[Psidev-pi-dev] New version 4.1.25 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are the new/changed terms for the version 4.1.25 of the
psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


@Felipe: I left out PTMProphet:PTM Score (see Eric's last email):
"
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
"

If you need such PTMProphet metrics, then please send me a list with
proposal for their exact name and definitions.



New CV terms in version 4.1.25 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:1001456 ! analysis 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

[Term]
id: MS:1003016
name: ProteinProphet:peptide weight
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

[Term]
id: MS:1003017
name: ProteinProphet:peptide group weight
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

[Term]
id: MS:1003018
name: Philosopher
def: "General proteomics processing toolkit for shotgun proteomics." 
[https://philosopher.nesvilab.org/]
is_a: MS:1001456 ! analysis software



Changed CV terms in version 4.1.25 of psi-ms.obo:
=================================================
************ adde 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

Building ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

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

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

www.medizinisches-proteom-center.de