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

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Hi Gerhard, many thanks for agreeing to take over and for putting all this
together. First, regarding timing. I think it would be great if you could
collect feedback over the next few days and then put out a new proposed
revision, and then give us a chance to discuss it at the MSSWG call on
Tuesday (17:00 your time; please join us if you can!). Once the results
from that discussion have taken place, then it would be best to make any
final necessary revisions and then commit. Would that be okay?

Here are some responses to your queries below:

> 2. Open questions (please email me further informations):
> =========================================================
> What are the datatypes for the following terms?
>
> MS:1001919 (ProteomeXchange primary accession number)

This should just be "ProteomeXchange accession number" as proposed by
Juanan, no? I don't know where "primary" came from. This should be an
positive integer like "123". I think this is what Juanan had in mind?
Please correct if I misunderstood this!

> MS:1001920 (ProteomeXchange secondary identifier)

This should just be "ProteomeXchange identifier" as proposed by Juanan,
no? I don't know where "secondary" came from. This should be a string like
"PXD000123"

> MS:1001921 (ProteomeXchange primary accession version number)

This should just be "ProteomeXchange accession version number " as
proposed by Juanan, no? I don't know where "primary" came from. This
should be a positive integer like "4"

> MS:1001927 (Tranche file hash)

This should be an xsd:string

> MS:1001928 (Tranche project hash)

This should be an xsd:string

Thanks,
Eric

> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Wednesday, January 25, 2012 6:33 AM
> To: psi...@li...; psidev-pi-
> de...@li...; Mass spectrometry standard development
> Subject: [Psidev-ms-vocab] Release candidate for the next release of
> psi-ms.obo
>
> 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