psidev-ms-dev

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

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

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

Hi Gerhard, many thanks for putting this together. It will be great to
finalize this next week. One suggestion I'll make is to include the
original publication of each of the scoring algorithm definitions. I think
each one probably derives from an original single publication. It would
also be good to use the same punctuation/capitalization as the original
paper as the term name.

Thanks!
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Friday, March 09, 2012 5:19 AM
> To: psi...@li...; psidev-pi-
> de...@li...; Mass spectrometry standard development
> Subject: [Psidev-ms-vocab] Open psi-ms.obo term proposals to discuss at
> HUPO-PSI meeting in San Diego next week
>
> 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...
> Web:	http://www.medizinisches-proteom-center.de