[Psidev-ms-dev] Release candidate 3.55.0_rc2

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Dear proteomics community,

attached there's the release candidate 3.55.0_rc2 of
the psi-ms.obo file. It contains new terms for
the MZmine and Maltcms frameworks.

In addition most of the purgatory terms are obsoleted
now, some moved to other branches and 10 terms are still
left in the purgatory branch, because these terms are still
referenced by other terms.

Changed CV terms in version 3.55.0_rc2 of psi-ms.obo:
=====================================================
************ Moved from purgatory --> measurement method
[Term]
id: MS:1000205
name: selected ion monitoring
def: "The operation of a mass spectrometer in which the intensities of
several specific m/z values are recorded rather than the entire mass
spectrum." [PSI:MS]
synonym: "MIM" RELATED []
synonym: "Multiple Ion Monitoring" EXACT []
synonym: "SIM" EXACT []
is_a: MS:1000596 ! measurement method

************ Moved from purgatory --> measurement method
[Term]
id: MS:1000206
name: selected reaction monitoring
def: "Data acquired from specific product ions corresponding to m/z
selected precursor ions recorded via multiple stages of mass
spectrometry. Selected reaction monitoring can be performed in time or
in space." [PSI:MS]
synonym: "MRM" RELATED []
synonym: "Multiple Reaction Monitoring" RELATED []
synonym: "SRM" EXACT []
is_a: MS:1000596 ! measurement method

************ Now under ion type
[Term]
id: MS:1000368
name: metastable ion
def: "An ion that is formed with internal energy higher than the
threshold for dissociation but with a lifetime great enough to allow it
to exit the ion source and enter the mass spectrometer where it
dissociates before detection." [PSI:MS]
is_a: MS:1002343 ! ion type

************ Now under ion type
[Term]
id: MS:1000378
name: stable ion
def: "An ion with internal energy sufficiently low that it does not
rearrange or dissociate prior to detection in a mass spectrometer." [PSI:MS]
is_a: MS:1002343 ! ion type

************ Now under ion type
[Term]
id: MS:1000379
name: unstable ion
def: "An ion with sufficient energy to dissociate within the ion
source." [PSI:MS]
is_a: MS:1002343 ! ion type

************ Renamed: gas -> gaseous sample state
[Term]
id: MS:1000048
name: gaseous sample state
def: "State if the sample is in gaseous form." [PSI:MS]
is_a: MS:1000003 ! sample state

************ Renamed: liquid -> liquid sample state
[Term]
id: MS:1000049
name: liquid sample state
def: "State if the sample is in liquid form." [PSI:MS]
is_a: MS:1000003 ! sample state

************ Renamed: solid -> solid sample state
[Term]
id: MS:1000050
name: solid sample state
def: "State if the sample is in solid form." [PSI:MS]
is_a: MS:1000003 ! sample state

************ OBSOLETED PURGATORY TERMS
MS:1000002	sample name	
MS:1000010	analyzer type	
MS:1000023	isolation width	
MS:1000054	chromatography	
MS:1000097	constant neutral mass loss	
MS:1000098	multiple ion monitoring
MS:1000100	precursor ion scan	
MS:1000101	product ion scan	
MS:1000155	ELEMENT2	
MS:1000214	electron energy obsolete	
MS:1000244	consecutive reaction monitoring	
MS:1000292	mass spectrograph obsolete
MS:1000295	mattauch-herzog geometry	
MS:1000296	nier-johnson geometry	
MS:1000297	paul ion trap
MS:1000299	quistor
MS:1000313	scan m/z range?	
MS:1000323	constant neutral loss scan	
MS:1000324	constant neutral gain scan	
MS:1000338	nth generation product ion scan	
MS:1000352	secondary electron	
MS:1000425	ion energy loss spectrum	
MS:1000454	instrument additional description	
MS:1000461	additional description	
MS:1000479	purgatory	
MS:1000552	maldi spot identifier	
MS:1001051	multiple enzyme combination rules
MS:1001115	scan number(s)
MS:1001213	search result details
MS:1001326	add_others

************************************************************
************ TERMS STILL IN THE PURGATORY BRANCH
The following 10 terms are still in the purgatory branch.
It was not possible to obsolete them, because other terms
still refer to them:

ID			name							
	referenced by
=============================================================
MS:1000268 mass spectrometry
	MS:1000020 scanning method
	MS:1000263 isotope ratio mass spectrometry
MS:1000293 mass spectrometer
	MS:1000226 molecular beam mass spectrometry
	MS:1000238 accelerator mass spectrometry
	MS:1000256 high-field asymmetric waveform ion mobility spectrometry
	MS:1000260 ion kinetic energy spectrometry
	MS:1000261 ion mobility spectrometry
	MS:1000267 mass analyzed ion kinetic energy spectrometry
	MS:1000269 mass spectrometry/mass spectrometry
	MS:1000277 residual gas analyzer
	MS:1000287 time-of-flight mass spectrometer
	MS:1000289 double-focusing mass spectrometer
	MS:1000290 hybrid mass spectrometer
	MS:1000298 prolate traochoidal mass spectrometer
	MS:1000301 sector mass spectrometer
	MS:1000302 tandem mass spectrometer
	MS:1000303 transmission quadrupole mass spectrometer
	MS:1000306 dynamic mass spectrometry
MS:1000329 linked scan
	MS:1000330 linked scan at constant b/e
	MS:1000331 Linked Scan at Constant E2/V
	MS:1000332 Linked Scan at Constant B2/E
	MS:1000333 Linked Scan at Constant B[1-(E/E0)]^1/2 / E
MS:1000365 ion?
	MS:1000437 ion reaction
	MS:1000506 ion role
	MS:1000507 ion attribute
	MS:1000508 ion chemical type
MS:1000444 m/z Separation Method
	MS:1000234 mass resolving power(already obsolete)
	MS:1000305 cyclotron motion
	MS:1000314 mass selective axial ejection
	MS:1000315 mass selective instability
	MS:1000316 mathieu stability diagram
	MS:1000317 orthogonal extraction
	MS:1000318 resonance ion ejection
MS:1000445 sequential m/z separation method
	MS:1000270 multiple stage mass spectrometry
	MS:1000321 2E Mass Spectrum
	MS:1000334 MS/MS in Time
	MS:1000335 MS/MS in Space
	MS:1000336 neutral loss
MS:1000459 spectrum instrument description
	MS:1000037 polarity (already obsolete)
MS:1000013 resolution type
	MS:1000088 constant
	MS:1000089 proportional
MS:1000017 scan function
	MS:1000090 mass scan
	MS:1000091 selected ion detection
MS:1000020 scanning method
	MS:1000498 full scan
	MS:1000791 enhanced resolution scan (already obsolete)

************************************************************
************ TERMS OVERLAPPING WITH INCLUDED ONTOLOGIES
B. In order to ensure non-orthogonality (redundancy)
   between the CV terms and its imports, the following
   terms in psi-ms.obo were made obsolete. Please use
   the corresponding terms from the unit.obo resp.
   PATO.obo instead.

ID in psi-ms.obo name in unit.obo ID in unit.obo name in unit.obo
=================================================================
MS:1000212       dalton           UO:0000221     dalton		
MS:1000137       electron volt    UO:0000266     electronvolt		
MS:1000046       energy unit      UO:0000111     energy unit		
MS:1000464       mass unit        UO:0000002     mass unit		
MS:1000038       minute           UO:0000031     minute		
MS:1000039       second           UO:0000010     second		
MS:1000550       time unit        UO:0000003     time unit		
MS:1000460       unit             UO:0000000     unit

ID in psi-ms.obo name in unit.obo ID in PATO.obo name in PATO.obo
=================================================================
MS:1000095       linear           PATO:0001199   linear
MS:1000037       polarity         PATO:0002186   polarity
MS:1000843       wavelength       PATO:0001242   wavelength

New CV terms in version 3.55.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002342
name: MZmine
def: "A framework for differential analysis of mass spectrometry data."
[PMID:16403790, PMID:20650010]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002343
name: ion type
def: "A framework for differential analysis of mass spectrometry data."
[PSI:PI]
is_a: MS:1000365 ! ion?

[Term]
id: MS:1002344
name: Maltcms
def: "Modular Application Toolkit for Chromatography Mass-Spectrometry
is an application framework mainly for developers." [PSI:PI,
http://maltcms.sf.net]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

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