[Psidev-ms-dev] Open psi-ms.obo term proposals to discuss at HUPO-PSI meeting in San Diego next week

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

Dear proteomics community,

attached there's the psi-ms.obo release candidate 3.21.0_rc2 as a basis for
discussion on the HUPO PSI meeting next week in San Diego.

It contains some new terms proposed by Andy Jones concerning the ion 
mobility
resp. Henk van den Toorn concerning post translational modification scoring.

In addition Terry Farah and Sean L. Seymour will make a proposal of some 
CV terms
belonging to protein grouping to us (see also the attached Powerpoint 
and Excel files).


Newly added CV terms:
=====================
[Term]
id: MS:1001966
name: product ion mobility
def: "The mobility of an MS2 product ion, as measured by ion mobility 
mass spectrometry." [PSI:MS]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001967
name: product ion drift time
def: "The ion drift time of an MS2 product ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000028 ! millisecond

[Term]
id: MS:1001968
name: PTM scoring algorithm name
def: "Name of the algorithm used for post-translational modification 
scoring." [PSI:MS]
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001969
name: pRS score
def: "Peptide score based on the cumulative binomial probability that 
the observed match is a random event." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001970
name: pRS sequence probability
def: "Probability that the isoform is correct." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001971
name: pRS site probability
def: "For each phosphorylation site, this value is an estimate of the 
probability that the site is truly phosphorylated." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001972
name: PTM score
def: "Posttranslational modification score." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001973
name: a-score
def: "A-Score for peptide phosphorylation site location." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001974
name: h-score
def: "H-Score for peptide phosphorylation site location." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001975
name: delta score
def: "Phosphorylation site localization delta score." [PSI:MS]
is_a: MS:1001968 ! PTM scoring algorithm name

[Term]
id: MS:1001976
name: PTM scoring algorithm version
def: "Version of the post-translational modification scoring algorithm." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001977
name: PTM scoring value
def: "Score value for post-translational modification." [PSI:MS]
xref: value-type:xsd\:float "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

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...
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