psidev-ms-dev

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

[Gerhard M. <Ger...@ru...>]

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

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

[Eric D. <ede...@sy...>]

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

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

[Juan A. V. <ju...@eb...>]

Hi all,

Thanks to Eric and Pierre-Alain for their feedback. You were right about the lack of consistency in the naming.

After thinking a bit more about it, I think that at least for the moment there is no need to have a 'ProteomeXchange secondary identifier". If it is finally needed, we can add it at a later stage when it is clear what it can be.

-The ProteomeXchange accession number should be a string. It will have this structure: PXD00123. I have removed the 'primary' from the name and changed slightly the definition.
- ProteomeXchange accession number version number is an integer and I have corrected the name of the term.  PXD00123.1
- I agree with Pierre-Alain's proposal for keyword.

I have added the string type for the Tranche related terms, as suggested by Eric.

And yes, about the publication, we can use the PubMed ID.

The other terms will be created in the PRIDE CV.

Cheers,

Juanan



[Term]
id: MS:1001919
name: ProteomeXchange accession number
def: "Unique 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

PLEASE DELETE
[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 accession number version number
def: "Version number of a ProteomeXchange accession number." [PSI:PI]
xref: value-type:xsd\:positiveInteger "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



On 26 Jan 2012, at 07:49, pierre-alain binz wrote:

> 
> Hi Eric, these PX accession change proposals came from me:
> I was not comfortable with the original proposal from Juan:
> 
> ProteomeXchange accession number
> ProteomeXchange identifier
> ProteomeXchange accession version number
> 
> As there might be incoherence and lacking precision between  term names 
> and definitions: From the proposed definitions
> - the accession number, defined as "Main identifier of a ProteomeXchange 
> dataset.", might not be a "number",
> - the identifier, defined as "Secondary identifier of a ProteomeXchange 
> dataset." might be a number,
> - the accession version number, defined as "Version number of a 
> ProteomeXchange accession number" is badly termed. It should be either 
> an "accession number version number" and therefore force the value to be 
> a number or an "accession number version" and the datatype defined if 
> the value should be a number or not.
> See also my email from monday 23.
> 
> 
> Cheers
> Pierre-Alain
> 
> On 25.01.2012 18:24, Eric Deutsch wrote:
>> 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
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-d2d
>> _______________________________________________
>> Psidev-ms-vocab mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
> 
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Psidev-ms-vocab mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab