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

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

Hi Gerhard, Felipe, thanks for this proposal, I have a few suggested
amendments, below in red (and *** in case color doesn't come through):



-----Original Message-----
From: mayerg97 via Psidev-ms-vocab <psi...@li...>

Dear proteomics/metabolomics community,



following are the new/changed terms for the release candidate 4.1.25_rc1 of
the psi-ms.obo file.





New CV terms in version 4.1.25_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1003011

name: pFind

def: "Sequence-tag-based search engine pFind." [PMID:30295672]

is_a: MS:1001456 ! analysis software



[Term]

id: MS:1003012

name: KSDP score

def: "Kernel mass spectral dot product scoring function." [PMID:15044235]

is_a: MS:1001143 ! PSM-level search engine specific statistic

relationship: has_order MS:1002108 ! higher score better



[Term]

id: MS:1003013

name: i3tms

def: "i3-tms search engine and data-analysis software." [PSI:PI]

is_a: MS:1001456 ! analysis software



[Term]

id: MS:1003014

name: MSFragger

def: "A database search-based peptide identification tool." [PMID:28394336]

is_a: MS:1002286 ! Trans-Proteomic Pipeline software



[Term]

id: MS:1003015

name: razor peptide

def: "A peptide which is shared between protein groups and assigned to

the protein group with the largest number of identified peptides." [PSI:PI]

is_a: MS:1000860 ! peptide



*** Begin

The following term should not be added as is. PTMProphet doesn’t have a
“PTM Score”.

x [Term]

x id: MS:1003016

x name: PTMProphet:PTM Score

x def: "The PTM score from PTMProphet software." [PSI:MS]

x xref: value-type:xsd\:string "The allowed value-type for this CV term."

X is_a: MS:1001968 ! PTM localization PSM-level statistic

X relationship: has_regexp MS:1002505 ! regular expression for modification
localization scoring

*** PTM Prophet has quite a substantial number of metrics.

At the PSM level, we have:

normalized information content

number of localized modifications

At the site level, we have:

               modification localization probability

               O-score

M-score

So I think we may actually want 5 terms, not a single term (and not called
PTM Score).

@Felipe, are you eager to write terms, or were you just thinking that we
will need something eventually?

The paper is currently under revision. I suggest we exclude 3016 from this
RC, and circle back in a few weeks to provide a more complete set of terms
and definitions. Does that sound okay?

*** End





[Term]

id: MS:1003017

name: ProteinProphet:peptide weight

def: "Peptide weight used for FDR filtering." [PSI:PI]

***def: "Fraction of peptide evidence attributable to a protein or a set of
indistinguishable proteins." [PSI:PI]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1002490 ! peptide-level scoring

is_a: MS:1001153 ! search engine specific score

relationship: has_order MS:1002108 ! higher score better

relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

*** NOTE: Although some may use this for filtering, any score could
potentially be used for filtering, and I suggest that a potential use
should not be part of the definition, or else 100 other terms would also be
characterized as “for FDR filtering” (but I discourage that)



[Term]

id: MS:1003018

name: ProteinProphet:peptide group weight

def: "Peptide group weight used for FDR filtering." [PSI:PI]

***def: "Fraction of peptide evidence attributable to a group of proteins."
[PSI:PI]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1002490 ! peptide-level scoring

is_a: MS:1001153 ! search engine specific score

relationship: has_order MS:1002108 ! higher score better

relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive





Changed CV terms in version 4.1.25_rc1 of psi-ms.obo:

=====================================================

************ added synonym 'InterProphet'

[Term]

id: MS:1002288

name: iProphet

def: "A program in the TPP that calculates distinct peptide

probabilities based on several lines of corroborating evidence including

search results from multiple search engines via the pepXML format."

[PMID:21876204]

synonym: "InterProphet" EXACT []

is_a: MS:1002286 ! Trans-Proteomic Pipeline software



Best Regards,

Gerhard



-- 



----------------------------------------------------------------------



Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER



Scientific assistant



Medizinisches Proteom-Center



DEPARTMENT Medical Bioinformatics



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Fon +49 (0)234 32-29272 | Fax +49 (0)234 32-14554



E-mail ger...@ru...



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