psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] New release candidate 3.73.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.73.0_rc1 of the psi-ms.obo file.

It contains new terms for localization score thresholds, added string 
value-types
for PTM location scores, and some updated definitions for PTM site 
location terms.


Changed CV terms in version 3.73.0 _rc1 of psi-ms.obo:
======================================================
************ Updated the definitions of the following terms:
[Term]
id: MS:1001969
name: phosphoRS score
def: "phosphoRS score for PTM site location at the PSM-level." 
[DOI:10.1021/pr200611n, PMID:22073976]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1001985
name: Ascore
def: "A-score for PTM site location at the PSM-level." 
[DOI:10.1038/nbt1240, PMID:16964243]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002536
name: D-Score
def: "D-Score for PTM site location at the PSM-level." 
[DOI:10.1002/pmic.201200408, PMID:23307401]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002537
name: MD-Score
def: "MD-Score for PTM site location at the PSM-level." 
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002550
name: peptide:phosphoRS score
def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002551
name: peptide:Ascore
def: "A-score score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002553
name: peptide:D-Score
def: "D-Score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002554
name: peptide:MD-Score
def: "MD-Score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

************ Renamed from 'order' --> 'modification index'
[Term]
id: MS:1002504
name: modification index
def: "The order of modifications to be referenced elsewhere in the 
document." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

************ Added string value-type\:string and
************ relationship: has_regexp MS:10012505 ! regular expression 
for modification localization scoring
************ to all PSM-level PTM localization score's and
************ to all peptide-level PTM localization score's, e.g.
[Term]
id: MS:1002551
name: peptide:Ascore
def: "A-score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring



New CV terms in version 3.73.0_rc1 of psi-ms.obo:
=================================================
************ New terms for PTM localization score thresholds.
[Term]
id: MS:1002555
name: PTM localization score threshold
def: "Threshold for PTM site location score." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002556
name: Ascore threshold
def: "Threshold for Ascore PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002557
name: D-Score threshold
def: "Threshold for D-score PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002558
name: MD-Score threshold
def: "Threshold for MD-score PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002559
name: H-Score threshold
def: "Threshold for H-score PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:10025560
name: DeBunker:score threshold
def: "Threshold for DeBunker PTM site location score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002561
name: Mascot:PTM site assignment confidence threshold
def: "Threshold for Mascot PTM site assignment confidence." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002562
name: MSQuant:PTM-score threshold
def: "Threshold for MSQuant:PTM-score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002563
name: MaxQuant:PTM Score threshold
def: "Threshold for MaxQuant:PTM Score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002564
name: MaxQuant:P-site localization probability threshold
def: "Threshold for MaxQuant:P-site localization probability." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002565
name: MaxQuant:PTM Delta Score threshold
def: "Threshold for MaxQuant:PTM Delta Score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002566
name: MaxQuant:Phospho (STY) Probabilities threshold
def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002567
name: phosphoRS score threshold
def: "Threshold for phosphoRS score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002568
name: phosphoRS site probability threshold
def: "Threshold for phosphoRS site probability." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.72.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new version 3.72.0 of the psi-ms.obo file.

It contains obsoletions for ProteomeDiscoverer static and dynamic 
modification
terms, PTM localization scoring, PeptideShaker confidence levels, the xi 
cross-
linking software, for spectral counting indices and for peptide-level PTM
localization scoring.


Changed CV terms in version 3.72.0 of psi-ms.obo:
=================================================
************ Renamed from "PTM localization score"
************         ---> "PSM-level PTM localization score"
[Term]
id: MS:1001968
name: PSM-level PTM localization score
def: "A score that assign confidence to the localization of an amino 
acid modification on a peptide sequence at the PSM-level." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

************ Obsoleted the following terms
id: MS:1002078 (ProteomeDiscoverer:1. Static Modification)
id: MS:1002079 (ProteomeDiscoverer:2. Static Modification)
id: MS:1002330 (ProteomeDiscoverer:3. Static Modification)
id: MS:1001720 (ProteomeDiscoverer:1. Dynamic Modification)
id: MS:1001721 (ProteomeDiscoverer:2. Dynamic Modification)
id: MS:1001722 (ProteomeDiscoverer:3. Dynamic Modification)
id: MS:1001723 (ProteomeDiscoverer:4. Dynamic Modification)
id: MS:1002331 (ProteomeDiscoverer:5. Dynamic Modification)


New CV terms in version 3.72.0 of psi-ms.obo:
=============================================
************ New terms for PTM localization scoring
[Term]
id: MS:1002539
name: D-Score
def: "D-Score for phosphorylation site location at the PSM-level." 
[DOI:10.1002/pmic.201200408, PMID:23307401]
is_a: MS:1001968 ! PSM-level PTM localization score

[Term]
id: MS:1002540
name: MD-Score
def: "MD-Score for phosphorylation site location at the PSM-level." 
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
is_a: MS:1001968 ! PSM-level PTM localization score

************ New terms for PeptideShaker confidence levels
[Term]
id: MS:1002538
name: PTM localization confidence metric
def: "Localization confidence metric for a post translational 
modification (PTM)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002539
name: PeptideShaker PTM confidence type
def: "PeptideShaker quality criteria for the confidence of PTM 
localizations." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002538 ! PTM localization confidence metric

[Term]
id: MS:1002540
name: PeptideShaker PSM confidence type
def: "PeptideShaker quality criteria for the confidence of PSM's." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification confidence metric

[Term]
id: MS:1002541
name: PeptideShaker peptide confidence type
def: "PeptideShaker quality criteria for the confidence of peptide 
identifications." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide identification confidence metric

[Term]
id: MS:1002542
name: PeptideShaker protein confidence type
def: "PeptideShaker quality criteria for the confidence of protein 
identifications." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric

************ New terms related to the xi cross-linking software
[Term]
id: MS:1002543
name: xiFDR
def: "Target/Decoy based FDR estimation for cross-linking 
peptide-identifications." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002544
name: xi
def: "Search engine for cross-linked peptides." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002545
name: xi:score
def: "The xi result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002546
name: Skyline mzQuantML converter
def: "A software package to convert Skyline report to mzQuantML." 
[PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/]
is_a: MS:1001139 ! quantitation software name
is_a: MS:1001456 ! analysis software

************ New spectral counting quantification data types
[Term]
id: MS:1002547
name: normalized spectral abundance factor
def: "A normalized spectral abundance factor (NSAF)." 
[DOI:10.1021/pr060161n, PMID:16944946]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002548
name: distributed normalized spectral abundance factor
def: "A distributed normalized spectral abundance factor (dNSAF." 
[DOI:10.1021/ac9023999, PMID:20166708]
is_a: MS:1001805 ! quantification datatype

************ New terms for peptide-level PTM localization scoring
[Term]
id: MS:1002549
name: peptide-level PTM localization score
def: "A score that assign confidence to the localization of an amino 
acid modification on a peptide sequence at the peptide-level." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002550
name: peptide:phosphoRS score
def: "Peptide score based on the cumulative binomial probability that 
the observed match is a random event at the peptide-level." [PSI:PI]
is_a: MS:1002549 ! peptide-level PTM localization score

[Term]
id: MS:1002551
name: peptide:Ascore
def: "Ascore score for peptide phosphorylation site location at the 
peptide-level." [PSI:PI]
is_a: MS:1002549 ! peptide-level PTM localization score

[Term]
id: MS:1002552
name: peptide:H-Score
def: "H-Score for peptide phosphorylation site location at the 
peptide-level." [PSI:PI]
is_a: MS:1002549 ! peptide-level PTM localization score

[Term]
id: MS:1002553
name: peptide:D-Score
def: "D-Score for phosphorylation site location at the peptide-level." 
[PSI:PI]
is_a: MS:1002549 ! peptide-level PTM localization score

[Term]
id: MS:1002554
name: peptide:MD-Score
def: "MD-Score for phosphorylation site location at the peptide-level." 
[PSI:PI]
is_a: MS:1002549 ! peptide-level PTM localization score

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.72.0_rc3 of psi-ms.obo

[Lutz F. <lfi...@st...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[Psidev-ms-dev] Release candidate 3.72.0_rc3 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.72.0_rc3 of the psi-ms.obo file.

It contains new terms for ProteomeDiscoverer, PTM localization scoring,
PeptideShaker confidence levels, the xi cross-linking software, for
spectral counting indices and for peptide-level PTM localization scoring.


Changed CV terms in version 3.72.0_rc3 of psi-ms.obo:
=====================================================
************ Renamed from "PTM localization score"
************         ---> "PSM-level PTM localization score"
[Term]
id: MS:1001968
name: PSM-level PTM localization score
def: "A score that assign confidence to the localization of an amino 
acid modification on a peptide sequence at the PSM-level." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details


New CV terms in version 3.72.0_rc3 of psi-ms.obo:
=================================================
************ New terms for ProteomeDiscoverer dynamic modifications
[Term]
id: MS:1002536
name: ProteomeDiscoverer:6th Dynamic Modification
def: "ProteomeDiscoverer's 6th dynamic post-translational modification 
(PTM) input parameter." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002537
name: ProteomeDiscoverer:7th Dynamic Modification
def: "ProteomeDiscoverer's 7th dynamic post-translational modification 
(PTM) input parameter." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002538
name: ProteomeDiscoverer:8th Dynamic Modification
def: "ProteomeDiscoverer's 8th dynamic post-translational modification 
(PTM) input parameter." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

************ New terms for PTM localization scoring
[Term]
id: MS:1002539
name: D-Score
def: "D-Score for phosphorylation site location at the PSM-level." 
[DOI:10.1002/pmic.201200408, PMID:23307401]
is_a: MS:1001968 ! PSM-level PTM localization score

[Term]
id: MS:1002540
name: MD-Score
def: "MD-Score for phosphorylation site location at the PSM-level." 
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
is_a: MS:1001968 ! PSM-level PTM localization score

************ New terms for PeptideShaker confidence levels
[Term]
id: MS:1002541
name: PTM localization confidence metric
def: "Localization confidence metric for a post translational 
modification (PTM)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002542
name: PeptideShaker PTM confidence type
def: "PeptideShaker quality criteria for the confidence of PTM 
localizations." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002541 ! PTM localization confidence metric

[Term]
id: MS:1002543
name: PeptideShaker PSM confidence type
def: "PeptideShaker quality criteria for the confidence of PSM's." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification confidence metric

[Term]
id: MS:1002544
name: PeptideShaker peptide confidence type
def: "PeptideShaker quality criteria for the confidence of peptide 
identifications." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide identification confidence metric

[Term]
id: MS:1002545
name: PeptideShaker protein confidence type
def: "PeptideShaker quality criteria for the confidence of protein 
identifications." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric

************ New terms related to the xi cross-linking software
[Term]
id: MS:1002546
name: xiFDR
def: "Target/Decoy based FDR estimation for cross-linking 
peptide-identifications." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002547
name: xi
def: "Search engine for cross-linked peptides." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002548
name: xi:score
def: "The xi result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002549
name: Skyline mzQuantML converter
def: "A software package to convert Skyline report to mzQuantML." 
[PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/]
is_a: MS:1001139 ! quantitation software name
is_a: MS:1001456 ! analysis software

************ New spectral counting quantification data types
[Term]
id: MS:1002550
name: normalized spectral abundance factor
def: "A normalized spectral abundance factor (NSAF)." 
[DOI:10.1021/pr060161n, PMID:16944946]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002551
name: distributed normalized spectral abundance factor
def: "A distributed normalized spectral abundance factor (dNSAF." 
[DOI:10.1021/ac9023999, PMID:20166708]
is_a: MS:1001805 ! quantification datatype

************ New terms for peptide-level PTM localization scoring
[Term]
id: MS:1002552
name: peptide-level PTM localization score
def: "A score that assign confidence to the localization of an amino 
acid modification on a peptide sequence at the peptide-level." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002553
name: peptide:phosphoRS score
def: "Peptide score based on the cumulative binomial probability that 
the observed match is a random event at the peptide-level." [PSI:PI]
is_a: MS:1002552 ! peptide-level PTM localization score

[Term]
id: MS:1002554
name: peptide:Ascore
def: "Ascore score for peptide phosphorylation site location at the 
peptide-level." [PSI:PI]
is_a: MS:1002552 ! peptide-level PTM localization score

[Term]
id: MS:1002555
name: peptide:H-Score
def: "H-Score for peptide phosphorylation site location at the 
peptide-level." [PSI:PI]
is_a: MS:1002552 ! peptide-level PTM localization score

[Term]
id: MS:1002556
name: peptide:D-Score
def: "D-Score for phosphorylation site location at the peptide-level." 
[PSI:PI]
is_a: MS:1002552 ! peptide-level PTM localization score

[Term]
id: MS:1002557
name: peptide:MD-Score
def: "MD-Score for phosphorylation site location at the peptide-level." 
[PSI:PI]
is_a: MS:1002552 ! peptide-level PTM localization score

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Registration is open for PSI meeting 2015 in Seattle

[Juan A. V. <ju...@eb...>]

Dear all,

The registration for the  2015 meeting (http://www.psidev.info/content/hupo-psi-meeting-2015 <http://www.psidev.info/content/hupo-psi-meeting-2015>) is now open. In fact, some people already got registered.

So, please get registered if you are planning to attend. It will help us in the general planning of the meeting.

The direct URL for the registration is:

http://www.psidev.info/content/registration-psi-cosmos-meeting-2015#overlay-context=content/hupo-psi-meeting-2015 <http://www.psidev.info/content/registration-psi-cosmos-meeting-2015#overlay-context=content/hupo-psi-meeting-2015>

Best regards,

Juan Antonio

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.72.0_rc2 of psi-ms.obo

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

Hi Gerhard, many thanks for handling all these new terms. I have some
concerns about this series:

id: MS:1002536
name: ProteomeDiscoverer:6. Dynamic Modification
def: "Determine 6th dynamic post-translational modifications (PTMs)."
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

1) Do these really need to be enumerated? 6th? 7th? 8th? What about 9th? We
have no 9th? Can't we just have a single term that is
ProteomeDiscoverer:Dynamic Modification?
2) The use of "6." to mean "6th" is unusual. I think this is just a German
thing. I don't think other countries do this, or do they? The US does not. I
think just staying with "6th" would be better (if we absolutely must have
enumeration).
3) Why do we need the verb "Determine"? Do all other input parameters have
"Determine" in the definition? It seems to me that a better definition would
be "ProteomeDiscoverer's 6th dynamic post-translational modification (PTM)
input parameter."
4) I'm also concerned by the proliferation of highly specialized terms when
a single generic one would do. Can we not just have a single "variable mass
modification" term instead of dozens of engine specific ones? I suppose
different engines specify them in different formats, but writing out
engine-specific formatted data in engine-specific terms, just creates a
problem for reading software, rather than normalizing it at the writer
level.

What do you all think?

Maybe we can discuss at the call tomorrow.

Thanks,
Eric



-----Original Message-----
From: mayerg97 [mailto:ger...@ru...]
Sent: Wednesday, February 04, 2015 5:46 AM
To: psi...@li...;
psi...@li...; psi...@li...
Subject: [Psidev-ms-vocab] Release candidate 3.72.0_rc2 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.72.0_rc2 of the psi-ms.obo file.

It contains new terms for ProteomeDiscoverer, PTM localization scoring,
PeptideShaker confidence level ,the xi cross-linking software.


Changed CV terms in version 3.72.0_rc2 of psi-ms.obo:
=====================================================
************ No changed terms


New CV terms in version 3.72.0_rc2 of psi-ms.obo:
=================================================
************ New terms for ProteomeDiscoverer dynamic modifications [Term]
id: MS:1002536
name: ProteomeDiscoverer:6. Dynamic Modification
def: "Determine 6th dynamic post-translational modifications (PTMs)."
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002537
name: ProteomeDiscoverer:7. Dynamic Modification
def: "Determine 7th dynamic post-translational modifications (PTMs)."
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002538
name: ProteomeDiscoverer:8. Dynamic Modification
def: "Determine 8th dynamic post-translational modifications (PTMs)."
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

************ New terms for PTM localization scoring [Term]
id: MS:1002540
name: D-Score
def: "D-Score for phosphorylation site location."
[DOI:10.1002/pmic.201200408, PMID:23307401]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1002541
name: MD-Score
def: "MD-Score for phosphorylation site location."
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
is_a: MS:1001968 ! PTM localization score

************ New term for PeptideShaker confidence levels [Term]
id: MS:1002542
name: PeptideShaker protein confidence type
def: "PeptideShaker quality criteria for the confidence of PTM
localizations." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric

************ New terms related to the xi cross-linking software [Term]
id: MS:1002543
name: xiFDR
def: "Target/Decoy based FDR estimation for cross-linking
peptide-identifications." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002544
name: xi
def: "Search engine for cross-linked peptides." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002545
name: xi:score
def: "The xi result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002546
name: Skyline mzQuantML converter
def: "A software package to convert Skyline report to mzQuantML."
[PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/]
is_a: MS:1001139 ! quantitation software name
is_a: MS:1001456 ! analysis software

************ New spectral counting quantification data types [Term]
id: MS:1002547
name: normalized spectral abundance factor
def: "A normalized spectral abundance factor (NSAF)."
[DOI:10.1021/pr060161n, PMID:16944946]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002548
name: distributed normalized spectral abundance factor
def: "A distributed normalized spectral abundance factor (dNSAF."
[DOI:10.1021/ac9023999, PMID:20166708]
is_a: MS:1001805 ! quantification datatype

Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics /
Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.72.0_rc2 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.72.0_rc2 of the psi-ms.obo file.

It contains new terms for ProteomeDiscoverer, PTM localization scoring,
PeptideShaker confidence level ,the xi cross-linking software.


Changed CV terms in version 3.72.0_rc2 of psi-ms.obo:
=====================================================
************ No changed terms


New CV terms in version 3.72.0_rc2 of psi-ms.obo:
=================================================
************ New terms for ProteomeDiscoverer dynamic modifications
[Term]
id: MS:1002536
name: ProteomeDiscoverer:6. Dynamic Modification
def: "Determine 6th dynamic post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002537
name: ProteomeDiscoverer:7. Dynamic Modification
def: "Determine 7th dynamic post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002538
name: ProteomeDiscoverer:8. Dynamic Modification
def: "Determine 8th dynamic post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

************ New terms for PTM localization scoring
[Term]
id: MS:1002540
name: D-Score
def: "D-Score for phosphorylation site location." 
[DOI:10.1002/pmic.201200408, PMID:23307401]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1002541
name: MD-Score
def: "MD-Score for phosphorylation site location." 
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
is_a: MS:1001968 ! PTM localization score

************ New term for PeptideShaker confidence levels
[Term]
id: MS:1002542
name: PeptideShaker protein confidence type
def: "PeptideShaker quality criteria for the confidence of PTM 
localizations." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric

************ New terms related to the xi cross-linking software
[Term]
id: MS:1002543
name: xiFDR
def: "Target/Decoy based FDR estimation for cross-linking 
peptide-identifications." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002544
name: xi
def: "Search engine for cross-linked peptides." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002545
name: xi:score
def: "The xi result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002546
name: Skyline mzQuantML converter
def: "A software package to convert Skyline report to mzQuantML." 
[PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/]
is_a: MS:1001139 ! quantitation software name
is_a: MS:1001456 ! analysis software

************ New spectral counting quantification data types
[Term]
id: MS:1002547
name: normalized spectral abundance factor
def: "A normalized spectral abundance factor (NSAF)." 
[DOI:10.1021/pr060161n, PMID:16944946]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002548
name: distributed normalized spectral abundance factor
def: "A distributed normalized spectral abundance factor (dNSAF." 
[DOI:10.1021/ac9023999, PMID:20166708]
is_a: MS:1001805 ! quantification datatype

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.72.0_rc1 of psi-ms.obo

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

Hi Gerhard, many thanks for continuing to work on this! Regarding the new
proposed terms, I think we already have a term for A-score:, term 1985:

http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS:1001985&termName=Ascore:Ascore

Or is the new proposed one different? If so, we should clearly differentiate
in the definitions.

Thanks,
Eric




-----Original Message-----
From: mayerg97 [mailto:ger...@ru...]
Sent: Thursday, January 29, 2015 7:00 AM
To: psi...@li...;
psi...@li...; psi...@li...
Subject: [Psidev-pi-dev] Release candidate 3.72.0_rc1 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.72.0_rc1 of the psi-ms.obo file.
It contains new terms for ProteomeDiscoverer, PTM localization scoring,
PeptideShaker confidence level and the xi cross-linking software.


Changed CV terms in version 3.72.0_rc1 of psi-ms.obo:
=====================================================
************ No changed terms


New CV terms in version 3.72.0_rc1 of psi-ms.obo:
=================================================
************ New terms for ProteomeDiscoverer dynamic modifications
[Term]
id: MS:1002536
name: ProteomeDiscoverer:6. Dynamic Modification
def: "Determine 6th dynamic post-translational modifications (PTMs)."
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002537
name: ProteomeDiscoverer:7. Dynamic Modification
def: "Determine 7th dynamic post-translational modifications (PTMs)."
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002538
name: ProteomeDiscoverer:8. Dynamic Modification
def: "Determine 8th dynamic post-translational modifications (PTMs)."
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

************ New terms for PTM localization scoring
[Term]
id: MS:1002539
name: A-Score
def: "A-Score for phosphorylation site location."
[DOI:10.1021/pr1006813, PMID:20836569]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1002540
name: D-Score
def: "D-Score for phosphorylation site location."
[DOI:10.1002/pmic.201200408, PMID:23307401]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1002541
name: MD-Score
def: "MD-Score for phosphorylation site location."
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
is_a: MS:1001968 ! PTM localization score

************ New term for PeptideShaker confidence levels
[Term]
id: MS:1002542
name: PeptideShaker protein confidence type
def: "PeptideShaker quality criteria for the confidence of PTM
localizations." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric

************ New terms related to the xi cross-linking software
[Term]
id: MS:1002543
name: xiFDR
def: "Target/Decoy based FDR estimation for cross-linking
peptide-identifications." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002544
name: xi
def: "Search engine for cross-linked peptides." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002545
name: xi:score
def: "The xi result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.72.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.72.0_rc1 of the psi-ms.obo file.
It contains new terms for ProteomeDiscoverer, PTM localization scoring,
PeptideShaker confidence level and the xi cross-linking software.


Changed CV terms in version 3.72.0_rc1 of psi-ms.obo:
=====================================================
************ No changed terms


New CV terms in version 3.72.0_rc1 of psi-ms.obo:
=================================================
************ New terms for ProteomeDiscoverer dynamic modifications
[Term]
id: MS:1002536
name: ProteomeDiscoverer:6. Dynamic Modification
def: "Determine 6th dynamic post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002537
name: ProteomeDiscoverer:7. Dynamic Modification
def: "Determine 7th dynamic post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002538
name: ProteomeDiscoverer:8. Dynamic Modification
def: "Determine 8th dynamic post-translational modifications (PTMs)." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

************ New terms for PTM localization scoring
[Term]
id: MS:1002539
name: A-Score
def: "A-Score for phosphorylation site location." 
[DOI:10.1021/pr1006813, PMID:20836569]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1002540
name: D-Score
def: "D-Score for phosphorylation site location." 
[DOI:10.1002/pmic.201200408, PMID:23307401]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1002541
name: MD-Score
def: "MD-Score for phosphorylation site location." 
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
is_a: MS:1001968 ! PTM localization score

************ New term for PeptideShaker confidence levels
[Term]
id: MS:1002542
name: PeptideShaker protein confidence type
def: "PeptideShaker quality criteria for the confidence of PTM 
localizations." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric

************ New terms related to the xi cross-linking software
[Term]
id: MS:1002543
name: xiFDR
def: "Target/Decoy based FDR estimation for cross-linking 
peptide-identifications." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002544
name: xi
def: "Search engine for cross-linked peptides." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002545
name: xi:score
def: "The xi result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] iPRG2015 - Deadline extended!

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

Hi everyone, in case you have not seen it via other channels, the deadline
for the latest iPRG study has been extended. So if you were wanting to
participate, but ran out of time, here is a fresh chance to turn back the
clock and prepare your contribution.  I would highly encourage you to
participate, this is fun!



Regards,

Eric





*From:* spc...@go... [mailto:
spc...@go...] *On Behalf Of *Henry Lam
*Sent:* Tuesday, January 27, 2015 10:07 PM
*To:* spc...@go...
*Subject:* [spctools-discuss] iPRG2015 - Deadline extended!



Dear potential participants,



iPRG conducts annual or bi-annual community study on proteomics data
analysis. This year, the study focuses on label-free quantitation methods.



The study instructions are here:



http://www.abrf.org/ResearchGroups/ProteomicsInformaticsResearchGroup/Studies/iPRG2015_Study_Instructions_FINAL.PDF



To allow more time for you to finish the data analysis, the deadline for
submitting your iPRG 2015 results will be extended to Feb. 13, 2015
(Friday).



Given the extra time, please consider submitting multiple entries if you
want to explore different methods. Please also pass this notice to your
friends and colleagues and encourage them to try!



One participant alerted us that the Skyline peak intensity table was
non-unique (i.e. some peptides have duplicate lines). A table with the
duplicates removed (SkylineIntensities_unique.tsv) has been uploaded to the
same directory in the same FTP site (ftp.peptideatlas.org). If you are
using that file as your input, you may want to try to apply your method to
the new "unique" table to see if your results change.



Sincerely,



The ABRF Proteome Informatics Research Group (iPRG)

Eugene Kapp – Walter and Eliza Hall Institute of Medical Research (Co-chair)
Henry Lam – Hong Kong University of Science and Technology (Co-chair)
Brett Phinney – UC Davis (ABRF Executive Board Liaison)
John Cottrell – Matrix Science Ltd
Michael Hoopmann – Institute for Systems Biology
Sangtae Kim – Pacific Northwest National Laboratory
Thomas Neubert – New York University
Magnus Palmblad – Leiden University Medical Center
Olga Vitek – Northeastern University
Sue Weintraub – University of Texas Health Science Center at San Antonio



-- 
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an
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Re: [Psidev-ms-dev] [Psidev-pi-dev] Need help regarding uploading of Mass Spectrometry proteomics data and gel images.

[Yasset Perez-R. <yp...@eb...>]

Dear Mousami:
    Be in contact with pri...@eb..., they will help you.
Regards

Yasset
On 18/12/2014 11:06, Mousami Srivastava wrote:
> Dear Sir / Madam,
>
> Greetings from Mousami.
>
> I'm working as a Graduate Scholar from Defence Institute of Physiology 
> and Allied Sciences (DIPAS). Our Team had worked with the Proteomics 
> experiment to identify biomarkers and we have generated mass 
> spectrometry results and gel images. We worked with Brukers 
> Corporation Maldi TOF Mass spectrometry instruments.
>
> Now Reviewers are expecting that we have to upload all our work to the 
> public repository. We are also interested with the same.
>
> Could you please help us in uploading our MS work and gel images to 
> the public repository.
>
>
>
> -- 
> Regards,
> Mousami Srivastava
> Email : sm....@gm... <mailto:sm....@gm...>
> srv...@ya... <mailto:srv...@ya...>
> Mob. No.: +91-9013728894
> Research Scholar
> DIPAS, DRDO
> Delhi
> India
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
Yasset Perez-Riverol PhD.
Bioinformatician
Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Twitter: @ypriverol

[Psidev-ms-dev] iPRG 2015 launched

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

Hi everyone, in case you have not seen it via other channels, the latest
iPRG study has been launched. I was on the committee in the past, but no
longer am. But, of course, I strongly support as wide a participation as
possible! I would encourage you to participate!



Regards,

Eric




——————————————————————————————


The Proteome Informatics (iPRG) 2015 study is officially launched today!

The Proteome Informatics Research Group (iPRG) of the Association of
Biomolecular Resource Facilities (ABRF) invites you to participate in a
collaborative data analysis study to evaluate software and statistical
methods for label-free quantitation. Participants will be asked to detect
proteins that exhibit significant differences in abundance in a yeast
whole-cell lysate and report protein abundance ratios between pairs of four
samples, each represented by three technical replicates, analyzed by a
quadrupole-orbitrap mass spectrometer. The study will primarily focus on
post-identification processing steps, such as filtering false positives,
computing the quantitative metrics, assembling peptide-level information to
estimate protein abundance ratios, and statistical assessment

To participate in this study, please go to:

http://www.abrf.org/index.cfm/group.show/ProteomicsInformaticsResearchGroup.53.htm

Sincerely,

The ABRF Proteome Informatics Research Group (iPRG)

Eugene Kapp – Walter and Eliza Hall Institute of Medical Research (Co-chair)
Henry Lam – Hong Kong University of Science and Technology (Co-chair)
Brett Phinney – UC Davis (ABRF Executive Board Liaison)
John Cottrell – Matrix Science Ltd
Michael Hoopmann – Institute for Systems Biology
Sangtae Kim – Pacific Northwest National Laboratory
Thomas Neubert – New York University
Magnus Palmblad – Leiden University Medical Center
Olga Vitek – Northeastern University
Sue Weintraub – University of Texas Health Science Center at San Antonio

[Psidev-ms-dev] HUPO PSI 2015 spring workshop in Seattle April 13, 14, 15

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

Hi everyone, I am pleased to announce that the 2015 HUPO PSI spring
workshop will be hosted in Seattle at the Institute for Systems Biology on
April 13, 14, 15. Our registration page will open in January, but please
mark your calendars now for full-day sessions all 3 days and plan on
joining us in Seattle to continue important work on standards.



Regards,

Eric

[Psidev-ms-dev] FW: mzML Perl implementation

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

[Hi everyone, I may have deleted this post in the approval queue by
accident. See post by Felipe below]



Thank you for making these tools available, Felipe!



*From:* Felipe da Veiga Leprevost [mailto:fe...@le...]
*Sent:* Saturday, November 15, 2014 3:06 AM
*To:* psi...@li...
*Subject:* mzML Perl implementation



Dear all,



I wish to inform you that we have now a Perl parser implementation for the
mzML format, available at:



https://metacpan.org/pod/distribution/MzML-Parser/README.pod

https://github.com/Leprevost/MzML-Parser



The parser can organize the mzML file into a series of nested objects,
following strictly the standard schema. This is the first release of the
module and future versions will bring more features like advanced methods
to easily extract some of the deeply nested information.



Also, I am planning to release Perl modules for TraML, mzIdenML, MzQuantML
and mzTab.





best regards and keep the good work!



--

Felipe da Veiga Leprevost, PhD.

www.leprevost.com.br

Laboratory for Proteomics and Protein Engineering.

Fiocruz, Brazil.

[Psidev-ms-dev] mzML Perl implementation

[Felipe da V. L. <fe...@le...>]

Dear all,

I wish to inform you that we have now a Perl parser implementation for
the mzML format, available at:

https://metacpan.org/pod/distribution/MzML-Parser/README.pod
https://github.com/Leprevost/MzML-Parser

The parser can organize the mzML file into a series of nested objects,
following strictly the standard schema. This is the first release of the
module and future versions will bring more features like advanced
methods to easily extract some of the deeply nested information.

Also, I am planning to release Perl modules for TraML, mzIdenML,
MzQuantML and mzTab.


best regards and keep the good work!

--
Felipe da Veiga Leprevost, PhD. www.leprevost.com.br Laboratory for
Proteomics and Protein Engineering. Fiocruz, Brazil.

[Psidev-ms-dev] New version 3.71.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new version 3.71.0 of the psi-ms.obo file.
It contains two new CV terms for scores of the ProLuCID software.


Changed CV terms in version 3.71.0 of psi-ms.obo:
=================================================
************ Removed the value-type, since used only as parent-term
[Term]
id: MS:1000044
name: dissociation method
def: "Fragmentation method used for dissociation or fragmentation." [PSI:MS]
synonym: "Activation Method" RELATED []
relationship: part_of MS:1000456 ! precursor activation


New CV terms in version 3.71.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002534
name: ProLuCID:xcorr
def: "The ProLuCID result 'XCorr'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002535
name: ProLuCID:deltacn
def: "The ProLuCID result 'DeltaCn'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.71.0_rc1 od psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.71.0_rc1 of the psi-ms.obo file.
It contains two new CV terms for scores of the ProLuCID software.


Changed CV terms in version 3.71.0_rc1 of psi-ms.obo:
=====================================================
************ Removed the value-type, since used only as parent-term
[Term]
id: MS:1000044
name: dissociation method
def: "Fragmentation method used for dissociation or fragmentation." [PSI:MS]
synonym: "Activation Method" RELATED []
relationship: part_of MS:1000456 ! precursor activation


New CV terms in version 3.71.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002534
name: ProLuCID:xcorr
def: "The ProLuCID result 'XCorr'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002535
name: ProLuCID:deltacn
def: "The ProLuCID result 'DeltaCn'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.70.0 of psi-ms.obo

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

Thank you, Gerhard!





*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Monday, November 03, 2014 5:35 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.70.0 of
psi-ms.obo



Dear proteomics community,

sorry, a mistake crept in in the last version 3.70.0

Attached you find the corrected version 3.70.1 of the psi-ms.obo file.
It contains corrections for the is_a relationships for the terms
MS:1002362 and MS:1002367


Changed CV terms in version 3.70.1 of psi-ms.obo:
=================================================
************ is_a: MS:1001192 ! peptide identification confidence metric
************ changed to
************ is_a: MS:1001092 ! peptide identification confidence metric
[Term]
id: MS:1002362
name: distinct peptide-level probability
def: "Probability that the reported distinct peptide sequence (irrespective
of mass modifications) has been correctly identified via the referenced
PSMs." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide identification confidence metric
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ is_a: MS:1001192 ! protein identification confidence metric
************ changed to
************ is_a: MS:1001198 ! protein identification confidence metric
[Term]
id: MS:1002367
name: probability for proteins
def: "Probability that a specific protein sequence has been correctly
identified from the PSM and distinct peptide evidence, and based on the
available protein sequences presented to the analysis software." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive


New CV terms in version 3.70.1 of psi-ms.obo:
=============================================
No new CV terms

Best Regards,
Gerhard


Am 03.11.2014 um 09:53 schrieb Fredrik Levander:

Dear Gerard et al,

There seems to have been a change in the is_a relation to 'Expect value'
for some of the peptide and protein probability terms
(MS:1002362,MS:1002367) with this update.  However, they don't seem to be
expect values by their definitions, so I was wondering whether this is an
accidental change?

Best Regards

Fredrik

On 2014-11-03 09:24, mayerg97 wrote:

Dear proteomics community,

attached is the new version 3.70.0 of the psi-ms.obo file.

It contains a new term for the AB SCIEX TripleTOF 6600 and corrections for
the
is_a relationships of four terms:


Changed CV terms in version 3.70.0 of psi-ms.obo:
=================================================
************ is_a: MS:1000138 ! percent collision energy
************ changed to
************ is_a: MS:1000138 ! normalized collision energy
[Term]
id: MS:1002218
name: percent collision energy ramp start
def: "Collision energy at the start of the collision energy ramp in
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! normalized collision energy
relationship: has_units UO:0000187 ! percent


************ is_a: MS:1000138 ! percent collision energy
************ changed to
************ is_a: MS:1000138 ! normalized collision energy
[Term]
id: MS:1002219
name: percent collision energy ramp end
def: "Collision energy at the end of the collision energy ramp in percent,
normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! normalized collision energy
relationship: has_units UO:0000187 ! percent


************ is_a: MS:1001192 ! peptide identification confidence metric
************ changed to
************ is_a: MS:1001192 ! Expect value
[Term]
id: MS:1002362
name: distinct peptide-level probability
def: "Probability that the reported distinct peptide sequence (irrespective
of mass modifications) has been correctly identified via the referenced
PSMs." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001192 ! Expect value
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive


************ is_a: MS:1001192 ! protein identification confidence metric
************ changed to
************ is_a: MS:1001192 ! Expect value
[Term]
id: MS:1002367
name: probability for proteins
def: "Probability that a specific protein sequence has been correctly
identified from the PSM and distinct peptide evidence, and based on the
available protein sequences presented to the analysis software." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001192 ! Expect value
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive



New CV terms in version 3.70.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002533
name: TripleTOF 6600
def: "AB SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight
mass spectrometer." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

Best Regards,
Gerhard




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-- 

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer

Bioinformatics / Biostatistics

Medizinisches-Proteom-Center (MPC)

Ruhr-Universität Bochum

Zentrum für klinische Forschung I (ZKF I), E.049a

Universitätsstraße 150

D-44801 Bochum

 Phone:  +49(0)234/32-21006

Fax:    +49(0)234/32-14554

Email:  ger...@ru...

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

[Psidev-ms-dev] New version 3.70.0 of psi-ms.obo

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

Dear proteomics community,

attached is the new version 3.70.0 of the psi-ms.obo file.

It contains a new term for the AB SCIEX TripleTOF 6600 and corrections 
for the
is_a relationships of four terms:


Changed CV terms in version 3.70.0 of psi-ms.obo:
=================================================
************ is_a: MS:1000138 ! percent collision energy
************ changed to
************ is_a: MS:1000138 ! normalized collision energy
[Term]
id: MS:1002218
name: percent collision energy ramp start
def: "Collision energy at the start of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! normalized collision energy
relationship: has_units UO:0000187 ! percent


************ is_a: MS:1000138 ! percent collision energy
************ changed to
************ is_a: MS:1000138 ! normalized collision energy
[Term]
id: MS:1002219
name: percent collision energy ramp end
def: "Collision energy at the end of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! normalized collision energy
relationship: has_units UO:0000187 ! percent


************ is_a: MS:1001192 ! peptide identification confidence metric
************ changed to
************ is_a: MS:1001192 ! Expect value
[Term]
id: MS:1002362
name: distinct peptide-level probability
def: "Probability that the reported distinct peptide sequence 
(irrespective of mass modifications) has been correctly identified via 
the referenced PSMs." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001192 ! Expect value
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive


************ is_a: MS:1001192 ! protein identification confidence metric
************ changed to
************ is_a: MS:1001192 ! Expect value
[Term]
id: MS:1002367
name: probability for proteins
def: "Probability that a specific protein sequence has been correctly 
identified from the PSM and distinct peptide evidence, and based on the 
available protein sequences presented to the analysis software." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001192 ! Expect value
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive



New CV terms in version 3.70.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002533
name: TripleTOF 6600
def: "AB SCIEX TripleTOF 6600, a quadrupole - quadrupole - 
time-of-flight mass spectrometer." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.70.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached is the release candidate 3.70.0_rc1 of the psi-ms.obo file.

It contains a new term for the AB SCIEX TripleTOF 6600.


New CV terms in version 3.70.0_rc1 of psi-ms.obo:
=================================================

[Term]
id: MS:1002533
name: TripleTOF 6600
def: "AB SCIEX TripleTOF 6600, a quadrupole - quadrupole - 
time-of-flight mass spectrometer." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.69.0 of psi-ms.obo

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

Dear proteomics community,

attached the new version 3.69.0 of the psi-ms.obo file.

It contains corrections of the is_a relations for some MS-GF scores
and two new UIMF format terms.


Changed CV terms in version 3.69.0 of psi-ms.obo:
=================================================
************     is_a: MS:1001872 ! distinct peptide-level e-value
************ --> is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1002052
name: MS-GF:SpecEValue
def: "MS-GF spectral E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better


************     is_a: MS:1001872 ! distinct peptide-level e-value
************ --> is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1002053
name: MS-GF:EValue
def: "MS-GF E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better


************     is_a: MS:1001868 ! distinct peptide-level q-value
************ --> is_a: MS:1002354 ! PSM-level q-value
[Term]
id: MS:1002054
name: MS-GF:QValue
def: "MS-GF Q-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002354 ! PSM-level q-value

************ Added relationship: has_order MS:1002108 ! higher score better
[Term]
id: MS:1002394
name: PIA:protein score
def: "The score given to a protein by any protein inference." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
relationship: has_order MS:1002108 ! higher score better


New CV terms in version 3.69.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002531
name: UIMF format
def: "SQLite-based file format created at Pacific Northwest National 
Lab. It stores an intermediate analysis of ion-mobility mass 
spectrometry data." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002532
name: UIMF nativeID format
def: "Native format defined by frame=xsd:nonNegativeInteger 
scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.69.0_rc2 of psi-ms.obo

[Mayer, G. <may...@ru...>]

Dear proteomics community,

attached the release candidate 3.69.0_rc2 of the psi-ms.obo file.

It contains corrections of the is_a relations for some MS-GF scores
and two new UIMF format terms.


Changed CV terms in version 3.69.0_rc2 of psi-ms.obo:
=====================================================
************     is_a: MS:1001872 ! distinct peptide-level e-value
************ --> is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1002052
name: MS-GF:SpecEValue
def: "MS-GF spectral E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better


************     is_a: MS:1001872 ! distinct peptide-level e-value
************ --> is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1002053
name: MS-GF:EValue
def: "MS-GF E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better


************     is_a: MS:1001868 ! distinct peptide-level q-value
************ --> is_a: MS:1002354 ! PSM-level q-value
[Term]
id: MS:1002054
name: MS-GF:QValue
def: "MS-GF Q-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002354 ! PSM-level q-value

************ Added relationship: has_order MS:1002108 ! higher score better
[Term]
id: MS:1002394
name: PIA:protein score
def: "The score given to a protein by any protein inference." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
relationship: has_order MS:1002108 ! higher score better


New CV terms in version 3.69.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002531
name: UIMF format
def: "SQLite-based file format created at Pacific Northwest National 
Lab. It stores an intermediate analysis of ion-mobility mass 
spectrometry data." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002532
name: UIMF nativeID format
def: "Native format defined by frame=xsd:nonNegativeInteger 
scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format


Best Regards,
Gerhard

[Psidev-ms-dev] Release candidate 3.69.0_rc1 of psi-ms.obo file

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

Dear proteomics community,

attached the release candidate 3.69.0_rc1 of the psi-ms.obo file.

It contains corrections of the is_a relations for some MS-GF scores.


Changed CV terms in version 3.69.0_rc1 of psi-ms.obo:
=====================================================
************     is_a: MS:1001872 ! distinct peptide-level e-value
************ --> is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1002052
name: MS-GF:SpecEValue
def: "MS-GF spectral E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better


************     is_a: MS:1001872 ! distinct peptide-level e-value
************ --> is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1002053
name: MS-GF:EValue
def: "MS-GF E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better


************     is_a: MS:1001868 ! distinct peptide-level q-value
************ --> is_a: MS:1002354 ! PSM-level q-value
[Term]
id: MS:1002054
name: MS-GF:QValue
def: "MS-GF Q-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002354 ! PSM-level q-value


New CV terms in version 3.69.0_rc1 of psi-ms.obo:
=================================================
No new terms

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.68.0 of psi-ms.obo

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

Dear proteomics community,

attached the new version 3.68.0 of the psi-ms.obo file.

It contains two new binary data arrays and a de-obsoletion of the term 
"sample name".

Changed CV terms in version 3.68.0 of psi-ms.obo:
=================================================
************ De-obsoleted the term "sample name"
[Term]
id: MS:1000002
name: sample name
def: "A reference string relevant to the sample under study." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute


New CV terms in version 3.68.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002529
name: resolution array
def: "A data array of resolution values." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002530
name: baseline array
def: "A data array of signal baseline values (the signal in the absence 
of analytes)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.68.0_rc1 of psi-ms.obo file

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

Dear proteomics community,

attached there is the release candidate 3.68.0_rc1 of the psi-ms.obo file.

It contains two new binary data arrays and a de-obsoletion of the term 
"sample name".


Changed CV terms in version 3.68.0_rc1 of psi-ms.obo:
=====================================================
************ De-obsoleted the term "sample name"
[Term]
id: MS:1000002
name: sample name
def: "A reference string relevant to the sample under study." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute


New CV terms in version 3.68.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002529
name: resolution array
def: "A data array of resolution values." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002530
name: baseline array
def: "A data array of signal baseline values (the signal in the absence 
of analytes)." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000513 ! binary data array

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de