[Psidev-ms-dev] Release candidate for the next release of psi-ms.obo

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Hello all,

I took over the CV maintenance of the psi-ms.obo file from David.

David, in the name of the community I would like to thank you so much 
for your efforts in
maintaining the CV during the last year.

In the following you find a list of all requests and proposals which I 
found in 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".

Please check if the list is complete and the terms are correctly defined.
At point 2.) I have also listed some open questions for added terms, for 
which I hope to get answers
from the community. Any feedback and further suggestions are appreciated.
If there are no further objections and / or discussions I plan to 
release the new version next tuesday (Jan 31th).

In the attachment you'll find the obo file of the v3.17.0 release candidate.

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)

************ A new relation in "precolated plate": now also a "sample 
plate type"
[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):
=========================================================
What are the datatypes for the following terms?

MS:1001919 (ProteomeXchange primary accession number)
MS:1001920 (ProteomeXchange secondary identifier)
MS:1001921 (ProteomeXchange primary accession version number)
MS:1001927 (Tranche file hash)
MS:1001928 (Tranche project hash)

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: elastase
def: "Enzyme elastase. Cleaves after A, L, I or V, except when P is 
after A, L, I or V." [PSI:MS]
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. Cleaves after P." [PSI:MS]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=P)

[Term]
id: MS:1001917
name: staphylococcal protease
def: "Staphylococcal protease. Cleaves after E." [PSI:MS]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=E)

[Term]
id: MS:1001918
name: jodobenzoate
def: "Chemical Jodobenzoate. Cleaves after W." [PSI:MS]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=W)

[Term]
id: MS:1001919
name: ProteomeXchange primary accession number
def: "Main identifier of a ProteomeXchange dataset." [PSI:PI]
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001920
name: ProteomeXchange secondary identifier
def: "Secondary identifier of a ProteomeXchange dataset." [PSI:PI]
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1001921
name: ProteomeXchange primary accession version number
def: "Version number of a ProteomeXchange accession number." [PSI:PI]
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]
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]
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 []

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