[Psidev-ms-dev] Release candidate 3.74.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.74.0_rc1 of the psi-ms.obo file.


Changed CV terms in version 3.74.0_rc1 of psi-ms.obo:
=====================================================
************ Changed is_a relationship from 'quality estimation method 
details'
************ --> 'statistical threshold'
[Term]
id: MS:1001494
name: no threshold
def: "In case no threshold was used." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

************ Added links to the paper in the definition
[Term]
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which 
must match the number of clusters that pass the threshold in the file." 
[DOI:10.1002/pmic.201400080, PMID:25092112]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein cluster details

************ Removed the suffix UNDER DISCUSSION from the following two 
terms
[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is the final set of identifications to be interpreted by 
consuming software. Amongst the set of SpectrumIdentificationList(s) 
that are flagged with the term, each spectrum must not be referenced 
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is not the final set of identifications to be interpreted by 
consuming software. This term should be used when results are provided 
from multiple search engines for the results from each search engine 
before they are combined to give consensus identifications. Amongst the 
set of SpectrumIdentificationList(s) that are flagged with the term, 
each spectrum may be referenced from more than one 
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details


New CV terms in version 3.74.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002569
name: ProteomeDiscoverer:Number of Spectra Processed At Once
def: "Number of spectra processed at once in a ProteomeDiscoverer 
search." [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:1002570
name: sequence multiply subsumable protein
def: "A protein for which the matched peptide sequences are the same, or 
a subset of, the matched peptide sequences for two or more other 
proteins combined. These other proteins need not all be in the same 
group." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002571
name: spectrum multiply subsumable protein
def: "A protein for which the matched spectra are the same, or a subset 
of, the matched spectra for two or more other proteins combined. These 
other proteins need not all be in the same group." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship

************ Two new terms for finer granulated distinction between the 
diffe-
************ rent statistical threshold types, needed for mapping file rules
[Term]
id: MS:1002572
name: protein detection statistical threshold
def: "Estimated statistical threshold used for protein detection." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002573
name: spectrum identification statistical threshold
def: "Estimated statistical threshold used for spectrum identification." 
[PSI:MS]
is_a: MS:1002482 ! statistical 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