[Psidev-ms-dev] Release candidate 3.52.0_rc3 of psi-ms.obo

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Dear proteomics community,

attached there's the release candidate 3.52.0_rc3 of the psi-ms.obo file.

It contains scores and some new ProteomeDiscoverer 1.4 input parameters.
e.g. for MS Amanda.
In addition it defines some terms for converter software.

Changed CV terms in version 3.52.0_rc3 of psi-ms.obo:
=====================================================
************ Added boolean data type
[Term]
id: MS:1001194
name: quality estimation with decoy database
def: "Quality estimation by decoy database." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001060 ! quality estimation method details

New CV terms in version 3.52.0_rc3 of psi-ms.obo:
=================================================
[Term]
id: MS:1002316
name: ProteomeDiscoverer:Amanda:high confidence threshold
def: "Strict confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002317
name: ProteomeDiscoverer:Amanda:middle confidence threshold
def: "Relaxed confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002318
name: ProteomeDiscoverer:automatic workload
def: "Flag indicating automatic estimation of the workload level." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002319
name: Amanda:AmandaScore
def: "The Amanda score of the scoring function for a PSM." [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

[Term]
id: MS:1002320
name: ProteomeDiscoverer:max differential modifications
def: "Maximum dynamic modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002321
name: ProteomeDiscoverer:max equal modifications
def: "Maximum equal modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002322
name: ProteomeDiscoverer:min peptide length
def: "Minimum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002323
name: ProteomeDiscoverer:max peptide length
def: "Maximum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002324
name: ProteomeDiscoverer:max number neutral loss
def: "Maximum number of same neutral losses." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002325
name: ProteomeDiscoverer:max number neutral loss modifications
def: "Max number of same neutral losses of modifications." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002326
name: ProteomeDiscoverer:use flanking ions
def: "Flag for usage of flanking ions." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002327
name: ProteomeDiscoverer:max number of same modifs
def: "The maximum number of possible equal modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002328
name: ProteomeDiscoverer:perform deisotoping
def: "Defines whether a simple deisotoping shall be performed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002329
name: ProteomeDiscoverer:ion settings
def: "Specifies the fragment ions and neutral losses that are
calculated." [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:1002330
name: ProteomeDiscoverer:3. Static Modification
def: "Determine 3rd static (fixed) post-translational modifications
(PTMs)." [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:1002331
name: ProteomeDiscoverer:5. Dynamic Modification
def: "Determine 5th dynamic (variable) post-translational modifications
(PTMs)." [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:1002332
name: lab head
def: "The laboratory head responsible for a submitted dataset." [PSI:PI]
is_a: MS:1002037 ! dataset submitter

[Term]
id: MS:1002333
name: converter software
def: "The used conversion software." [PSI:PI]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002334
name: ProCon
def: "Proteomics Conversion tool." [PSI:PI,
http://www.medizinisches-proteom-center.de/procon]
is_a: MS:1002333 ! converter software

[Term]
id: MS:1002335
name: PRIDE Converter2
def: "Proteomics Conversion tool." [PMID:22949509]
is_a: MS:1002333 ! converter software

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatik / Biostatistik
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