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

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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
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