MS:1001046
name: Sequest:sort by dCn
def: "Sort order of Sequest search results by the delta of the 
normalized correlation score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001047
name: Sequest:sort by dM
def: "Sort order of Sequest search results by the difference between a 
theoretically calculated and the corresponding experimentally measured 
molecular mass M." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001048
name: Sequest:sort by Ions
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001049
name: Sequest:sort by MH+
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001050
name: Sequest:sort by P
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001052
name: Sequest:sort by PreviousAminoAcid
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001053
name: Sequest:sort by Ref
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001059
name: Sequest:sort by RSp
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001068
name: Sequest:sort by Sp
def: "Sort order of Sequest search results by the Sp score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001069
name: Sequest:sort by TIC
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001070
name: Sequest:sort by Scan
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001071
name: Sequest:sort by Sequence
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001072
name: Sequest:sort by Sf
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001086
name: Sequest:sort by XCorr
def: "Sort order of Sequest search results by the correlation score." 
[PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001094
name: Sequest:sort by z
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV


New CV terms in version 3.43.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002213
name: conclusive protein
def: "A protein identified by at least one unique (distinct, discrete) 
peptide (peptides are considered different only if they can be 
distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002214
name: indistinguishable protein
def: "A member of a group of proteins sharing all peptides that are 
exclusive to the group (peptides are considered different only if they 
can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002215
name: non-conclusive protein
def: "A protein sharing all its matched peptides with either conclusive 
or indistinguishable proteins (peptides are considered different only if 
they can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002216
name: ambiguous group member
def: "A protein sharing at least one peptide not matched to either 
conclusive or indistinguishable proteins (peptides are considered 
different only if they can be distinguished by evidence in mass 
spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

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] Empty mzML files

[John C. <jmc...@gm...>]

This page (http://www.psidev.info/mzml_1_0_0%20) says to send feedback
about mzML here. So I am doing that.

I think it would be beneficial to allow empty indexed mzML files. It
looks like unindexed files can be empty, but this is the problematic
part of the indexed schema:

  <xs:complexType name="IndexListType">
    <xs:sequence>
      <xs:element minOccurs="1" maxOccurs="unbounded" name="index"
type="dx:IndexType">
        <xs:annotation>
          <xs:documentation>Index element containing one or more
offsets for random data access for the entity described in the 'name'
attribute.</xs:documentation>
        </xs:annotation>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="count" type="xs:nonNegativeInteger" use="required">
      <xs:annotation>
        <xs:documentation>Number of indices in this list.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>

The count attribute is nonNegative which means it can be zero (good),
but there is a minOccurs="1" on the index element.

It doesn't really seem like there is a new specification on the
horizon anytime soon, but I thought I would voice my opinion in case
there is a new specification some day.

More info:
http://sourceforge.net/mailarchive/message.php?msg_id=30214022

Thanks for your time,
-John

------------------------------------------------
John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
Bitbucket: https://bitbucket.org/jmchilton
Github: https://github.com/jmchilton
Web: http://jmchilton.net

[Psidev-ms-dev] New version 3.43.0 of psi-ms.obo

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

Dear proteomics community,

the psi-ms.obo file is updated to the new version 3.43.0.

It contains some terms for peptide grouping categories in PAnalyzer, 
requested by Gorka Prieto.
In addition, following Matt's proposal, the names of terms like 
"Sequest:sort_by_*" are changed to "Sequest:sort by *"


Changed CV terms in version 3.43.0 of psi-ms.obo:
=================================================
************ Changed the is_a relationship from
************ is_a: MS:1001198 ! protein identification confidence metric
************ --> is_a: MS:1001101 ! protein group or subset relationship
[Term]
id: MS:1001600
name: protein inference confidence category
def: "Confidence category of inferred protein (conclusive, non 
conclusive, ambiguous group or indistinguishable)." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship


************ Changed the names for the following terms following Matt's 
proposal from "sort_by_*" to "sort by *"
[Term]
id: MS:1001046
name: Sequest:sort by dCn
def: "Sort order of Sequest search results by the delta of the 
normalized correlation score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001047
name: Sequest:sort by dM
def: "Sort order of Sequest search results by the difference between a 
theoretically calculated and the corresponding experimentally measured 
molecular mass M." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001048
name: Sequest:sort by Ions
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001049
name: Sequest:sort by MH+
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001050
name: Sequest:sort by P
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001052
name: Sequest:sort by PreviousAminoAcid
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001053
name: Sequest:sort by Ref
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001059
name: Sequest:sort by RSp
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001068
name: Sequest:sort by Sp
def: "Sort order of Sequest search results by the Sp score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001069
name: Sequest:sort by TIC
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001070
name: Sequest:sort by Scan
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001071
name: Sequest:sort by Sequence
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001072
name: Sequest:sort by Sf
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001086
name: Sequest:sort by XCorr
def: "Sort order of Sequest search results by the correlation score." 
[PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001094
name: Sequest:sort by z
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV


New CV terms in version 3.43.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002213
name: conclusive protein
def: "A protein identified by at least one unique (distinct, discrete) 
peptide (peptides are considered different only if they can be 
distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002214
name: indistinguishable protein
def: "A member of a group of proteins sharing all peptides that are 
exclusive to the group (peptides are considered different only if they 
can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002215
name: non-conclusive protein
def: "A protein sharing all its matched peptides with either conclusive 
or indistinguishable proteins (peptides are considered different only if 
they can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002216
name: ambiguous group member
def: "A protein sharing at least one peptide not matched to either 
conclusive or indistinguishable proteins (peptides are considered 
different only if they can be distinguished by evidence in mass 
spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

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 3.43.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.43.0_rc1 of the psi-ms.obo file.

The terms between the ID's id: MS:1001591 (anchor protein) and id: 
MS:1001600 (protein inference confidence category)
are already under discussion since some time.

I remember we discussed them on our last HUPO spring meeting in San 
Diego and already in a discussion initiated by Terry Farrah
in August 2011 in this mailing list (see attached files).
When I remember it correctly Sean L. Seymour in San Diego announced that 
he wanted to circle around a Word file about this topic
(which until now I never saw / received).

Now Gorka Prieto asked for some terms for peptide grouping categories in 
PAnalyzer, which I included in this release candidate.

In addition, following Matt's proposal, the names of terms like 
"Sequest:sort_by_*" are changed to "Sequest:sort by *"


Changed CV terms in version 3.43.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the is_a relationship from
************ is_a: MS:1001198 ! protein identification confidence metric
************ --> is_a: MS:1001101 ! protein group or subset relationship
[Term]
id: MS:1001600
name: protein inference confidence category
def: "Confidence category of inferred protein (conclusive, non 
conclusive, ambiguous group or indistinguishable)." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship


************ Changed the names for the following terms following Matt's 
proposal from "sort_by_*" to "sort by *"
[Term]
id: MS:1001046
name: Sequest:sort by dCn
def: "Sort order of Sequest search results by the delta of the 
normalized correlation score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001047
name: Sequest:sort by dM
def: "Sort order of Sequest search results by the difference between a 
theoretically calculated and the corresponding experimentally measured 
molecular mass M." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001048
name: Sequest:sort by Ions
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001049
name: Sequest:sort by MH+
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001050
name: Sequest:sort by P
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001052
name: Sequest:sort by PreviousAminoAcid
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001053
name: Sequest:sort by Ref
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001059
name: Sequest:sort by RSp
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001068
name: Sequest:sort by Sp
def: "Sort order of Sequest search results by the Sp score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001069
name: Sequest:sort by TIC
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001070
name: Sequest:sort by Scan
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001071
name: Sequest:sort by Sequence
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001072
name: Sequest:sort by Sf
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001086
name: Sequest:sort by XCorr
def: "Sort order of Sequest search results by the correlation score." 
[PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001094
name: Sequest:sort by z
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV


New CV terms in version 3.43.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002213
name: conclusive protein
def: "A protein identified by at least one unique (distinct, discrete) 
peptide (peptides are considered different only if they can be 
distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002214
name: indistinguishable protein
def: "A member of a group of proteins sharing all peptides that are 
exclusive to the group (peptides are considered different only if they 
can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002215
name: non-conclusive protein
def: "A protein sharing all its matched peptides with either conclusive 
or indistinguishable proteins (peptides are considered different only if 
they can be distinguished by evidence in mass spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category

[Term]
id: MS:1002216
name: ambiguous group member
def: "A protein sharing at least one peptide not matched to either 
conclusive or indistinguishable proteins (peptides are considered 
different only if they can be distinguished by evidence in mass 
spectrum)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category


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 3.42.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.42.0_rc1 of the psi-ms.obo file.

It contains new terms for the TOPP software and added definitions for 
many terms.


Changed CV terms in version 3.42.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the name from 'number of counts' --> 'number of 
detector counts'
[Term]
id: MS:1000131
name: number of detector counts
def: "The number of counted events observed in one or a group of 
elements of a detector." [PSI:MS]
is_a: MS:1000043 ! intensity unit

************ Added the data type
[Term]
id: MS:1001879
name: offset voltage
def: "The potential difference between two adjacent interface voltages 
affecting in-source collision induced dissociation." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt

************ Added the definitions to the following terms
[Term]
id: MS:1001046
name: Sequest:sort_by_dCn
def: "Sort order of Sequest search results by the delta of the 
normalized correlation score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001047
name: Sequest:sort_by_dM
def: "Sort order of Sequest search results by the difference between a 
theoretically calculated and the corresponding experimentally measured 
molecular mass M." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001068
name: Sequest:sort_by_Sp
def: "Sort order of Sequest search results by the Sp score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001086
name: Sequest:sort_by_XCorr
def: "Sort order of Sequest search results by the correlation score." 
[PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001108
name: param: a ion
def: "Parameter information, type of product: a ion with charge on the 
N-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001118
name: param: b ion
def: "Parameter information, type of product: b ion with charge on the 
N-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001119
name: param: c ion
def: "Parameter information, type of product: c ion with charge on the 
N-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001143
name: search engine specific score for peptides
def: "Search engine specific peptide scores." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001146
name: param: a ion-NH3
def: "Parameter information, type of product: a ion with lost ammonium." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001149
name: param: b ion-NH3
def: "Parameter information, type of product: b ion with lost ammonium." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001151
name: param: y ion-NH3
def: "Parameter information, type of product: y ion with lost ammonium." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001201
name: DB MW filter maximum
def: "Maximum value of molecular weight filter." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
relationship: has_units UO:0000221 ! dalton
relationship: has_units UO:0000222 ! kilodalton

[Term]
id: MS:1001202
name: DB MW filter minimum
def: "Minimum value of molecular weight filter." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
relationship: has_units UO:0000221 ! dalton
relationship: has_units UO:0000222 ! kilodalton

[Term]
id: MS:1001203
name: DB PI filter maximum
def: "Maximum value of isoelectric point filter." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters

[Term]
id: MS:1001204
name: DB PI filter minimum
def: "Minimum value of isoelectric point filter." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters

[Term]
id: MS:1001245
name: PerSeptive PKS file
def: "PerSeptive peak list file format." 
[http://www.matrixscience.com/help/data_file_help.html#PKS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001246
name: Sciex API III file
def: "PE Sciex peak list file format." 
[http://www.matrixscience.com/help/data_file_help.html#API]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001249
name: search input details
def: "Details describing the search input." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1001251
name: Trypsin
def: "Enzyme trypsin." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P)

[Term]
id: MS:1001252
name: DB source EBI
def: "Database source EBI." [PSI:PI]
is_a: MS:1001012 ! database source

[Term]
id: MS:1001253
name: DB source NCBI
def: "Database source NCBI." [PSI:PI]
is_a: MS:1001012 ! database source

[Term]
id: MS:1001254
name: DB source UniProt
def: "Database source UniProt." [PSI:PI]
is_a: MS:1001012 ! database source

[Term]
id: MS:1001257
name: param: v ion
def: "Parameter information, type of product: side chain loss v ion." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001258
name: param: d ion
def: "Parameter information, type of product: side chain loss d ion." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001259
name: param: immonium ion
def: "Parameter information, type of product: immonium ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001260
name: param: w ion
def: "Parameter information, type of product: side chain loss w ion. 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001261
name: param: x ion
def: "Parameter information, type of product: x ion with charge on the 
C-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001262
name: param: y ion
def: "Parameter information, type of product: y ion with charge on the 
C-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001263
name: param: z ion
def: "Parameter information, type of product: z ion with charge on the 
C-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001304
name: Asp-N
def: "Endoproteinase Asp-N." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001273 ! (?=[BD])

[Term]
id: MS:1001305
name: Asp-N_ambic
def: "Enzyme Asp-N, Ammonium Bicarbonate (AmBic)." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001274 ! (?=[DE])

[Term]
id: MS:1001306
name: Chymotrypsin
def: "Enzyme chymotrypsin." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P)

[Term]
id: MS:1001308
name: Formic_acid
def: "Formic acid." [PubChem_Compound:284]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001334 ! ((?<=D))|((?=D))

[Term]
id: MS:1001309
name: Lys-C
def: "Endoproteinase Lys-C." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001335 ! (?<=K)(?!P)

[Term]
id: MS:1001365
name: frag: internal yb ion
def: "Fragmentation information, type of product: internal yb ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001366
name: frag: internal ya ion
def: "Fragmentation information, type of product: internal ya ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001367
name: frag: z+1 ion
def: "Fragmentation information, type of product: z+1 ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001368
name: frag: z+2 ion
def: "Fragmentation information, type of product: z+2 ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001373
name: Sequest:TIC
def: "Sequest total ion current." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001406
name: param: internal yb ion
def: "Parameter information, type of product: internal yb ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001407
name: param: internal ya ion
def: "Parameter information, type of product: internal ya ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001408
name: param: z+1 ion
def: "Parameter information, type of product: z+1 ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001409
name: param: z+2 ion
def: "Parameter information, type of product: z+2 ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001463
name: Phenyx XML format
def: "Phenyx open XML file format." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001464
name: DTASelect file
def: "DTASelect file." [PMID:12643522, 
http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001466
name: MS2 file
def: "MS2 file for MS/MS spectral data." [PMID:15317041, 
DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html]
is_a: MS:1001040 ! intermediate analysis format



New CV terms in version 3.42.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002154
name: DTAExtractor
def: "Extracts spectra of an MS run file to several files in DTA 
format." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002155
name: IDMerger
def: "Merges several protein/peptide identification files into one 
file." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002156
name: IDFileConverter
def: "Converts identification engine file formats." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002157
name: SpectraMerger
def: "Merges spectra from an LC/MS map, either by precursor or by RT 
blocks." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002158
name: MzTabExporter
def: "Exports various XML formats to an mzTab file." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002159
name: MassTraceExtractor
def: "Annotates mass traces in centroided LC/MS maps." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002160
name: PrecursorMassCorrector
def: "Correct the precursor entries of tandem MS scans." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002161
name: HighResPrecursorMassCorrector
def: "Performs precursor mz correction on centroided high resolution 
data." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002162
name: AdditiveSeries
def: "Computes an additive series to quantify a peptide in a set of 
samples." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002163
name: Decharger
def: "Decharges and merges different feature charge variants of the same 
chemical entity." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002164
name: EICExtractor
def: "Quantifies signals at given positions in (raw or picked) LC/MS 
maps." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002165
name: TOPP feature finder
def: "Feature finder component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002166
name: FeatureFinderCentroided
def: "Detects two-dimensional features in centroided LC-MS data." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002167
name: FeatureFinderRaw
def: "Detects two-dimensional features in uncentroided LC-MS data." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002168
name: FeatureFinderIsotopeWavelet
def: "Detects two-dimensional features in uncentroided LC-MS data with a 
wavelet algorithm." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002169
name: FeatureFinderMetabo
def: "Detects two-dimensional features in centroided LC-MS data of 
metabolites." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002170
name: FeatureFinderMRM
def: "Quantifies features LC-MS/MS MRM data." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002171
name: ProteinQuantifier
def: "Computes protein abundances from annotated feature/consensus 
maps." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002172
name: ConsensusMapNormalizer
def: "Normalizes maps of one consensus XML file (after linking)." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002173
name: MapRTTransformer
def: "Applies retention time transformations to maps." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002174
name: TOPP feature linker
def: "Feature linker component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002175
name: FeatureLinkerLabeled
def: "Groups corresponding isotope-labeled features in a feature map." 
[PSI:PI]
is_a: MS:1002174 ! TOPP feature linker

[Term]
id: MS:1002176
name: FeatureLinkerUnlabeled
def: "Groups corresponding features from multiple maps." [PSI:PI]
is_a: MS:1002174 ! TOPP feature linker

[Term]
id: MS:1002177
name: FeatureLinkerUnlabeledQT
def: "Groups corresponding features from multiple maps using a quality 
threshold clustering approach." [PSI:PI]
is_a: MS:1002174 ! TOPP feature linker

[Term]
id: MS:1002178
name: CompNovo
def: "Performs a peptide/protein identification with the CompNovo 
engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002179
name: CompNovoCID
def: "Performs a peptide/protein identification with the CompNovo engine 
in collission-induced dissociation (CID) mode." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002180
name: TOPP software adaptor
def: "Software adaptor to an external program in the TOPP software." 
[PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002181
name: InspectAdapter
def: "Identifies MS/MS spectra using the external program Inspect." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002182
name: MascotAdapter
def: "Identifies MS/MS spectra using the external program Mascot." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002183
name: MascotAdapterOnline
def: "Identifies MS/MS spectra using the online version of the external 
program Mascot." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002184
name: OMSSAAdapter
def: "Identifies MS/MS spectra using the external program OMSSA." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002185
name: PepNovoAdapter
def: "Identifies MS/MS spectra using the external program PepNovo." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002186
name: XTandemAdapter
def: "Identifies MS/MS spectra using the external program XTandem." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002187
name: SpecLibSearcher
def: "Identifies peptide MS/MS spectra by spectral matching with a 
searchable spectral library." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002188
name: ConsensusID
def: "Computes a consensus identification from peptide identifications 
of several identification engines." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002189
name: IDConflictResolver
def: "Resolves ambiguous annotations of features with peptide 
identifications." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002190
name: IDFilter
def: "Filters results from protein or peptide identification engines 
based on different criteria." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002191
name: IDMapper
def: "Assigns protein/peptide identifications to feature or consensus 
features." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002192
name: IDPosteriorErrorProbability
def: "Estimates posterior error probabilities using a mixture model." 
[PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002193
name: IDRTCalibration
def: "Calibrate Retention times of peptide hits to standards." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002194
name: PeptideIndexer
def: "Refreshes the protein references for all peptide hits." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002195
name: PrecursorIonSelector
def: "A tool for precursor ion selection based on identification 
results." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002196
name: MRMMapper
def: "MRMMapper maps measured chromatograms (mzML) and the transitions 
used (TraML)." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002197
name: TOPP OpenSwath component
def: "OpenSwath component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002198
name: OpenSwathAnalyzer
def: "Picks peaks and finds features in an SRM experiment." [PSI:PI]
is_a: MS:1002197 ! TOPP OpenSwath component

[Term]
id: MS:1002199
name: OpenSwathChromatogramExtractor
def: "Extract chromatograms (XIC) from a MS2 map file." [PSI:PI]
is_a: MS:1002197 ! TOPP OpenSwath component

[Term]
id: MS:1002200
name: OpenSwathDecoyGenerator
def: "Generates decoys according to different models for a specific 
TraML." [PSI:PI]
is_a: MS:1002197 ! TOPP OpenSwath component

[Term]
id: MS:1002201
name: OpenSwathFeatureXMLToTSV
def: "Converts a featureXML to a mProphet tsv (tab separated values)." 
[PSI:PI]
is_a: MS:1002197 !TOPP OpenSwath component

[Term]
id: MS:1002202
name: OpenSwathRTNormalizer
def: "Generates a transformation file for retention time space into 
normalized space." [PSI:PI]
is_a: MS:1002197 ! TOPP OpenSwath component

[Term]
id: MS:1002203
name: TOPP-ProteinInference
def: "Infer proteins from a list of (high-confidence) peptides." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002204
name: TOPP-FalseDiscoveryRate
def: "Estimates the false discovery rate on peptide and protein level 
using decoy searches." [PSI:PI]
is_a: MS:1000752 ! TOPP software


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] Needed additions to the PSI-MS CV

[Magnus A. <mag...@bi...>]

Dear PSI-MS developers.

I have just gone through the PSI-MS and PRIDE CVs with focus on the 
proteomics quantification method IPTL (IsobariQ peptide termini 
labeling) and its software IsobariQ described in these publications:


Isobaric peptide termini labeling for MS/MS-based quantitative proteomics.
Koehler CJ, Strozynski M, Kozielski F, Treumann A, Thiede B.
J Proteome Res. 2009 Sep;8(9):4333-41.
---
IsobariQ: software for isobaric quantitative proteomics using IPTL, 
iTRAQ, and TMT.
Arntzen MØ, Koehler CJ, Barsnes H, Berven FS, Treumann A, Thiede B.
J Proteome Res. 2011 Feb 4;10(2):913-20. Epub 2010 Nov 29.
---
Isobaric peptide termini labeling utilizing site-specific N-terminal 
succinylation.
Koehler CJ, Arntzen MØ, Strozynski M, Treumann A, Thiede B.
Anal Chem. 2011 Jun 15;83(12):4775-81. Epub 2011 May 16.
---
Quantitative proteome analysis using isobaric peptide termini labeling 
(IPTL).
Arntzen MO, Koehler CJ, Treumann A, Thiede B.
Methods Mol Biol. 2011;753:65-76.
---
Comparison of data analysis parameters and MS/MS fragmentation 
techniques for quantitative proteome analysis using isobaric peptide 
termini labeling (IPTL).
Koehler CJ, Arntzen MØ, Treumann A, Thiede B.
Anal Bioanal Chem. 2012 Sep;404(4):1103-14. doi: 
10.1007/s00216-012-5949-z. Epub 2012 Mar 31.
---
A rapid approach for isobaric peptide termini labeling.
Koehler CJ, Arntzen MO, Treumann A, Thiede B.
Methods Mol Biol. 2012;893:129-41.


As IPTL and IsobariQ are currently having a growing number of users it 
would be nice to implement CVs describing specific features of this 
methodology.
I have now made a list of CV-terms needed and would be glad to help 
implement and describe these terms in the CV.

Do you know where could I submit my additions (both PSI-MS and PRIDE 
CVs) and what information is needed per term in order to implement this?


Kind regards,

Magnus Ø. Arntzen
Cell Death Proteomics Group
The biotechnology centre of Oslo/University of Oslo
Norway

Re: [Psidev-ms-dev] FW: Re: LSID

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

On Fri, 2012-11-23 at 13:52 +0000, Jones, Andy wrote:
...
> From: Chris Taylor <chr...@gm...>
...
> On 21/11/2012 16:57, Robles, Steve wrote:
> > I need to create LSIDs for the id attribute of the mzML element. Most 
> > examples that I have seen use urn:lsid:psidev.info:mzML. with 
> > something like a file name appended (i.e.
> > id="urn:lsid:psidev.info:mzML.instanceDocuments.tiny1" ).
That LSID is slightly off.
You can check your LSID via 
http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester/?q=urn%3Alsid%3Apsidev.info%3AmzML%3AinstanceDocuments.tiny1&submit=Go

> > I was wondering if our software could also use 
> > urn:lsid:psidev.info:mzML in the ID or if we need to register someplace or use something else?
According to the above LSID checker psidev.info 
is not a registered authority. I whacked your LSID even more,
and then you get:

http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester/?q=urn%3Alsid%3Aubio.org%3AmzML%3AinstanceDocuments.tiny1&submit=Go

In short, you can use whatever as <authority>, 
unless you need that LSID to actually *work* in a LSID sense
as seen here: http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester/?q=urn:lsid:ipni.org:names:20012728-1:1.1

Note: I never used LSID, and the above is mostly guesswork.

Yours,
Steffen

-- 
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

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.41.0 of psi-ms-obo

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

Hi Gerhard, many thanks for your continued work on this. If I recall
correctly, "number of counts" is a *unit* term. The unit ontology doesn't
contain such a unit, so we added this to our ontology to serve as a unit.
It should be analogous to 'number of electrons' in a detector, but for a
case where we don't know that the unit is electrons, but just "counts".
Maybe we should change it to "number of detector counts". This is
primarily used to specify the units of intensities of spectra. I think to
be semantically correct, this term should not have any child terms except
for ones directly related to this concept.

Regards,
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Wednesday, November 28, 2012 4:09 AM
To: psi...@li...;
psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-vocab] New version 3.41.0 of psi-ms-obo

Dear proteomics community,

attached there's the new version 3.41.0 of the psi-ms.obo file.

To the CV terms used in <AnalysisSummary> of mzQuantML, the datatype
xsd\:boolean was added.

In addition it contains some new terms (identification file format
attribute, numerator data type attribute and denominator data type
attribute) for mzQuantML validation and the replacement of some 'TOPP
software'-related terms by newer terms.

Some Remarks:
=============
1) The term MS:1000131 (number of counts) is a parent term only
    Therefore it has no data type.
2) The term MS:1001842 (peptide PSM count) now has an integer data type
3) The new term MS:1002153 (protein level PSM counts) can now
    be used to specify the number of counts on the protein level


Changed CV terms in version 3.41.0 of psi-ms.obo:
=================================================
************ Added a xsd\:double data type to all 'quantification
datatype' (MS:1001805) childs,
************ except for spectral count values, which now have a
xsd\:integer data type


************ Changed the name from 'protein group/subset relationship'
--> 'protein group or subset relationship'
[Term]
id: MS:1001101
name: protein group or subset relationship
def: "Protein group or subset relationships." [PSI:PI]
is_a: MS:1001085 ! protein result details

************ Added a xsd\:boolean data type to the following terms [Term]
id: MS:1002001
name: MS1 label-based raw feature quantitation
def: "MS1 label-based raw feature quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002002
name: MS1 label-based peptide level quantitation
def: "MS1 label-based peptide level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002003
name: MS1 label-based protein level quantitation
def: "MS1 label-based protein level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002004
name: MS1 label-based proteingroup level quantitation
def: "MS1 label-based proteingroup level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002019
name: label-free raw feature quantitation
def: "Label-free raw feature quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002020
name: label-free peptide level quantitation
def: "Label-free peptide level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002021
name: label-free protein level quantitation
def: "Label-free protein level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002022
name: label-free proteingroup level quantitation
def: "Label-free proteingroup level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002024
name: MS2 tag-based feature level quantitation
def: "MS2 tag-based feature level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002025
name: MS2 tag-based peptide level quantitation
def: "MS2 tag-based peptide level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002026
name: MS2 tag-based protein level quantitation
def: "MS2 tag-based protein level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002027
name: MS2 tag-based proteingroup level quantitation
def: "MS2 tag-based proteingroup level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis

************ Added an integer data type to the next term [Term]
id: MS:1001842
name: peptide PSM count
def: "The number of MS/MS spectra identified for this peptide in spectral
counting." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

************ Renamed from 'method file attribute' --> 'method file format
attribute'
[Term]
id: MS:1002128
name: method file format attribute
def: "Attribute describing a method file format." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

************ Changed the definition for the next term [Term]
id: MS:1002129
name: ITRAQAnalyzer
def: "Software for iTRAQ workflow. Extracts and normalizes iTRAQ
information from an MS experiment."
[http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release
/html/TOPP__ITRAQAnalyzer.html]
is_a: MS:1001139 ! quantitation software name
is_a: MS:1000752 ! TOPP software


************ The following four terms for the TOPP software are made
obsolete, because the were replaced by new terms:
[Term]
id: MS:1000760
name: MapAligner
def: "OBSOLETE Corrects retention time distortions between maps." [PSI:MS]
comment: This term was made obsolete, because it is replaced by the
terms under the 'TOPP map aligner' (MS:1002147) branch.
is_a: MS:1000752 ! TOPP software
is_obsolete: true

[Term]
id: MS:1000762
name: NoiseFilter
def: "OBSOLETE Removes noise from profile spectra by using different
smoothing techniques." [PSI:MS]
comment: This term was made obsolete, because it is replaced by the
terms under the 'TOPP noise filter' (MS:1002131) branch.
is_a: MS:1000752 ! TOPP software
is_obsolete: true

[Term]
id: MS:1000763
name: PeakPicker
def: "OBSOLETE Finds mass spectrometric peaks in profile mass spectra."
[PSI:MS]
comment: This term was made obsolete, because it is replaced by the
terms under the 'TOPP peak picker' (MS:1002134) branch.
is_a: MS:1000752 ! TOPP software
is_obsolete: true

[Term]
id: MS:1000765
name: SpectraFilter
def: "OBSOLETE Applies a filter to peak spectra." [PSI:MS]
comment: This term was made obsolete, because it is replaced by the
terms under the 'TOPP spectra filter' (MS:1002137) branch.
is_a: MS:1000752 ! TOPP software
is_obsolete: true


New CV terms in version 3.41.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002130
name: identification file format attribute
def: "Attribute describing an identification file format." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002131
name: TOPP noise filter
def: "Noise filter component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002132
name: NoiseFilterGaussian
def: "Removes noise from profile spectra by using gaussian filter
smoothing techniques." [PSI:PI]
is_a: MS:1002131 ! TOPP noise filter

[Term]
id: MS:1002133
name: NoiseFilterSGolay
def: "Removes noise from profile spectra by using golay filter smoothing
techniques." [PSI:PI]
is_a: MS:1002131 ! TOPP noise filter

[Term]
id: MS:1002134
name: TOPP peak picker
def: "Peak picker component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002135
name: PeakPickerHiRes
def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:PI]
is_a: MS:1002134 ! TOPP peak picker

[Term]
id: MS:1002136
name: PeakPickerWavelet
def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:PI]
is_a: MS:1002134 ! TOPP peak picker

[Term]
id: MS:1002137
name: TOPP spectra filter
def: "Spectra filter component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002138
name: SpectraFilterBernNorm
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002139
name: SpectraFilterMarkerMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002140
name: SpectraFilterNLargest
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002141
name: SpectraFilterNormalizer
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002142
name: SpectraFilterParentPeakMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002143
name: SpectraFilterScaler
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002144
name: SpectraFilterSqrtMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002145
name: SpectraFilterThresholdMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002146
name: SpectraFilterWindowMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002147
name: TOPP map aligner
def: "Map aligner component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002148
name: MapAlignerIdentification
def: "Corrects retention time distortions between maps based on common
peptide identifications." [PSI:PI]
is_a: MS:1002147 ! TOPP map aligner

[Term]
id: MS:1002149
name: MapAlignerPoseClustering
def: "Corrects retention time distortions between maps using a pose
clustering approach." [PSI:PI]
is_a: MS:1002147 ! TOPP map aligner

[Term]
id: MS:1002150
name: MapAlignerSpectrum
def: "Corrects retention time distortions between maps by spectrum
alignment." [PSI:PI]
is_a: MS:1002147 ! TOPP map aligner

[Term]
id: MS:1002151
name: numerator data type attribute
def: "Attribute describing the data type of the numerator of a ratio."
[PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002152
name: denominator data type attribute
def: "Attribute describing the data type of the denominator of a ratio."
[PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002153
name: protein level PSM counts
def: "The number of spectra identified for this protein in spectral
counting." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

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 3.41.0 of psi-ms-obo

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

Dear proteomics community,

attached there's the new version 3.41.0 of the psi-ms.obo file.

To the CV terms used in <AnalysisSummary> of mzQuantML, the datatype 
xsd\:boolean was added.

In addition it contains some new terms (identification file format 
attribute, numerator data type attribute and
denominator data type attribute) for mzQuantML validation
and the replacement of some 'TOPP software'-related terms by newer terms.

Some Remarks:
=============
1) The term MS:1000131 (number of counts) is a parent term only
    Therefore it has no data type.
2) The term MS:1001842 (peptide PSM count) now has an integer data type
3) The new term MS:1002153 (protein level PSM counts) can now
    be used to specify the number of counts on the protein level


Changed CV terms in version 3.41.0 of psi-ms.obo:
=================================================
************ Added a xsd\:double data type to all 'quantification 
datatype' (MS:1001805) childs,
************ except for spectral count values, which now have a 
xsd\:integer data type


************ Changed the name from 'protein group/subset relationship' 
--> 'protein group or subset relationship'
[Term]
id: MS:1001101
name: protein group or subset relationship
def: "Protein group or subset relationships." [PSI:PI]
is_a: MS:1001085 ! protein result details

************ Added a xsd\:boolean data type to the following terms
[Term]
id: MS:1002001
name: MS1 label-based raw feature quantitation
def: "MS1 label-based raw feature quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002002
name: MS1 label-based peptide level quantitation
def: "MS1 label-based peptide level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002003
name: MS1 label-based protein level quantitation
def: "MS1 label-based protein level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002004
name: MS1 label-based proteingroup level quantitation
def: "MS1 label-based proteingroup level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002019
name: label-free raw feature quantitation
def: "Label-free raw feature quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002020
name: label-free peptide level quantitation
def: "Label-free peptide level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002021
name: label-free protein level quantitation
def: "Label-free protein level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002022
name: label-free proteingroup level quantitation
def: "Label-free proteingroup level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002024
name: MS2 tag-based feature level quantitation
def: "MS2 tag-based feature level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002025
name: MS2 tag-based peptide level quantitation
def: "MS2 tag-based peptide level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002026
name: MS2 tag-based protein level quantitation
def: "MS2 tag-based protein level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002027
name: MS2 tag-based proteingroup level quantitation
def: "MS2 tag-based proteingroup level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis

************ Added an integer data type to the next term
[Term]
id: MS:1001842
name: peptide PSM count
def: "The number of MS/MS spectra identified for this peptide in 
spectral counting." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

************ Renamed from 'method file attribute' --> 'method file 
format attribute'
[Term]
id: MS:1002128
name: method file format attribute
def: "Attribute describing a method file format." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

************ Changed the definition for the next term
[Term]
id: MS:1002129
name: ITRAQAnalyzer
def: "Software for iTRAQ workflow. Extracts and normalizes iTRAQ 
information from an MS experiment." 
[http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP__ITRAQAnalyzer.html]
is_a: MS:1001139 ! quantitation software name
is_a: MS:1000752 ! TOPP software


************ The following four terms for the TOPP software are made 
obsolete, because the were replaced by new terms:
[Term]
id: MS:1000760
name: MapAligner
def: "OBSOLETE Corrects retention time distortions between maps." [PSI:MS]
comment: This term was made obsolete, because it is replaced by the 
terms under the 'TOPP map aligner' (MS:1002147) branch.
is_a: MS:1000752 ! TOPP software
is_obsolete: true

[Term]
id: MS:1000762
name: NoiseFilter
def: "OBSOLETE Removes noise from profile spectra by using different 
smoothing techniques." [PSI:MS]
comment: This term was made obsolete, because it is replaced by the 
terms under the 'TOPP noise filter' (MS:1002131) branch.
is_a: MS:1000752 ! TOPP software
is_obsolete: true

[Term]
id: MS:1000763
name: PeakPicker
def: "OBSOLETE Finds mass spectrometric peaks in profile mass spectra." 
[PSI:MS]
comment: This term was made obsolete, because it is replaced by the 
terms under the 'TOPP peak picker' (MS:1002134) branch.
is_a: MS:1000752 ! TOPP software
is_obsolete: true

[Term]
id: MS:1000765
name: SpectraFilter
def: "OBSOLETE Applies a filter to peak spectra." [PSI:MS]
comment: This term was made obsolete, because it is replaced by the 
terms under the 'TOPP spectra filter' (MS:1002137) branch.
is_a: MS:1000752 ! TOPP software
is_obsolete: true


New CV terms in version 3.41.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002130
name: identification file format attribute
def: "Attribute describing an identification file format." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002131
name: TOPP noise filter
def: "Noise filter component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002132
name: NoiseFilterGaussian
def: "Removes noise from profile spectra by using gaussian filter 
smoothing techniques." [PSI:PI]
is_a: MS:1002131 ! TOPP noise filter

[Term]
id: MS:1002133
name: NoiseFilterSGolay
def: "Removes noise from profile spectra by using golay filter smoothing 
techniques." [PSI:PI]
is_a: MS:1002131 ! TOPP noise filter

[Term]
id: MS:1002134
name: TOPP peak picker
def: "Peak picker component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002135
name: PeakPickerHiRes
def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:PI]
is_a: MS:1002134 ! TOPP peak picker

[Term]
id: MS:1002136
name: PeakPickerWavelet
def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:PI]
is_a: MS:1002134 ! TOPP peak picker

[Term]
id: MS:1002137
name: TOPP spectra filter
def: "Spectra filter component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002138
name: SpectraFilterBernNorm
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002139
name: SpectraFilterMarkerMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002140
name: SpectraFilterNLargest
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002141
name: SpectraFilterNormalizer
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002142
name: SpectraFilterParentPeakMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002143
name: SpectraFilterScaler
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002144
name: SpectraFilterSqrtMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002145
name: SpectraFilterThresholdMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002146
name: SpectraFilterWindowMower
def: "Applies a filter to peak spectra." [PSI:PI]
is_a: MS:1002137 ! TOPP spectra filter

[Term]
id: MS:1002147
name: TOPP map aligner
def: "Map aligner component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002148
name: MapAlignerIdentification
def: "Corrects retention time distortions between maps based on common 
peptide identifications." [PSI:PI]
is_a: MS:1002147 ! TOPP map aligner

[Term]
id: MS:1002149
name: MapAlignerPoseClustering
def: "Corrects retention time distortions between maps using a pose 
clustering approach." [PSI:PI]
is_a: MS:1002147 ! TOPP map aligner

[Term]
id: MS:1002150
name: MapAlignerSpectrum
def: "Corrects retention time distortions between maps by spectrum 
alignment." [PSI:PI]
is_a: MS:1002147 ! TOPP map aligner

[Term]
id: MS:1002151
name: numerator data type attribute
def: "Attribute describing the data type of the numerator of a ratio." 
[PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002152
name: denominator data type attribute
def: "Attribute describing the data type of the denominator of a ratio." 
[PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002153
name: protein level PSM counts
def: "The number of spectra identified for this protein in spectral 
counting." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

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] CV validator

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

Thanks – I’ve updated the mzq mapping file with the correct location and reported the broken links to the webmaster,
Cheers
Andy

From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: 26 November 2012 10:10
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] CV validator

Hi Andy,

there is a version under http://www.psidev.info/sites/default/files/CvMapping.xsd

Cheers,
Gerhard


Am 26.11.2012 10:57, schrieb Jones, Andy:
Hi all,
Anyone know where this file can be located: http://www.psidev.info/files/validator/CvMapping.xsd, the link is broken and so I guess we may not have been validating the structure of the recent mapping files developed?
Cheers
Andy




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--

---

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...<mailto:Ger...@ru...>

Web:    http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] CV validator

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

Hi Andy,

there is a version under 
http://www.psidev.info/sites/default/files/CvMapping.xsd

Cheers,
Gerhard


Am 26.11.2012 10:57, schrieb Jones, Andy:
>
> Hi all,
>
> Anyone know where this file can be located: 
> http://www.psidev.info/files/validator/CvMapping.xsd 
> <http://www.psidev.info/files/validator/CvMapping.xsd>, the link is 
> broken and so I guess we may not have been validating the structure of 
> the recent mapping files developed?
>
> Cheers
>
> Andy
>
>
>
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

-- 
---
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] CV validator

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

Hi all,
Anyone know where this file can be located: http://www.psidev.info/files/validator/CvMapping.xsd, the link is broken and so I guess we may not have been validating the structure of the recent mapping files developed?
Cheers
Andy

[Psidev-ms-dev] FW: Re: LSID

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

Hi all,

Anyone able to help with this mzML / LSID related query?
Best wishes
Andy

-----Original Message-----
From: Chris Taylor [mailto:chr...@gm...] 
Sent: 22 November 2012 13:20
To: Jones, Andy
Subject: Fwd: Re: LSID

Hiya,

Thought I'd pass this one your way -- the thread is hopefully self-explanatory. Hope you're well and all that.

Cheers, Chris.


-------- Original Message --------
Subject: Re: LSID
Date: Thu, 22 Nov 2012 13:17:30 +0000
From: Chris Taylor <chr...@gm...>
To: Robles, Steve <Ste...@le...>
CC: chr...@eb... <chr...@eb...>

Hi Steve,

I'm not directly involved with PSI any more, but I'll pass the question along to someone I know -- you should hear shortly, but failing that you could also try the discussion list here (last section): http://is.gd/6nTyLm

Best wishes, Chris.


On 21/11/2012 16:57, Robles, Steve wrote:
> Hi Chris,
>
> I’m not sure if you are the correct person to be contacting but maybe 
> you can redirect me to them.
>
> I need to create LSIDs for the id attribute of the mzML element. Most 
> examples that I have seen use urn:lsid:psidev.info:mzML. with 
> something like a file name appended (i.e.
> id="urn:lsid:psidev.info:mzML.instanceDocuments.tiny1" ).
>
> I was wondering if our software could also use 
> urn:lsid:psidev.info:mzML in the ID or if we need to register someplace or use something else?
> There is a lot of information on LSID but it not all clear.
>
> Thank you,
>
> *Steven Robles *| Software design engineer ste...@le...
>
> LECOLOGO3.png*
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Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.40.0_rc1 of psi-ms.obo

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

Thanks Gerhard
Pierre-Alain

On 21.11.2012 16:37, Gerhard Mayer wrote:
> Dear proteomics community,
>
> attached there's the release candidate 3.40.0_rc1 of the psi-ms.obo file.
>
> It contains the new term 'database UniProtKB' as parent of the two 
> terms 'database UniProtKB/Swiss-Prot' and 'database UniProtKB/TrEMBL'.
> as well as added definitions for all Phenyx - related terms (Thanks 
> Pierre-Alain for providing them).
>
> Furthermore definitions to the ProteinExtractor-related terms are now 
> available.
>
>
> Changed CV terms in version 3.40.0_rc1 of psi-ms.obo:
> =====================================================
> ************ Added the definitions to the following terms
> [Term]
> id: MS:1001207
> name: Mascot
> def: "The name of the Mascot search engine." [PSI:PI]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1001208
> name: Sequest
> def: "The name of the Sequest search engine." [PSI:PI]
> is_a: MS:1001456 ! analysis software
>
> ************ Changed the is_a relationship of the following two terms 
> into is_a: MS:1002126 ! database UniProtKB
> [Term]
> id: MS:1001104
> name: database UniProtKB/Swiss-Prot
> def: "The name of the UniProtKB/Swiss-Prot knowledgebase." [PSI:PI]
> is_a: MS:1002126 ! database UniProtKB
>
> [Term]
> id: MS:1002060
> name: database UniProtKB/TrEMBL
> def: "The name of the UniProtKB/TrEMBL database." [PSI:PI]
> is_a: MS:1002126 ! database UniProtKB
>
> ************ Added the definitions to the following Phenyx-related terms
> [Term]
> id: MS:1001209
> name: Phenyx
> def: "The name of the Phenyx search engine." [PSI:PI]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1001375
> name: Phenyx:Instrument Type
> def: "The instrument type parameter value in Phenyx." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001376
> name: Phenyx:Scoring Model
> def: "The selected scoring model in Phenyx." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001377
> name: Phenyx:Default Parent Charge
> def: "The default parent charge value in Phenyx." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001378
> name: Phenyx:Trust Parent Charge
> def: "The parameter in Phenyx that specifies if the experimental 
> charge state is to be considered as correct." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001379
> name: Phenyx:Turbo
> def: "The turbo mode parameter in Phenyx." [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001380
> name: Phenyx:Turbo:ErrorTol
> def: "The maximal allowed fragment m/z error filter considered in the 
> turbo mode of Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001381
> name: Phenyx:Turbo:Coverage
> def: "The minimal peptide sequence coverage value, expressed in 
> percent, considered in the turbo mode of Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001382
> name: Phenyx:Turbo:Series
> def: "The list of ion series considered in the turbo mode of Phenyx." 
> [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001383
> name: Phenyx:MinPepLength
> def: "The minimal number of residues for a peptide to be considered 
> for a valid identification in Phenyx." [PSI:PI]
> xref: value-type:xsd\:positiveInteger "The allowed value-type for this 
> CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001384
> name: Phenyx:MinPepzscore
> def: "The minimal peptide z-score for a peptide to be considered for a 
> valid identification in Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001385
> name: Phenyx:MaxPepPvalue
> def: "The maximal peptide p-value for a peptide to be considered for a 
> valid identification in Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001386
> name: Phenyx:AC Score
> def: "The minimal protein score required for a protein database entry 
> to be displayed in the list of identified proteins in Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001387
> name: Phenyx:Conflict Resolution
> def: "The parameter in Phenyx that specifies if the conflict 
> resolution algorithm is to be used." [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
> is_a: MS:1002097 ! Phenyx input parameter
>
> [Term]
> id: MS:1001388
> name: Phenyx:AC
> def: "The primary sequence database identifier of a protein in 
> Phenyx." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001116 ! single protein result details
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1001389
> name: Phenyx:ID
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> def: "A secondary sequence database identifier of a protein in 
> Phenyx." [PSI:PI]
> is_a: MS:1001116 ! single protein result details
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1001390
> name: Phenyx:Score
> def: "The protein score of a protein match in Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001116 ! single protein result details
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1001393
> name: Phenyx:Auto
> def: "The value of the automatic peptide acceptance filter in Phenyx. 
> " [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1001394
> name: Phenyx:User
> def: "The value of the user-defined peptide acceptance filter in 
> Phenyx." [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1001395
> name: Phenyx:Pepzscore
> def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1001396
> name: Phenyx:PepPvalue
> def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
> is_a: MS:1001870 ! p-value for peptides
>
> [Term]
> id: MS:1001397
> name: Phenyx:NumberOfMC
> def: "The number of missed cleavages of a peptide sequence in Phenyx." 
> [PSI:PI]
> xref: value-type:xsd\:positiveInteger "The allowed value-type for this 
> CV term."
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> [Term]
> id: MS:1001398
> name: Phenyx:Modif
> def: "The expression of the nature and position(s) of modified 
> residue(s) on a matched peptide sequence in Phenyx." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001153 ! search engine specific score
>
> ************ Added the definitions to the following 
> ProteinExtractor-related terms
> [Term]
> id: MS:1001431
> name: ProteinExtractor:MascotPeptideScoreThreshold
> def: "Only peptides with scores higher than that threshold are taken 
> into account in Mascot scoring for calculation of the ProteinExtractor 
> metascore." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001432
> name: ProteinExtractor:MascotUniqueScore
> def: "In the final result each protein must have at least one peptide 
> above this Mascot score threshold in ProteinExtractor metascore 
> calculation." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001434
> name: ProteinExtractor:MascotWeighting
> def: "Influence of Mascot search engine in the process of merging the 
> search engine specific protein lists into the global protein list of 
> ProteinExtractor." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001436
> name: ProteinExtractor:SequestPeptideScoreThreshold
> def: "Only peptides with scores higher than that threshold are taken 
> into account in Sequest scoring for calculation of the 
> ProteinExtractor metascore." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001437
> name: ProteinExtractor:SequestUniqueScore
> def: "In the final result each protein must have at least one peptide 
> above this Sequest score threshold in ProteinExtractor metascore 
> calculation." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001438
> name: ProteinExtractor:SequestWeighting
> def: "Influence of Sequest search engine in the process of merging the 
> search engine specific protein lists into the global protein list of 
> ProteinExtractor." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001440
> name: ProteinExtractor:ProteinSolverPeptideScoreThreshold
> def: "Only peptides with scores higher than that threshold are taken 
> into account in ProteinSolver scoring for calculation of the 
> ProteinExtractor metascore." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001441
> name: ProteinExtractor:ProteinSolverUniqueScore
> def: "In the final result each protein must have at least one peptide 
> above this ProteinSolver score threshold in ProteinExtractor metascore 
> calculation." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001442
> name: ProteinExtractor:ProteinSolverWeighting
> def: "Influence of ProteinSolver search engine in the process of 
> merging the search engine specific protein lists into the global 
> protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001444
> name: ProteinExtractor:PhenyxPeptideScoreThreshold
> def: "Only peptides with scores higher than that threshold are taken 
> into account in Phenyx scoring for calculation of the ProteinExtractor 
> metascore." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001445
> name: ProteinExtractor:PhenyxUniqueScore
> def: "In the final result each protein must have at least one peptide 
> above this Phenyx score threshold in ProteinExtractor metascore 
> calculation." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> [Term]
> id: MS:1001446
> name: ProteinExtractor:PhenyxWeighting
> def: "Influence of Phenyx search engine in the process of merging the 
> search engine specific protein lists into the global protein list of 
> ProteinExtractor." [DOI:10.4172/jpb.1000056]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002098 ! ProteinExtractor input parameter
>
> ************ The names of the following terms were changed to begin 
> with lower case letters
> ************ to be consistent with the 'Guidelines for the development 
> of Controlled Vocabularies'
> [Term]
> id: MS:1001807
> name: study variable attribute
> def: "Attribute describing a study variable." [PSI:MS]
> is_a: MS:1001806 ! quantification object attribute
>
> [Term]
> id: MS:1001817
> name: raw file attribute
> def: "Attribute describing a raw file." [PSI:MS]
> is_a: MS:1001806 ! quantification object attribute
>
> [Term]
> id: MS:1001823
> name: raw files group attribute
> def: "Attribute describing, how raw files build a raw file group." 
> [PSI:MS]
> is_a: MS:1001806 ! quantification object attribute
>
> [Term]
> id: MS:1001825
> name: feature list attribute
> def: "Attribute describing a feature list." [PSI:MS]
> is_a: MS:1001806 ! quantification object attribute
>
> ************ Changed is_a: MS:1002006 ! MRM transition type --> is_a: 
> MS:1002006 ! SRM transition type
> [Term]
> id: MS:1002008
> name: decoy SRM transition
> def: "A transition not expected to be present in the sample and used 
> to calculate statistical confidence of target transition detections in 
> some workflows." [PSI:MS]
> synonym: "decoy MRM transition" EXACT []
> is_a: MS:1002006 ! SRM transition type
>
>
>
> New CV terms in version 3.40.0_rc1 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002126
> name: database UniProtKB
> def: "The name of the UniProtKB knowledgebase." [PSI:PI]
> is_a: MS:1001013 ! database name
>
>
> Best Regards,
> Gerhard
>
>
>
> ------------------------------------------------------------------------------
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[Psidev-ms-dev] Release candidate 3.40.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.40.0_rc1 of the psi-ms.obo file.

It contains the new term 'database UniProtKB' as parent of the two terms 
'database UniProtKB/Swiss-Prot' and 'database UniProtKB/TrEMBL'.
as well as added definitions for all Phenyx - related terms (Thanks 
Pierre-Alain for providing them).

Furthermore definitions to the ProteinExtractor-related terms are now 
available.


Changed CV terms in version 3.40.0_rc1 of psi-ms.obo:
=====================================================
************ Added the definitions to the following terms
[Term]
id: MS:1001207
name: Mascot
def: "The name of the Mascot search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001208
name: Sequest
def: "The name of the Sequest search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

************ Changed the is_a relationship of the following two terms 
into is_a: MS:1002126 ! database UniProtKB
[Term]
id: MS:1001104
name: database UniProtKB/Swiss-Prot
def: "The name of the UniProtKB/Swiss-Prot knowledgebase." [PSI:PI]
is_a: MS:1002126 ! database UniProtKB

[Term]
id: MS:1002060
name: database UniProtKB/TrEMBL
def: "The name of the UniProtKB/TrEMBL database." [PSI:PI]
is_a: MS:1002126 ! database UniProtKB

************ Added the definitions to the following Phenyx-related terms
[Term]
id: MS:1001209
name: Phenyx
def: "The name of the Phenyx search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001375
name: Phenyx:Instrument Type
def: "The instrument type parameter value in Phenyx." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001376
name: Phenyx:Scoring Model
def: "The selected scoring model in Phenyx." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001377
name: Phenyx:Default Parent Charge
def: "The default parent charge value in Phenyx." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001378
name: Phenyx:Trust Parent Charge
def: "The parameter in Phenyx that specifies if the experimental charge 
state is to be considered as correct." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001379
name: Phenyx:Turbo
def: "The turbo mode parameter in Phenyx." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001380
name: Phenyx:Turbo:ErrorTol
def: "The maximal allowed fragment m/z error filter considered in the 
turbo mode of Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001381
name: Phenyx:Turbo:Coverage
def: "The minimal peptide sequence coverage value, expressed in percent, 
considered in the turbo mode of Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001382
name: Phenyx:Turbo:Series
def: "The list of ion series considered in the turbo mode of Phenyx." 
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001383
name: Phenyx:MinPepLength
def: "The minimal number of residues for a peptide to be considered for 
a valid identification in Phenyx." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this 
CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001384
name: Phenyx:MinPepzscore
def: "The minimal peptide z-score for a peptide to be considered for a 
valid identification in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001385
name: Phenyx:MaxPepPvalue
def: "The maximal peptide p-value for a peptide to be considered for a 
valid identification in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001386
name: Phenyx:AC Score
def: "The minimal protein score required for a protein database entry to 
be displayed in the list of identified proteins in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001387
name: Phenyx:Conflict Resolution
def: "The parameter in Phenyx that specifies if the conflict resolution 
algorithm is to be used." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001388
name: Phenyx:AC
def: "The primary sequence database identifier of a protein in Phenyx." 
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001389
name: Phenyx:ID
xref: value-type:xsd\:string "The allowed value-type for this CV term."
def: "A secondary sequence database identifier of a protein in Phenyx." 
[PSI:PI]
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001390
name: Phenyx:Score
def: "The protein score of a protein match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001393
name: Phenyx:Auto
def: "The value of the automatic peptide acceptance filter in Phenyx. " 
[PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001394
name: Phenyx:User
def: "The value of the user-defined peptide acceptance filter in 
Phenyx." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001395
name: Phenyx:Pepzscore
def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001396
name: Phenyx:PepPvalue
def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001870 ! p-value for peptides

[Term]
id: MS:1001397
name: Phenyx:NumberOfMC
def: "The number of missed cleavages of a peptide sequence in Phenyx." 
[PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this 
CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001398
name: Phenyx:Modif
def: "The expression of the nature and position(s) of modified 
residue(s) on a matched peptide sequence in Phenyx." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

************ Added the definitions to the following 
ProteinExtractor-related terms
[Term]
id: MS:1001431
name: ProteinExtractor:MascotPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken 
into account in Mascot scoring for calculation of the ProteinExtractor 
metascore." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001432
name: ProteinExtractor:MascotUniqueScore
def: "In the final result each protein must have at least one peptide 
above this Mascot score threshold in ProteinExtractor metascore 
calculation." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001434
name: ProteinExtractor:MascotWeighting
def: "Influence of Mascot search engine in the process of merging the 
search engine specific protein lists into the global protein list of 
ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001436
name: ProteinExtractor:SequestPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken 
into account in Sequest scoring for calculation of the ProteinExtractor 
metascore." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001437
name: ProteinExtractor:SequestUniqueScore
def: "In the final result each protein must have at least one peptide 
above this Sequest score threshold in ProteinExtractor metascore 
calculation." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001438
name: ProteinExtractor:SequestWeighting
def: "Influence of Sequest search engine in the process of merging the 
search engine specific protein lists into the global protein list of 
ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001440
name: ProteinExtractor:ProteinSolverPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken 
into account in ProteinSolver scoring for calculation of the 
ProteinExtractor metascore." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001441
name: ProteinExtractor:ProteinSolverUniqueScore
def: "In the final result each protein must have at least one peptide 
above this ProteinSolver score threshold in ProteinExtractor metascore 
calculation." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001442
name: ProteinExtractor:ProteinSolverWeighting
def: "Influence of ProteinSolver search engine in the process of merging 
the search engine specific protein lists into the global protein list of 
ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001444
name: ProteinExtractor:PhenyxPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken 
into account in Phenyx scoring for calculation of the ProteinExtractor 
metascore." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001445
name: ProteinExtractor:PhenyxUniqueScore
def: "In the final result each protein must have at least one peptide 
above this Phenyx score threshold in ProteinExtractor metascore 
calculation." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001446
name: ProteinExtractor:PhenyxWeighting
def: "Influence of Phenyx search engine in the process of merging the 
search engine specific protein lists into the global protein list of 
ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

************ The names of the following terms were changed to begin with 
lower case letters
************ to be consistent with the 'Guidelines for the development 
of Controlled Vocabularies'
[Term]
id: MS:1001807
name: study variable attribute
def: "Attribute describing a study variable." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1001817
name: raw file attribute
def: "Attribute describing a raw file." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1001823
name: raw files group attribute
def: "Attribute describing, how raw files build a raw file group." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1001825
name: feature list attribute
def: "Attribute describing a feature list." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

************ Changed is_a: MS:1002006 ! MRM transition type --> is_a: 
MS:1002006 ! SRM transition type
[Term]
id: MS:1002008
name: decoy SRM transition
def: "A transition not expected to be present in the sample and used to 
calculate statistical confidence of target transition detections in some 
workflows." [PSI:MS]
synonym: "decoy MRM transition" EXACT []
is_a: MS:1002006 ! SRM transition type



New CV terms in version 3.40.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002126
name: database UniProtKB
def: "The name of the UniProtKB knowledgebase." [PSI:PI]
is_a: MS:1001013 ! database name


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 3.39.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.39.0 of the psi-ms.obo file.
It contains only one new term (combined FDRScore).

I decided not to forward round the whole list for discussion,
since it seems to be very clear and specialised and Andy asked me
the favour to add it on short notice.


Changed CV terms in version 3.39.0 of psi-ms.obo:
=================================================
No changed CV terms


New CV terms in version 3.39.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002125
name: combined FDRScore
def: "Quality measurement score." [PMID:19253293]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details


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 3.38.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.38.0 of the psi-ms.obo file.

It contains changed terms for Mascot parameters (added the missing 
definitions).
Also the definitions to database and role terms are newly added.

In addition it contains two terms proposed by Julian to specify if 
higher or lower scores are better,
which are now part_of MS:1001153 ! search engine specific score

Furthermore some new terms for mzQuantML validation and terms for the 
sofware packages XTracker and ProteoSuite are added.

The term 'tab delimited text file' is now a child of 'intermediate 
analysis format' as discussed in the last mzQuantML telco.
The 'decoy DB derived from' tree was made obsolete.

I added also the updated list of terms with lacking definitions.
Your contributions for them, are as always welcome.


Changed CV terms in version 3.38.0 of psi-ms.obo:
=================================================
************ Changes name from Feature attribute --> feature attribute 
(changed to lower case)
[Term]
id: MS:1001828
name: feature attribute
def: "Attribute describing a Feature." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

************ Added definitions to the mascot terms MS:1001316 until 
MS:1001325
************ Thanks Ville, for providing them
[Term]
id: MS:1001316
name: Mascot:SigThreshold
def: "Significance threshold below which the p-value of a peptide match 
must lie to be considered statistically significant (default 0.05)." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001317
name: Mascot:MaxProteinHits
def: "The number of protein hits to display in the report. If 'Auto', 
all protein hits that have a protein score exceeding the average peptide 
identity threshold are reported. Otherwise an integer at least 1." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001318
name: Mascot:ProteinScoringMethod
def: "Mascot protein scoring method; either 'Standard' or 'MudPIT'." 
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001319
name: Mascot:MinMSMSThreshold
def: "Mascot peptide match ion score threshold. If between 0 and 1, then 
peptide matches whose expect value exceeds the thresholds are 
suppressed; if at least 1, then peptide matches whose ion score is below 
the threshold are suppressed." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001320
name: Mascot:ShowHomologousProteinsWithSamePeptides
def: "If true, show (sequence or spectrum) same-set proteins. Otherwise 
they are suppressed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001321
name: Mascot:ShowHomologousProteinsWithSubsetOfPeptides
def: "If true, show (sequence or spectrum) sub-set and subsumable 
proteins. Otherwise they are suppressed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001322
name: Mascot:RequireBoldRed
def: "Only used in Peptide Summary and Select Summary reports. If true, 
a peptide match must be 'bold red' to be included in the report; bold 
red means the peptide is a top ranking match in a query and appears for 
the first time (in linear order) in the list of protein hits." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001323
name: Mascot:UseUnigeneClustering
def: "If true, then the search results are against a nucleic acid 
database and Unigene clustering is enabled. Otherwise UniGene clustering 
is not in use." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001324
name: Mascot:IncludeErrorTolerantMatches
def: "If true, then the search results are error tolerant and peptide 
matches from the second pass are included in search results. Otherwise 
no error tolerant peptide matches are included." 
[http://www.matrixscience.com/help/error_tolerant_help.html]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001325
name: Mascot:ShowDecoyMatches
def: "If true, then the search results are against an automatically 
generated decoy database and the reported peptide matches and protein 
hits come from the decoy database. Otherwise peptide matches and protein 
hits come from the original database." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

************ added the is_a relation in order to allow the use for 
mzQuantML validation
[Term]
id: MS:1000884
name: protein attribute
def: "An nonphysical attribute describing a specific protein." [PSI:MS]
relationship: part_of MS:1000882 ! protein
is_a: MS:1001806 ! quantification object attribute

************ Added definition to the following database terms
[Term]
id: MS:1001084
name: database nr
def: "Non-redundant GenBank sequence database." [PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001104
name: database UniProtKB/Swiss-Prot
def: "Swiss-Prot protein sequence database." [PSI:PI]
is_a: MS:1001013 ! UniProtKB/database name

[Term]
id: MS:1001142
name: database IPI_human
def: "International Protein Index database for Homo sapiens sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001178
name: database EST
def: "Expressed sequence tag nucleotide sequence database." [PSI:PI]
is_a: MS:1001079 ! database type nucleotide

[Term]
id: MS:1001285
name: database IPI_mouse
def: "International Protein Index database for Mus musculus sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001286
name: database IPI_rat
def: "International Protein Index database for Rattus norvegicus 
sequences." [PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001287
name: database IPI_zebrafish
def: "International Protein Index database for Danio rerio sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001288
name: database IPI_chicken
def: "International Protein Index database for Gallus gallus sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001289
name: database IPI_cow
def: "International Protein Index database for Bos taurus sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001290
name: database IPI_arabidopsis
def: "International Protein Index database for Arabidopsis thaliana 
sequences." [PSI:PI]
is_a: MS:1001013 ! database name

************ obsoleted the 'decoy DB derived from' tree
[Term]
id: MS:1001284
name: decoy DB derived from
def: "OBSOLETE The name of the database, the search database was derived 
from." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001450 ! decoy DB details
is_obsolete: true

[Term]
id: MS:1001291
name: decoy DB from nr
def: "OBSOLETE Decoy database from a non-redundant GenBank sequence 
database." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001292
name: decoy DB from IPI_rat
def: "OBSOLETE Decoy database from a International Protein Index 
database for Rattus norvegicus." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001293
name: decoy DB from IPI_mouse
def: "OBSOLETE Decoy database from a International Protein Index 
database for Mus musculus." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001294
name: decoy DB from IPI_arabidopsis
def: "OBSOLETE Decoy database from a International Protein Index 
database for Arabidopsis thaliana." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001295
name: decoy DB from EST
def: "OBSOLETE Decoy database from an expressed sequence tag nucleotide 
sequence database." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001296
name: decoy DB from IPI_zebrafish
def: "OBSOLETE Decoy database from a International Protein Index 
database for Danio rerio." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001297
name: decoy DB from UniProtKB/Swiss-Prot
def: "OBSOLETE Decoy database from a Swiss-Prot protein sequence 
database." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001298
name: decoy DB from IPI_chicken
def: "OBSOLETE Decoy database from a International Protein Index 
database for Gallus gallus." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001299
name: decoy DB from IPI_cow
def: "OBSOLETE Decoy database from a International Protein Index 
database for Bos taurus." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001300
name: decoy DB from IPI_human
def: "OBSOLETE Decoy database from a International Protein Index 
database for Homo sapiens." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1002060
name: database UniProtKB/TrEMBL
def: "TrEMBL protein sequence database." [PSI:PI]
is_a: MS:1001013 ! UniProtKB/database name

[Term]
id: MS:1002061
name: decoy DB from UniProtKB/TrEMBL
def: "OBSOLETE Decoy database from a TrEMBL protein sequence database." 
[PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

************ Added a boolean value type for the three following terms
[Term]
id: MS:1002015
name: spectral count peptide level quantitation
def: "Spectral count peptide level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002016
name: spectral count protein level quantitation
def: "Spectral count protein level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002017
name: spectral count proteingroup level quantitation
def: "Spectral count proteingroup level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis

************ Added definitions to the following five terms
[Term]
id: MS:1001267
name: software vendor
def: "Software vendor role." [PSI:PI]
is_a: MS:1001266 ! role type

[Term]
id: MS:1001268
name: programmer
def: "Programmer role." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001269
name: instrument vendor
def: "Instrument vendor role." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001270
name: lab personnel
def: "Lab personnel role." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001271
name: researcher
def: "Researcher role." [PSI:PI]
is_a: MS:1001266 ! role type

************ Changed the name from 'quantitation software comment / 
customizations' to 'quantitation software comment or customizations'
[Term]
id: MS:1001832
name: quantitation software comment or customizations
def: "Quantitation software comment or any customizations to the default 
setup of the software." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information

************ 'tab delimited text file' is now a child of 'intermediate 
analysis format'
[Term]
id: MS:1000914
name: tab delimited text file
def: "A file that has two or more columns of tabular data where each 
column is separated by a TAB character." [PSI:MS]
is_a: MS:1001459 ! file format
is_a: MS:1001040 ! intermediate analysis format

************ Added the definitions to the following 4 terms
[Term]
id: MS:1001430
name: ProteinExtractor:UseMascot
def: "Flag indicating to include Mascot scoring for calculation of the 
ProteinExtractor metascore." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001435
name: ProteinExtractor:UseSequest
def: "Flag indicating to include Sequest scoring for calculation of the 
ProteinExtractor metascore." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001439
name: ProteinExtractor:UseProteinSolver
def: "Flag indicating to include ProteinSolver scoring for calculation 
of the ProteinExtractor metascore." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001443
name: ProteinExtractor:UsePhenyx
def: "Flag indicating to include Phenyx scoring for calculation of the 
ProteinExtractor metascore." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter


New Typedef in version 3.38.0 of psi-ms.obo:
============================================
[Typedef]
id: has_order
name: has_order

New CV terms in version 3.38.0 of psi-ms.obo:
=============================================
************ The next two terms were proposed by Julian to indicate if a 
higher or lower score is better.
************ TODO: We should later add a
************ has_order: MS:1002108 ! higher score better
************ or
************ has_order: MS:1002109 ! lower score better
************ to all peptide resp. protein scores.
************ e.g.
************
************ [Term]
************ id: MS:1001155
************ name: Sequest:xcorr
************ def: "The SEQUEST result 'XCorr'." [PSI:PI]
************ xref: value-type:xsd\:double "The allowed value-type for 
this CV term."
************ is_a: MS:1001143 ! search engine specific score for peptides
************ is_a: MS:1001153 ! search engine specific score
************ has_order: MS:1002108 ! higher score better

[Term]
id: MS:1002108
name: higher score better
def: "Indicates that a higher score is better." [PSI:PI]
relationship: part_of MS:1001153 ! search engine specific score

[Term]
id: MS:1002109
name: lower score better
def: "Indicates that a lower score is better." [PSI:PI]
relationship: part_of MS:1001153 ! search engine specific score


************ The following terms are intended for mzQuantML validation 
and mzQuantML MIAPE conformance checking
************ TODO: Add child terms for them later.
[Term]
id: MS:1002110
name: assay attribute
def: "Attribute describing an assay." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002111
name: assay label attribute
def: "Attribute describing an assay label." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002112
name: protein group list attribute
def: "Attribute describing a protein group list." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002113
name: protein group attribute
def: "Attribute describing a protein group." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002114
name: protein list attribute
def: "Attribute describing a protein list." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002115
name: peptide consensus list attribute
def: "Attribute describing a peptide consensus list." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002116
name: peptide consensus attribute
def: "Attribute describing a peptide consensus." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002117
name: small molecule list attribute
def: "Attribute describing a small mollecule list." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002118
name: small molecule attribute
def: "Attribute describing a small molecule." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002119
name: small molecule modification attribute
def: "Attribute describing a small molecule modification." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002120
name: experiment name
def: "The name for identifying an experiment." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002121
name: spectral count feature
def: "Dummy decribing a spectral count feature." [PSI:PI]
is_a: MS:1001828 ! feature attribute

[Term]
id: MS:1002122
name: counts reporting
def: "FeatureList of spectral counts." [PSI:PI]
is_a: MS:1001825 ! FeatureList attribute

[Term]
id: MS:1002123
name: x-Tracker
def: "x-Tracker generic tool for quantitative proteomics." 
[http://www.x-tracker.info/]
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002124
name: ProteoSuite
def: "ProteoSuite software for the analysis of quantitative proteomics 
data." [DOI:10.1089/omi.2012.0022, PMID:22804616, 
http://www.proteosuite.org/]
is_a: MS:1001139 ! quantitation software name

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] Better coverage for metabolomics and GC/MS in particular

[Oliver K. <oli...@un...>]

Steffen,

that's excellent news.

On 16.11.2012, at 12:41, Steffen Neumann <sne...@ip...> wrote:
> Really, what I'd like to have in the end is that 
> Metabolomics GC/MS data is archived as mzML, 
> rather than netCDF today. People start to use
> GC/[EI|APCI]-QTOF-MS or other interesting technologies,
> and I'd love to have mzML being a possible unified format.
I would certainly second that and we would be happy to support 
you there. As discussed at various occasions, we would also be 
happy to asssist when it comes to making mzQuantML and mzTab 
(even more) suitable formats for reporting quantitative 
metabolomics data.

Cheers,
 Oliver

Re: [Psidev-ms-dev] Better coverage for metabolomics and GC/MS in particular

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

Hi Nils and others, 

there are three aspects that immediately come to mind, 
and I am keeping a sourceforge tracker[1] for COSMOS 
(which I started only today, so very little content yet).

1) Add missing CV terms, which we already started 
   about a year ago with IIRC stuff like 
   MS:1002040 / inlet temperature. Also, we'd need to 
   complete the coverage of instruments in the CV.

   Most of these will be fairly trivial.

2) Add the GCxGC (and also cover LCxLC) we discussed a few weeks ago
   to the examples and the specification document, so that not only 
   maltcms can deal with it ;-)

3a) Improve support for software converters to mzML 
    for GC instruments, and document that. I heard 
    that LECO has mzML export somehow, but I haven't seen it 
    anywhere yet. Some companies (Waters GCT Premier, 
    Bruker APCI micrOTOF) can use the "normal" proteowizard converters.

    Again, that should be documented somewhere. 
    Maybe complete "Current and future support for mzML:"
    on http://www.psidev.info/mzml ?

3b) Improve support for software readers/data processing.
    So maltcms we can tick off already, xcms is fine as well,
    mzmine2 should be able to process the data. 
    I'd like to pursuade projects like pyMS [2] to 
    adopt stuff like pymzML [3] and so on. 

Really, what I'd like to have in the end is that 
Metabolomics GC/MS data is archived as mzML, 
rather than netCDF today. People start to use
GC/[EI|APCI]-QTOF-MS or other interesting technologies,
and I'd love to have mzML being a possible unified format.

Yours,
Steffen

[1] https://sourceforge.net/p/cosmos-fp7/tickets/    
[2] https://code.google.com/p/pyms/ 
[3] https://github.com/pymzml/pymzML

On Fri, 2012-11-16 at 12:16 +0100, Nils Hoffmann wrote:
> Sorry for the previous post in german, I was too fast in replying and
> hit 'the other' address :-).
> I would like to also congratulate Steffen on this project and I am looking
> forward to seeing his recommendations.
> 
> Nils
> 
> Am 16.11.2012 11:39, schrieb Nils Hoffmann:
> > Hi Steffen,
> > herzlichen Glückwunsch, das klingt nach sehr viel Arbeit im Vorfeld.
> > Welchen Aspekt von GC-MS Daten willst Du denn in mzML besser abdecken?
> >
> >
> > Gruß,
> > Nils
> > Am 16.11.2012 07:57, schrieb Steffen Neumann:
> >> Good morning,
> >>
> >> you may have seen my name on this list before,
> >> but recently we at the IPB received a new hat:
> >> namely the "COSMOS WP2 Standards Development" - hat,
> >> see also http://www.cosmos-fp7.eu/wp2
> >>
> >> One of the aims is to improve the handling of GC/MS data
> >> in mzML, so expect to see a few requests to add new instruments 
> >> and GC-specific terms to the psi-ms.obo
> >>
> >> We'll also later try to contribute to other PSI standards,
> >> to enable their adoption in the metabolomics community,
> >> stay tuned.
> >>
> >> I am looking forward to work with the PSI,
> >> and get metabolomics where proteomics already is
> >> in many aspects.
> >>
> >> Yours,
> >> Steffen
> >>
> >
> 
> 

-- 
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

Re: [Psidev-ms-dev] Better coverage for metabolomics and GC/MS in particular

[Nils H. <nil...@ce...>]

Sorry for the previous post in german, I was too fast in replying and
hit 'the other' address :-).
I would like to also congratulate Steffen on this project and I am looking
forward to seeing his recommendations.

Nils

Am 16.11.2012 11:39, schrieb Nils Hoffmann:
> Hi Steffen,
> herzlichen Glückwunsch, das klingt nach sehr viel Arbeit im Vorfeld.
> Welchen Aspekt von GC-MS Daten willst Du denn in mzML besser abdecken?
>
>
> Gruß,
> Nils
> Am 16.11.2012 07:57, schrieb Steffen Neumann:
>> Good morning,
>>
>> you may have seen my name on this list before,
>> but recently we at the IPB received a new hat:
>> namely the "COSMOS WP2 Standards Development" - hat,
>> see also http://www.cosmos-fp7.eu/wp2
>>
>> One of the aims is to improve the handling of GC/MS data
>> in mzML, so expect to see a few requests to add new instruments 
>> and GC-specific terms to the psi-ms.obo
>>
>> We'll also later try to contribute to other PSI standards,
>> to enable their adoption in the metabolomics community,
>> stay tuned.
>>
>> I am looking forward to work with the PSI,
>> and get metabolomics where proteomics already is
>> in many aspects.
>>
>> Yours,
>> Steffen
>>
>


-- 
Nils Hoffmann                                   phone:    +49-521-106-4342
Bielefeld University                            room:             U10-144
Faculty of Technology, Genome Informatics
P.O. Box 10 01 31
33501 Bielefeld, Germany
http://www.cebitec.uni-bielefeld.de/~hoffmann

Re: [Psidev-ms-dev] Better coverage for metabolomics and GC/MS in particular

[Nils H. <nil...@ce...>]

Hi Steffen,
herzlichen Glückwunsch, das klingt nach sehr viel Arbeit im Vorfeld.
Welchen Aspekt von GC-MS Daten willst Du denn in mzML besser abdecken?


Gruß,
Nils
Am 16.11.2012 07:57, schrieb Steffen Neumann:
> Good morning,
>
> you may have seen my name on this list before,
> but recently we at the IPB received a new hat:
> namely the "COSMOS WP2 Standards Development" - hat,
> see also http://www.cosmos-fp7.eu/wp2
>
> One of the aims is to improve the handling of GC/MS data
> in mzML, so expect to see a few requests to add new instruments 
> and GC-specific terms to the psi-ms.obo
>
> We'll also later try to contribute to other PSI standards,
> to enable their adoption in the metabolomics community,
> stay tuned.
>
> I am looking forward to work with the PSI,
> and get metabolomics where proteomics already is
> in many aspects.
>
> Yours,
> Steffen
>


-- 
Nils Hoffmann                                   phone:    +49-521-106-4342
Bielefeld University                            room:             U10-144
Faculty of Technology, Genome Informatics
P.O. Box 10 01 31
33501 Bielefeld, Germany
http://www.cebitec.uni-bielefeld.de/~hoffmann

Re: [Psidev-ms-dev] Better coverage for metabolomics and GC/MS in particular

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

Hi Steffen, this is fabulous news! We look forward to your continued
participation and collaboration with the PSI.

Best regards,
Eric



> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Thursday, November 15, 2012 10:57 PM
> To: psi...@li...
> Cc: psidev-ms-vocab
> Subject: [Psidev-ms-dev] Better coverage for metabolomics and GC/MS in
> particular
>
> Good morning,
>
> you may have seen my name on this list before,
> but recently we at the IPB received a new hat:
> namely the "COSMOS WP2 Standards Development" - hat,
> see also http://www.cosmos-fp7.eu/wp2
>
> One of the aims is to improve the handling of GC/MS data
> in mzML, so expect to see a few requests to add new instruments
> and GC-specific terms to the psi-ms.obo
>
> We'll also later try to contribute to other PSI standards,
> to enable their adoption in the metabolomics community,
> stay tuned.
>
> I am looking forward to work with the PSI,
> and get metabolomics where proteomics already is
> in many aspects.
>
> Yours,
> Steffen
>
> --
> 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
>
>
>
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[Psidev-ms-dev] Better coverage for metabolomics and GC/MS in particular

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

Good morning,

you may have seen my name on this list before,
but recently we at the IPB received a new hat:
namely the "COSMOS WP2 Standards Development" - hat,
see also http://www.cosmos-fp7.eu/wp2

One of the aims is to improve the handling of GC/MS data
in mzML, so expect to see a few requests to add new instruments 
and GC-specific terms to the psi-ms.obo

We'll also later try to contribute to other PSI standards,
to enable their adoption in the metabolomics community,
stay tuned.

I am looking forward to work with the PSI,
and get metabolomics where proteomics already is
in many aspects.

Yours,
Steffen

-- 
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

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

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

Hi Salva,

On 11 Nov 2012, at 15:38, Salvador Martínez de Bartolomé wrote:

> 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?

We will not 'substitute' but keep both formats as submission formats. The idea is to have mzIdentML 1.1 files supported at (around) March next year.


> Until when are you going to accept PRIDE XML files?

PRIDE XML will be supported for quite some years still. 

Cheers,

Juanan



> 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
>> 
>> 
>> 
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