[Psidev-ms-dev] Release Candidate 2 for psi-ms.obo v3.17.0

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Hello all,

in the attachment you'll find the obo file of the v3.17.0 release 
candidate 2
to be discussed at todays PSI MSS WG teleconference call (see email from 
Eric).

It contains all requests and proposals from the the ms-vocab list
since the last official release at Nov 24th, 2011 of the obo file 
(version 3.16.0).

In addition I made sure that each definition ends with a period (full 
stop) according to the
"Guidelines for the development of Controlled Vocabularies".

Likewise I putted the [Typedef] stanzas before the [Term] stanzas and in 
the header tags I made
sure that the 'import' tag occurs before the 'default-namespace' and 
that the 'remark' tags are
compliant with the order rules mentioned in the "OBO Flat File Format 
Specification, version 1.2".

Please check if the list is complete and the terms are correctly defined.
Any feedback and further suggestions are appreciated.

1. Changes to already existing CV terms:
========================================
************ Added Clostripain as synonym to "Arg-C" and the missing 
definition field
[Term]
id: MS:1001303
name: Arg-C
def: "Endoproteinase Arg-C." [PSI:PI]
synonym: "clostripain" EXACT []
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001272 ! (?<=R)(?!P)

************ Added the missing definition field
[Term]
id: MS:1001307
name: CNBr
def: "Cyanogen bromide." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001333 ! (?<=M)

************ def: field defined
[Term]
id: MS:1000836
name: dried dropplet
def: "Dried dropplet in MALDI matrix preparation." [PSI:MS]
is_a: MS:1000833 ! matrix application type

************ def: field defined
[Term]
id: MS:1000837
name: printed
def: "Printed MALDI matrix preparation." [PSI:MS]
is_a: MS:1000833 ! matrix application type

************ def: field defined
[Term]
id: MS:1000838
name: sprayed
def: "Sprayed MALDI matrix prerparation." [PSI:MS]
is_a: MS:1000833 ! matrix application type

************ A new relation in "precolated plate": now also a "sample 
plate type"; def: field defined
[Term]
id: MS:1000839
name: precoated plate
def: "Precoated plate." [PSI:MS]
is_a: MS:1000833 ! matrix application type
is_a: MS:1001938 ! sample plate type

************ "paul ion trap" is now obsolete, because redundant to 
quadrupole ion trap
[Term]
id: MS:1000297
name: paul ion trap
def: "OBSOLETE A device that permits the trapping of ions by means of an 
alternating current voltage. The ejection of ions with a m/z less than a 
prescribed value and retention of those with higher mass depends on the 
application of radio frequency voltages between a ring electrode and two 
end-cap electrodes to confine the ions in a circular path. The choice of 
these voltages determines the m/z below which ions are ejected." [PSI:MS]
comment: This term was made obsolete because it is redundant to 
quadrupole ion trap
synonym: "quadrupole ion trap" RELATED []
is_a: MS:1000479 ! purgatory
is_obsolete: true

************ "axial ejection linear ion trap" is now a linear ion trap
[Term]
id: MS:1000078
name: axial ejection linear ion trap
def: "A linear ion trap mass spectrometer where ions are ejected along
the axis of the analyzer." [PSI:MS]
is_a: MS:1000291 ! linear ion trap

************ "radial ejection linear ion trap" is now a linear ion trap
[Term]
id: MS:1000083
name: radial ejection linear ion trap
def: "A linear ion trap mass spectrometer where ions are ejected along
the radius of the analyzer." [PSI:MS]
is_a: MS:1000291 ! linear ion trap

2. Open questions (please email me further informations):
=========================================================
- How to represent the source (reference definitions) of the cleavage 
agents?

3. Newly added CV terms:
========================
[Term]
id: MS:1001914
name: pymzML
def: "Python module to interface mzML Data." [PSI:MS]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1001915
name: leukocyteelastase
def: "Enzyme leukocyte elastase (EC 3.4.21.37)." 
[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.37 
"BRENDA"]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=[ALIV])(?!P)

[Term]
id: MS:1001916
name: proline endopeptidase
def: "Enzyme proline endopeptidase (EC 3.4.21.26)." 
[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.26 
"BRENDA"]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=[HKR]P)(?!P)

[Term]
id: MS:1001917
name: glutamyl endopeptidase
def: "Enzyme Glutamyl endopeptidase (EC 3.4.21.19)." 
[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.19 
"BRENDA"]
synonym: "staphylococcal protease" EXACT []
synonym: "Glu-C" EXACT []
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=[^E]E)

[Term]
id: MS:1001918
name: 2-iodobenzoate
def: "Chemical iodobenzoate. Cleaves after W." 
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=4739928 
"PubChem"]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=W)

[Term]
id: MS:1001919
name: ProteomeXchange accession number
def: "Main identifier of a ProteomeXchange dataset." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001921
name: ProteomeXchange accession number version number
def: "Version number of a ProteomeXchange accession number." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001922
name: Digital Object Identifier (DOI)
def: "DOI unique identifier." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
relationship: has_regexp MS:1001176 ! (10\.(\d)+(\.(\d)*)?/[^\*].+)

[Term]
id: MS:1001923
name: external reference keyword
def: "Free text attribute that can enrich the information about an 
entity." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001924
name: journal article keyword
def: "Keyword present in a scientific publication." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001923 ! external reference keyword

[Term]
id: MS:1001925
name: submitter keyword
def: "Keyword assigned by the data submitter." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001923 ! external reference keyword

[Term]
id: MS:1001926
name: curator keyword
def: "Keyword assigned by a data curator." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001923 ! external reference keyword

[Term]
id: MS:1001927
name: Tranche file hash
def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001928
name: Tranche project hash
def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001929
name: PRIDE experiment URI
def: "URI that allows the access to one experiment in the PRIDE 
database." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001930
name: PRIDE project URI
def: "URI that allows the access to one project in the PRIDE database." 
[PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001931
name: source interface
def: "The source interface." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1001932
name: source interface model
def: "The source interface model." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001931 ! source interface

[Term]
id: MS:1001933
name: source sprayer
def: "The source sprayer." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1001934
name: source sprayer type
def: "The source sprayer type." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001933 ! source sprayer

[Term]
id: MS:1001935
name: source sprayer manufacturer
def: "The source sprayer manufacturer." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001933 ! source sprayer

[Term]
id: MS:1001936
name: source sprayer model
def: "The source sprayer model." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001933 ! source sprayer

[Term]
id: MS:1001937
name: sample plate
def: "Plate where the sample solution is spotted in a MALDI or similar 
instrument." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1001938
name: sample plate type
def: "The sample plate type." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001937 ! sample plate

[Term]
id: MS:1001939
name: stainless steel plate
def: "Stainless steel plate." [PSI:MS]
is_a: MS:1001938 ! sample plate type

[Term]
id: MS:1001940
name: coated glass plate
def: "Coated glass plate." [PSI:MS]
is_a: MS:1001938 ! sample plate type

[Term]
id: MS:1001941
name: electrospray supply type
def: "Whether the sprayer is fed or is loaded with sample once." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1001942
name: static supply electrospray
def: "The sprayer is loaded with sample once." [PSI:MS]
is_a: MS:1001941 ! electrospray supply type

[Term]
id: MS:1001943
name: fed supply electrospray
def: "The sprayer is continuously fed with sample." [PSI:MS]
is_a: MS:1001941 ! electrospray supply type

[Term]
id: MS:1001944
name: Collision cell exit potential
def: "Potential difference between Q2 and Q3 in a triple quadrupole 
instrument in volts." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000218 ! volt
synonym: "CXP" EXACT []

[Term]
id: MS:1001945
name: Pegasus 4D
def: "LECO nominal mass resolution time-of-flight GCxGC mass 
spectrometer." [PSI:MS]
is_a: MS:1001800 ! LECO instrument model

Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de