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From: Kessner, D. E. <Dar...@cs...> - 2008-02-06 18:58:58
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I would like to propose using standard acronyms in the CV term names
when it is clear what they mean.
We currently have:
<cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted laser
desorption ionization" value=""/>
<cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform ion
cyclotron resonance mass spectrometer" value=""/>
I think this is more readable:
<cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/>
<cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" value=""/>
The full name can still be available in the term description field.
I have an ulterior motive for this -- in the code generation of the
MSData library, the above terms become constants:
MS_matrix_assisted_laser_desorption_ionization = 1000075,
MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer =
1000079,
But I think the following is more programmer-friendly:
MS_MALDI = 1000075,
MS_FT_ICR_MS = 1000079,
Darren
Darren Kessner
Scientific Programmer
Dar...@cs...
310-423-9538
Spielberg Family Center for Applied Proteomics
Cedars-Sinai Medical Center
http://www.sfcap.cshs.org/
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From: Joshua T. <jt...@sy...> - 2008-02-06 19:59:54
|
Hi Darren, Speaking only for myself, I think that the "name" attribute should be optional in the file and not interfere with validation. I've never understood why the text string needs to exactly match the CV for validation; someone one the list had brought up other languages, etc. But I think it came up on the list before, and requiring strict mapping between accession numbers and text string seemed to be important for the format. At the least, acronyms would require additional 'mapping files' or something similar to be added to the specification, and the validator to be updated. Maybe someone more familiar with these tasks could step in. Maybe the CV could be expanded so that every entry had an additional "acronym" field. This brings up other questions, like would uniqueness be enforced, etc? Josh Kessner, Darren E. wrote: > I would like to propose using standard acronyms in the CV term names > when it is clear what they mean. > > > > We currently have: > > <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted laser > desorption ionization" value=""/> > > <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform ion > cyclotron resonance mass spectrometer" value=""/> > > > > I think this is more readable: > > <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> > > <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" value=""/> > > > > The full name can still be available in the term description field. > > > > I have an ulterior motive for this -- in the code generation of the > MSData library, the above terms become constants: > > MS_matrix_assisted_laser_desorption_ionization = 1000075, > > MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = > 1000079, > > > > But I think the following is more programmer-friendly: > > MS_MALDI = 1000075, > > MS_FT_ICR_MS = 1000079, > > > > > > > > Darren > > > > > > > > Darren Kessner > > Scientific Programmer > > Dar...@cs... <mailto:Dar...@cs...> > > 310-423-9538 > > > > Spielberg Family Center for Applied Proteomics > > Cedars-Sinai Medical Center > > http://www.sfcap.cshs.org/ > > > > > > IMPORTANT WARNING: This message is intended for the use of the person or > entity to which it is addressed and may contain information that is > privileged and confidential, the disclosure of which is governed by > applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivering it to the > intended recipient, you are hereby notified that any dissemination, > distribution or copying of this information is STRICTLY PROHIBITED. > > If you have received this message in error, please notify us immediately > by calling (310) 423-6428 and destroy the related message. Thank You for > your cooperation. > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Matthew C. <mat...@va...> - 2008-02-06 20:06:45
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The OBO has "exact_synonyms" like this: [Term] id: MS:1000079 name: fourier transform ion cyclotron resonance mass spectrometer def: "A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z." [PSI:MS] exact_synonym: "FT_ICR" [] is_a: MS:1000443 ! mass analyzer type Darren, I suggest you parse both the term name and its synonyms into a set for that term, and choose from it the shortest string to put in the enum. :) -Matt Joshua Tasman wrote: > Hi Darren, > > Speaking only for myself, I think that the "name" attribute should be optional in the file and not interfere with validation. I've never understood why the text string needs to exactly match the CV for validation; someone one the list had brought up other languages, etc. But I think it came up on the list before, and requiring strict mapping between accession numbers and text string seemed to be important for the format. > > At the least, acronyms would require additional 'mapping files' or something similar to be added to the specification, and the validator to be updated. Maybe someone more familiar with these tasks could step in. Maybe the CV could be expanded so that every entry had an additional "acronym" field. This brings up other questions, like would uniqueness be enforced, etc? > > Josh > > > Kessner, Darren E. wrote: > >> I would like to propose using standard acronyms in the CV term names >> when it is clear what they mean. >> >> >> >> We currently have: >> >> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted laser >> desorption ionization" value=""/> >> >> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform ion >> cyclotron resonance mass spectrometer" value=""/> >> >> >> >> I think this is more readable: >> >> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> >> >> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" value=""/> >> >> >> >> The full name can still be available in the term description field. >> >> >> >> I have an ulterior motive for this -- in the code generation of the >> MSData library, the above terms become constants: >> >> MS_matrix_assisted_laser_desorption_ionization = 1000075, >> >> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = >> 1000079, >> >> >> >> But I think the following is more programmer-friendly: >> >> MS_MALDI = 1000075, >> >> MS_FT_ICR_MS = 1000079, >> >> >> >> >> >> >> >> Darren >> >> >> >> >> >> >> >> Darren Kessner >> >> Scientific Programmer >> >> Dar...@cs... <mailto:Dar...@cs...> >> >> 310-423-9538 >> >> >> >> Spielberg Family Center for Applied Proteomics >> >> Cedars-Sinai Medical Center >> >> http://www.sfcap.cshs.org/ >> >> >> >> >> >> IMPORTANT WARNING: This message is intended for the use of the person or >> entity to which it is addressed and may contain information that is >> privileged and confidential, the disclosure of which is governed by >> applicable law. If the reader of this message is not the intended >> recipient, or the employee or agent responsible for delivering it to the >> intended recipient, you are hereby notified that any dissemination, >> distribution or copying of this information is STRICTLY PROHIBITED. >> >> If you have received this message in error, please notify us immediately >> by calling (310) 423-6428 and destroy the related message. Thank You for >> your cooperation. >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> > > |
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From: Kessner, D. E. <Dar...@cs...> - 2008-02-07 00:07:56
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Great -- thanks, Matt. I hadn't seen that. Darren -----Original Message----- From: psi...@li... [mailto:psi...@li...] On Behalf Of Matthew Chambers Sent: Wednesday, February 06, 2008 12:06 PM To: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] CV param readability The OBO has "exact_synonyms" like this: [Term] id: MS:1000079 name: fourier transform ion cyclotron resonance mass spectrometer def: "A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z." [PSI:MS] exact_synonym: "FT_ICR" [] is_a: MS:1000443 ! mass analyzer type Darren, I suggest you parse both the term name and its synonyms into a set for that term, and choose from it the shortest string to put in the enum. :) -Matt Joshua Tasman wrote: > Hi Darren, > > Speaking only for myself, I think that the "name" attribute should be optional in the file and not interfere with validation. I've never understood why the text string needs to exactly match the CV for validation; someone one the list had brought up other languages, etc. But I think it came up on the list before, and requiring strict mapping between accession numbers and text string seemed to be important for the format. > > At the least, acronyms would require additional 'mapping files' or something similar to be added to the specification, and the validator to be updated. Maybe someone more familiar with these tasks could step in. Maybe the CV could be expanded so that every entry had an additional "acronym" field. This brings up other questions, like would uniqueness be enforced, etc? > > Josh > > > Kessner, Darren E. wrote: > >> I would like to propose using standard acronyms in the CV term names >> when it is clear what they mean. >> >> >> >> We currently have: >> >> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted laser >> desorption ionization" value=""/> >> >> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform ion >> cyclotron resonance mass spectrometer" value=""/> >> >> >> >> I think this is more readable: >> >> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> >> >> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" value=""/> >> >> >> >> The full name can still be available in the term description field. >> >> >> >> I have an ulterior motive for this -- in the code generation of the >> MSData library, the above terms become constants: >> >> MS_matrix_assisted_laser_desorption_ionization = 1000075, >> >> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = >> 1000079, >> >> >> >> But I think the following is more programmer-friendly: >> >> MS_MALDI = 1000075, >> >> MS_FT_ICR_MS = 1000079, >> >> >> >> >> >> >> >> Darren >> >> >> >> >> >> >> >> Darren Kessner >> >> Scientific Programmer >> >> Dar...@cs... <mailto:Dar...@cs...> >> >> 310-423-9538 >> >> >> >> Spielberg Family Center for Applied Proteomics >> >> Cedars-Sinai Medical Center >> >> http://www.sfcap.cshs.org/ >> >> >> >> >> >> IMPORTANT WARNING: This message is intended for the use of the person or >> entity to which it is addressed and may contain information that is >> privileged and confidential, the disclosure of which is governed by >> applicable law. If the reader of this message is not the intended >> recipient, or the employee or agent responsible for delivering it to the >> intended recipient, you are hereby notified that any dissemination, >> distribution or copying of this information is STRICTLY PROHIBITED. >> >> If you have received this message in error, please notify us immediately >> by calling (310) 423-6428 and destroy the related message. Thank You for >> your cooperation. >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ - >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> > > ------------------------------------------------------------------------ - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. If you have received this message in error, please notify us immediately by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. |
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From: Eric D. <ede...@sy...> - 2008-02-12 21:36:07
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Hi Darren, is this issue closed or still open? There is the suggestion to use the shortest exact synonym for your purpose. Is that adequate? Regarding: > >> I would like to propose using standard acronyms in the CV term names > >> when it is clear what they mean. I believe is the policy of the PSI CV designers (not just the MS CV) that acronyms should NOT be used, but rather should be a synonym. Can anyone confirm that? Thanks, Eric > From: psi...@li... [mailto:psidev-ms-dev- > > The OBO has "exact_synonyms" like this: > > [Term] > id: MS:1000079 > name: fourier transform ion cyclotron resonance mass spectrometer > def: "A mass spectrometer based on the principle of ion cyclotron > resonance in which an ion in a magnetic field moves in a circular orbit at > a frequency characteristic of its m/z value. Ions are coherently excited > to a larger radius orbit using a pulse of radio frequency energy and their > image charge is detected on receiver plates as a time domain signal. > Fourier transformation of the time domain signal results in a frequency > domain signal which is converted to a mass spectrum based in the inverse > relationship between frequency and m/z." [PSI:MS] > exact_synonym: "FT_ICR" [] > is_a: MS:1000443 ! mass analyzer type > > Darren, I suggest you parse both the term name and its synonyms into a set > for that term, and choose from it the shortest string to put in the enum. > :) > > -Matt > > > Joshua Tasman wrote: > > Hi Darren, > > > > Speaking only for myself, I think that the "name" attribute should be > optional in the file and not interfere with validation. I've never > understood why the text string needs to exactly match the CV for > validation; someone one the list had brought up other languages, etc. But > I think it came up on the list before, and requiring strict mapping > between accession numbers and text string seemed to be important for the > format. > > > > At the least, acronyms would require additional 'mapping files' or > something similar to be added to the specification, and the validator to > be updated. Maybe someone more familiar with these tasks could step in. > Maybe the CV could be expanded so that every entry had an additional > "acronym" field. This brings up other questions, like would uniqueness be > enforced, etc? > > > > Josh > > > > > > Kessner, Darren E. wrote: > > > >> I would like to propose using standard acronyms in the CV term names > >> when it is clear what they mean. > >> > >> > >> > >> We currently have: > >> > >> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted > laser > >> desorption ionization" value=""/> > >> > >> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform > ion > >> cyclotron resonance mass spectrometer" value=""/> > >> > >> > >> > >> I think this is more readable: > >> > >> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> > >> > >> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" > value=""/> > >> > >> > >> > >> The full name can still be available in the term description field. > >> > >> > >> > >> I have an ulterior motive for this -- in the code generation of the > >> MSData library, the above terms become constants: > >> > >> MS_matrix_assisted_laser_desorption_ionization = 1000075, > >> > >> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = > >> 1000079, > >> > >> > >> > >> But I think the following is more programmer-friendly: > >> > >> MS_MALDI = 1000075, > >> > >> MS_FT_ICR_MS = 1000079, > >> > >> > >> > >> > >> > >> > >> > >> Darren > >> > >> > >> > >> > >> > >> > >> > >> Darren Kessner > >> > >> Scientific Programmer > >> > >> Dar...@cs... <mailto:Dar...@cs...> > >> > >> 310-423-9538 > >> > >> > >> > >> Spielberg Family Center for Applied Proteomics > >> > >> Cedars-Sinai Medical Center > >> > >> http://www.sfcap.cshs.org/ > >> > >> > >> > >> > >> > >> IMPORTANT WARNING: This message is intended for the use of the person > or > >> entity to which it is addressed and may contain information that is > >> privileged and confidential, the disclosure of which is governed by > >> applicable law. If the reader of this message is not the intended > >> recipient, or the employee or agent responsible for delivering it to > the > >> intended recipient, you are hereby notified that any dissemination, > >> distribution or copying of this information is STRICTLY PROHIBITED. > >> > >> If you have received this message in error, please notify us > immediately > >> by calling (310) 423-6428 and destroy the related message. Thank You > for > >> your cooperation. > >> > >> > >> ----------------------------------------------------------------------- > - > >> > >> ----------------------------------------------------------------------- > -- > >> This SF.net email is sponsored by: Microsoft > >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> > >> > >> ----------------------------------------------------------------------- > - > >> > >> _______________________________________________ > >> Psidev-ms-dev mailing list > >> Psi...@li... > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > >> > > > > > > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Kessner, D. E. <Dar...@cs...> - 2008-02-12 21:37:42
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Yes, it's closed -- synonyms are fine. Darren -----Original Message----- From: psi...@li... [mailto:psi...@li...] On Behalf Of Eric Deutsch Sent: Tuesday, February 12, 2008 1:36 PM To: Mass spectrometry standard development Cc: Eric Deutsch Subject: Re: [Psidev-ms-dev] CV param readability Hi Darren, is this issue closed or still open? There is the suggestion to use the shortest exact synonym for your purpose. Is that adequate? Regarding: > >> I would like to propose using standard acronyms in the CV term names > >> when it is clear what they mean. I believe is the policy of the PSI CV designers (not just the MS CV) that acronyms should NOT be used, but rather should be a synonym. Can anyone confirm that? Thanks, Eric > From: psi...@li... [mailto:psidev-ms-dev- > > The OBO has "exact_synonyms" like this: > > [Term] > id: MS:1000079 > name: fourier transform ion cyclotron resonance mass spectrometer > def: "A mass spectrometer based on the principle of ion cyclotron > resonance in which an ion in a magnetic field moves in a circular orbit at > a frequency characteristic of its m/z value. Ions are coherently excited > to a larger radius orbit using a pulse of radio frequency energy and their > image charge is detected on receiver plates as a time domain signal. > Fourier transformation of the time domain signal results in a frequency > domain signal which is converted to a mass spectrum based in the inverse > relationship between frequency and m/z." [PSI:MS] > exact_synonym: "FT_ICR" [] > is_a: MS:1000443 ! mass analyzer type > > Darren, I suggest you parse both the term name and its synonyms into a set > for that term, and choose from it the shortest string to put in the enum. > :) > > -Matt > > > Joshua Tasman wrote: > > Hi Darren, > > > > Speaking only for myself, I think that the "name" attribute should be > optional in the file and not interfere with validation. I've never > understood why the text string needs to exactly match the CV for > validation; someone one the list had brought up other languages, etc. But > I think it came up on the list before, and requiring strict mapping > between accession numbers and text string seemed to be important for the > format. > > > > At the least, acronyms would require additional 'mapping files' or > something similar to be added to the specification, and the validator to > be updated. Maybe someone more familiar with these tasks could step in. > Maybe the CV could be expanded so that every entry had an additional > "acronym" field. This brings up other questions, like would uniqueness be > enforced, etc? > > > > Josh > > > > > > Kessner, Darren E. wrote: > > > >> I would like to propose using standard acronyms in the CV term names > >> when it is clear what they mean. > >> > >> > >> > >> We currently have: > >> > >> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted > laser > >> desorption ionization" value=""/> > >> > >> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform > ion > >> cyclotron resonance mass spectrometer" value=""/> > >> > >> > >> > >> I think this is more readable: > >> > >> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> > >> > >> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" > value=""/> > >> > >> > >> > >> The full name can still be available in the term description field. > >> > >> > >> > >> I have an ulterior motive for this -- in the code generation of the > >> MSData library, the above terms become constants: > >> > >> MS_matrix_assisted_laser_desorption_ionization = 1000075, > >> > >> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = > >> 1000079, > >> > >> > >> > >> But I think the following is more programmer-friendly: > >> > >> MS_MALDI = 1000075, > >> > >> MS_FT_ICR_MS = 1000079, > >> > >> > >> > >> > >> > >> > >> > >> Darren > >> > >> > >> > >> > >> > >> > >> > >> Darren Kessner > >> > >> Scientific Programmer > >> > >> Dar...@cs... <mailto:Dar...@cs...> > >> > >> 310-423-9538 > >> > >> > >> > >> Spielberg Family Center for Applied Proteomics > >> > >> Cedars-Sinai Medical Center > >> > >> http://www.sfcap.cshs.org/ > >> > >> > >> > >> > >> > >> IMPORTANT WARNING: This message is intended for the use of the person > or > >> entity to which it is addressed and may contain information that is > >> privileged and confidential, the disclosure of which is governed by > >> applicable law. If the reader of this message is not the intended > >> recipient, or the employee or agent responsible for delivering it to > the > >> intended recipient, you are hereby notified that any dissemination, > >> distribution or copying of this information is STRICTLY PROHIBITED. > >> > >> If you have received this message in error, please notify us > immediately > >> by calling (310) 423-6428 and destroy the related message. Thank You > for > >> your cooperation. > >> > >> > >> ----------------------------------------------------------------------- > - > >> > >> ----------------------------------------------------------------------- > -- > >> This SF.net email is sponsored by: Microsoft > >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> > >> > >> ----------------------------------------------------------------------- > - > >> > >> _______________________________________________ > >> Psidev-ms-dev mailing list > >> Psi...@li... > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > >> > > > > > > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev ------------------------------------------------------------------------ - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. If you have received this message in error, please notify us immediately by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. |
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From: Kessner, D. E. <Dar...@cs...> - 2008-02-06 20:26:11
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I wasn't thinking about validation, since I'm ignoring the 'name' attribute. This is solely a readability issue, for the mzML and for MSData client code. Darren -----Original Message----- From: psi...@li... [mailto:psi...@li...] On Behalf Of Joshua Tasman Sent: Wednesday, February 06, 2008 12:00 PM To: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] CV param readability Hi Darren, Speaking only for myself, I think that the "name" attribute should be optional in the file and not interfere with validation. I've never understood why the text string needs to exactly match the CV for validation; someone one the list had brought up other languages, etc. But I think it came up on the list before, and requiring strict mapping between accession numbers and text string seemed to be important for the format. At the least, acronyms would require additional 'mapping files' or something similar to be added to the specification, and the validator to be updated. Maybe someone more familiar with these tasks could step in. Maybe the CV could be expanded so that every entry had an additional "acronym" field. This brings up other questions, like would uniqueness be enforced, etc? Josh Kessner, Darren E. wrote: > I would like to propose using standard acronyms in the CV term names > when it is clear what they mean. > > > > We currently have: > > <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted laser > desorption ionization" value=""/> > > <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform ion > cyclotron resonance mass spectrometer" value=""/> > > > > I think this is more readable: > > <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> > > <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" value=""/> > > > > The full name can still be available in the term description field. > > > > I have an ulterior motive for this -- in the code generation of the > MSData library, the above terms become constants: > > MS_matrix_assisted_laser_desorption_ionization = 1000075, > > MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = > 1000079, > > > > But I think the following is more programmer-friendly: > > MS_MALDI = 1000075, > > MS_FT_ICR_MS = 1000079, > > > > > > > > Darren > > > > > > > > Darren Kessner > > Scientific Programmer > > Dar...@cs... <mailto:Dar...@cs...> > > 310-423-9538 > > > > Spielberg Family Center for Applied Proteomics > > Cedars-Sinai Medical Center > > http://www.sfcap.cshs.org/ > > > > > > IMPORTANT WARNING: This message is intended for the use of the person or > entity to which it is addressed and may contain information that is > privileged and confidential, the disclosure of which is governed by > applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivering it to the > intended recipient, you are hereby notified that any dissemination, > distribution or copying of this information is STRICTLY PROHIBITED. > > If you have received this message in error, please notify us immediately > by calling (310) 423-6428 and destroy the related message. Thank You for > your cooperation. > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev ------------------------------------------------------------------------ - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. If you have received this message in error, please notify us immediately by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. |
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From: Joshua T. <jt...@sy...> - 2008-02-06 20:36:45
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Yes, but the official validator will complain if the 'name' string doesn't exactly match the CV, capitalization included. -Josh Kessner, Darren E. wrote: > I wasn't thinking about validation, since I'm ignoring the 'name' > attribute. > > This is solely a readability issue, for the mzML and for MSData client > code. > > > Darren > > > -----Original Message----- > From: psi...@li... > [mailto:psi...@li...] On Behalf Of Joshua > Tasman > Sent: Wednesday, February 06, 2008 12:00 PM > To: Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] CV param readability > > Hi Darren, > > Speaking only for myself, I think that the "name" attribute should be > optional in the file and not interfere with validation. I've never > understood why the text string needs to exactly match the CV for > validation; someone one the list had brought up other languages, etc. > But I think it came up on the list before, and requiring strict mapping > between accession numbers and text string seemed to be important for the > format. > > At the least, acronyms would require additional 'mapping files' or > something similar to be added to the specification, and the validator to > be updated. Maybe someone more familiar with these tasks could step in. > Maybe the CV could be expanded so that every entry had an additional > "acronym" field. This brings up other questions, like would uniqueness > be enforced, etc? > > Josh > > > Kessner, Darren E. wrote: >> I would like to propose using standard acronyms in the CV term names >> when it is clear what they mean. >> >> >> >> We currently have: >> >> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted > laser >> desorption ionization" value=""/> >> >> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform > ion >> cyclotron resonance mass spectrometer" value=""/> >> >> >> >> I think this is more readable: >> >> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> >> >> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" > value=""/> >> >> >> The full name can still be available in the term description field. >> >> >> >> I have an ulterior motive for this -- in the code generation of the >> MSData library, the above terms become constants: >> >> MS_matrix_assisted_laser_desorption_ionization = 1000075, >> >> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = >> 1000079, >> >> >> >> But I think the following is more programmer-friendly: >> >> MS_MALDI = 1000075, >> >> MS_FT_ICR_MS = 1000079, >> >> >> >> >> >> >> >> Darren >> >> >> >> >> >> >> >> Darren Kessner >> >> Scientific Programmer >> >> Dar...@cs... <mailto:Dar...@cs...> >> >> 310-423-9538 >> >> >> >> Spielberg Family Center for Applied Proteomics >> >> Cedars-Sinai Medical Center >> >> http://www.sfcap.cshs.org/ >> >> >> >> >> >> IMPORTANT WARNING: This message is intended for the use of the person > or >> entity to which it is addressed and may contain information that is >> privileged and confidential, the disclosure of which is governed by >> applicable law. If the reader of this message is not the intended >> recipient, or the employee or agent responsible for delivering it to > the >> intended recipient, you are hereby notified that any dissemination, >> distribution or copying of this information is STRICTLY PROHIBITED. >> >> If you have received this message in error, please notify us > immediately >> by calling (310) 423-6428 and destroy the related message. Thank You > for >> your cooperation. >> >> >> > ------------------------------------------------------------------------ >> > ------------------------------------------------------------------------ > - >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> >> >> > ------------------------------------------------------------------------ >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > ------------------------------------------------------------------------ > - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by > applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. > > If you have received this message in error, please notify us immediately > by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Lennart M. <len...@eb...> - 2008-02-07 10:31:17
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Hi Josh, > Yes, but the official validator will complain if the 'name' string doesn't exactly match the CV, capitalization included. This is incorrect (I actually tested it with version 0.99.1 of the semantic mzML validator we wrote and distributed in the kit). The tool validates solely on the CV accession numbers, because this is the only 'fixed quantity' (names have exact synonyms for instance), and the 'name' attribute is mainly in the standard format for readability reasons. So I think it's acceptable if people use acronyms instead of full versions, especially if they are present as exact synonyms in the CV. If the correct CV accession number is used for a term, there should never be a problem, since it has been decided throughout the PSI a long time ago (and I think we can all agree on this as well) that the accession number takes precedence over the name at all times. > > Kessner, Darren E. wrote: >> I wasn't thinking about validation, since I'm ignoring the 'name' >> attribute. >> >> This is solely a readability issue, for the mzML and for MSData client >> code. >> >> >> Darren >> >> >> -----Original Message----- >> From: psi...@li... >> [mailto:psi...@li...] On Behalf Of Joshua >> Tasman >> Sent: Wednesday, February 06, 2008 12:00 PM >> To: Mass spectrometry standard development >> Subject: Re: [Psidev-ms-dev] CV param readability >> >> Hi Darren, >> >> Speaking only for myself, I think that the "name" attribute should be >> optional in the file and not interfere with validation. I've never >> understood why the text string needs to exactly match the CV for >> validation; someone one the list had brought up other languages, etc. >> But I think it came up on the list before, and requiring strict mapping >> between accession numbers and text string seemed to be important for the >> format. >> >> At the least, acronyms would require additional 'mapping files' or >> something similar to be added to the specification, and the validator to >> be updated. Maybe someone more familiar with these tasks could step in. >> Maybe the CV could be expanded so that every entry had an additional >> "acronym" field. This brings up other questions, like would uniqueness >> be enforced, etc? >> >> Josh >> >> >> Kessner, Darren E. wrote: >>> I would like to propose using standard acronyms in the CV term names >>> when it is clear what they mean. >>> >>> >>> >>> We currently have: >>> >>> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted >> laser >>> desorption ionization" value=""/> >>> >>> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform >> ion >>> cyclotron resonance mass spectrometer" value=""/> >>> >>> >>> >>> I think this is more readable: >>> >>> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> >>> >>> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" >> value=""/> >>> >>> >>> The full name can still be available in the term description field. >>> >>> >>> >>> I have an ulterior motive for this -- in the code generation of the >>> MSData library, the above terms become constants: >>> >>> MS_matrix_assisted_laser_desorption_ionization = 1000075, >>> >>> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = >>> 1000079, >>> >>> >>> >>> But I think the following is more programmer-friendly: >>> >>> MS_MALDI = 1000075, >>> >>> MS_FT_ICR_MS = 1000079, >>> >>> >>> >>> >>> >>> >>> >>> Darren >>> >>> >>> >>> >>> >>> >>> >>> Darren Kessner >>> >>> Scientific Programmer >>> >>> Dar...@cs... <mailto:Dar...@cs...> >>> >>> 310-423-9538 >>> >>> >>> >>> Spielberg Family Center for Applied Proteomics >>> >>> Cedars-Sinai Medical Center >>> >>> http://www.sfcap.cshs.org/ >>> >>> >>> >>> >>> >>> IMPORTANT WARNING: This message is intended for the use of the person >> or >>> entity to which it is addressed and may contain information that is >>> privileged and confidential, the disclosure of which is governed by >>> applicable law. If the reader of this message is not the intended >>> recipient, or the employee or agent responsible for delivering it to >> the >>> intended recipient, you are hereby notified that any dissemination, >>> distribution or copying of this information is STRICTLY PROHIBITED. >>> >>> If you have received this message in error, please notify us >> immediately >>> by calling (310) 423-6428 and destroy the related message. Thank You >> for >>> your cooperation. >>> >>> >>> >> ------------------------------------------------------------------------ >> ------------------------------------------------------------------------ >> - >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> >>> >>> >> ------------------------------------------------------------------------ >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> ------------------------------------------------------------------------ >> - >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by >> applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. >> >> If you have received this message in error, please notify us immediately >> by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > |
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From: jtasman <jt...@sy...> - 2008-02-07 15:51:18
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Great, thanks for clearing that up. I must have been remembering a previous version of the validator. Josh Lennart Martens wrote: > Hi Josh, > > > >> Yes, but the official validator will complain if the 'name' string doesn't exactly match the CV, capitalization included. >> > > This is incorrect (I actually tested it with version 0.99.1 of the > semantic mzML validator we wrote and distributed in the kit). > > The tool validates solely on the CV accession numbers, because this is > the only 'fixed quantity' (names have exact synonyms for instance), and > the 'name' attribute is mainly in the standard format for readability > reasons. > > So I think it's acceptable if people use acronyms instead of full > versions, especially if they are present as exact synonyms in the CV. > If the correct CV accession number is used for a term, there should > never be a problem, since it has been decided throughout the PSI a long > time ago (and I think we can all agree on this as well) that the > accession number takes precedence over the name at all times. > > > >> Kessner, Darren E. wrote: >> >>> I wasn't thinking about validation, since I'm ignoring the 'name' >>> attribute. >>> >>> This is solely a readability issue, for the mzML and for MSData client >>> code. >>> >>> >>> Darren >>> >>> >>> -----Original Message----- >>> From: psi...@li... >>> [mailto:psi...@li...] On Behalf Of Joshua >>> Tasman >>> Sent: Wednesday, February 06, 2008 12:00 PM >>> To: Mass spectrometry standard development >>> Subject: Re: [Psidev-ms-dev] CV param readability >>> >>> Hi Darren, >>> >>> Speaking only for myself, I think that the "name" attribute should be >>> optional in the file and not interfere with validation. I've never >>> understood why the text string needs to exactly match the CV for >>> validation; someone one the list had brought up other languages, etc. >>> But I think it came up on the list before, and requiring strict mapping >>> between accession numbers and text string seemed to be important for the >>> format. >>> >>> At the least, acronyms would require additional 'mapping files' or >>> something similar to be added to the specification, and the validator to >>> be updated. Maybe someone more familiar with these tasks could step in. >>> Maybe the CV could be expanded so that every entry had an additional >>> "acronym" field. This brings up other questions, like would uniqueness >>> be enforced, etc? >>> >>> Josh >>> >>> >>> Kessner, Darren E. wrote: >>> >>>> I would like to propose using standard acronyms in the CV term names >>>> when it is clear what they mean. >>>> >>>> >>>> >>>> We currently have: >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted >>>> >>> laser >>> >>>> desorption ionization" value=""/> >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform >>>> >>> ion >>> >>>> cyclotron resonance mass spectrometer" value=""/> >>>> >>>> >>>> >>>> I think this is more readable: >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" >>>> >>> value=""/> >>> >>>> >>>> >>>> The full name can still be available in the term description field. >>>> >>>> >>>> >>>> I have an ulterior motive for this -- in the code generation of the >>>> MSData library, the above terms become constants: >>>> >>>> MS_matrix_assisted_laser_desorption_ionization = 1000075, >>>> >>>> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = >>>> 1000079, >>>> >>>> >>>> >>>> But I think the following is more programmer-friendly: >>>> >>>> MS_MALDI = 1000075, >>>> >>>> MS_FT_ICR_MS = 1000079, >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Darren >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Darren Kessner >>>> >>>> Scientific Programmer >>>> >>>> Dar...@cs... <mailto:Dar...@cs...> >>>> >>>> 310-423-9538 >>>> >>>> >>>> >>>> Spielberg Family Center for Applied Proteomics >>>> >>>> Cedars-Sinai Medical Center >>>> >>>> http://www.sfcap.cshs.org/ >>>> >>>> >>>> >>>> >>>> >>>> IMPORTANT WARNING: This message is intended for the use of the person >>>> >>> or >>> >>>> entity to which it is addressed and may contain information that is >>>> privileged and confidential, the disclosure of which is governed by >>>> applicable law. If the reader of this message is not the intended >>>> recipient, or the employee or agent responsible for delivering it to >>>> >>> the >>> >>>> intended recipient, you are hereby notified that any dissemination, >>>> distribution or copying of this information is STRICTLY PROHIBITED. >>>> >>>> If you have received this message in error, please notify us >>>> >>> immediately >>> >>>> by calling (310) 423-6428 and destroy the related message. Thank You >>>> >>> for >>> >>>> your cooperation. >>>> >>>> >>>> >>>> >>> ------------------------------------------------------------------------ >>> ------------------------------------------------------------------------ >>> - >>> >>>> This SF.net email is sponsored by: Microsoft >>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>> >>>> >>>> >>>> >>> ------------------------------------------------------------------------ >>> >>>> _______________________________________________ >>>> Psidev-ms-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>>> >>> ------------------------------------------------------------------------ >>> - >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by >>> applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. >>> >>> If you have received this message in error, please notify us immediately >>> by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. >>> >>> ------------------------------------------------------------------------- >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> >> > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > |
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From: Kessner, D. E. <Dar...@cs...> - 2008-02-07 16:56:43
|
Thank you to everyone for clearing up the issue for me! Darren -----Original Message----- From: psi...@li... [mailto:psi...@li...] On Behalf Of jtasman Sent: Thursday, February 07, 2008 7:51 AM To: len...@eb...; Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] CV param readability Great, thanks for clearing that up. I must have been remembering a previous version of the validator. Josh Lennart Martens wrote: > Hi Josh, > > > >> Yes, but the official validator will complain if the 'name' string doesn't exactly match the CV, capitalization included. >> > > This is incorrect (I actually tested it with version 0.99.1 of the > semantic mzML validator we wrote and distributed in the kit). > > The tool validates solely on the CV accession numbers, because this is > the only 'fixed quantity' (names have exact synonyms for instance), and > the 'name' attribute is mainly in the standard format for readability > reasons. > > So I think it's acceptable if people use acronyms instead of full > versions, especially if they are present as exact synonyms in the CV. > If the correct CV accession number is used for a term, there should > never be a problem, since it has been decided throughout the PSI a long > time ago (and I think we can all agree on this as well) that the > accession number takes precedence over the name at all times. > > > >> Kessner, Darren E. wrote: >> >>> I wasn't thinking about validation, since I'm ignoring the 'name' >>> attribute. >>> >>> This is solely a readability issue, for the mzML and for MSData client >>> code. >>> >>> >>> Darren >>> >>> >>> -----Original Message----- >>> From: psi...@li... >>> [mailto:psi...@li...] On Behalf Of Joshua >>> Tasman >>> Sent: Wednesday, February 06, 2008 12:00 PM >>> To: Mass spectrometry standard development >>> Subject: Re: [Psidev-ms-dev] CV param readability >>> >>> Hi Darren, >>> >>> Speaking only for myself, I think that the "name" attribute should be >>> optional in the file and not interfere with validation. I've never >>> understood why the text string needs to exactly match the CV for >>> validation; someone one the list had brought up other languages, etc. >>> But I think it came up on the list before, and requiring strict mapping >>> between accession numbers and text string seemed to be important for the >>> format. >>> >>> At the least, acronyms would require additional 'mapping files' or >>> something similar to be added to the specification, and the validator to >>> be updated. Maybe someone more familiar with these tasks could step in. >>> Maybe the CV could be expanded so that every entry had an additional >>> "acronym" field. This brings up other questions, like would uniqueness >>> be enforced, etc? >>> >>> Josh >>> >>> >>> Kessner, Darren E. wrote: >>> >>>> I would like to propose using standard acronyms in the CV term names >>>> when it is clear what they mean. >>>> >>>> >>>> >>>> We currently have: >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted >>>> >>> laser >>> >>>> desorption ionization" value=""/> >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform >>>> >>> ion >>> >>>> cyclotron resonance mass spectrometer" value=""/> >>>> >>>> >>>> >>>> I think this is more readable: >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" >>>> >>> value=""/> >>> >>>> >>>> >>>> The full name can still be available in the term description field. >>>> >>>> >>>> >>>> I have an ulterior motive for this -- in the code generation of the >>>> MSData library, the above terms become constants: >>>> >>>> MS_matrix_assisted_laser_desorption_ionization = 1000075, >>>> >>>> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = >>>> 1000079, >>>> >>>> >>>> >>>> But I think the following is more programmer-friendly: >>>> >>>> MS_MALDI = 1000075, >>>> >>>> MS_FT_ICR_MS = 1000079, >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Darren >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Darren Kessner >>>> >>>> Scientific Programmer >>>> >>>> Dar...@cs... <mailto:Dar...@cs...> >>>> >>>> 310-423-9538 >>>> >>>> >>>> >>>> Spielberg Family Center for Applied Proteomics >>>> >>>> Cedars-Sinai Medical Center >>>> >>>> http://www.sfcap.cshs.org/ >>>> >>>> >>>> >>>> >>>> >>>> IMPORTANT WARNING: This message is intended for the use of the person >>>> >>> or >>> >>>> entity to which it is addressed and may contain information that is >>>> privileged and confidential, the disclosure of which is governed by >>>> applicable law. If the reader of this message is not the intended >>>> recipient, or the employee or agent responsible for delivering it to >>>> >>> the >>> >>>> intended recipient, you are hereby notified that any dissemination, >>>> distribution or copying of this information is STRICTLY PROHIBITED. >>>> >>>> If you have received this message in error, please notify us >>>> >>> immediately >>> >>>> by calling (310) 423-6428 and destroy the related message. Thank You >>>> >>> for >>> >>>> your cooperation. >>>> >>>> >>>> >>>> >>> ------------------------------------------------------------------------ >>> ------------------------------------------------------------------------ >>> - >>> >>>> This SF.net email is sponsored by: Microsoft >>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>> >>>> >>>> >>>> >>> ------------------------------------------------------------------------ >>> >>>> _______________________________________________ >>>> Psidev-ms-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>>> >>> ------------------------------------------------------------------------ >>> - >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by >>> applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. >>> >>> If you have received this message in error, please notify us immediately >>> by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. >>> >>> ------------------------------------------------------------------------ - >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>> >> ------------------------------------------------------------------------ - >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> >> > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > ------------------------------------------------------------------------ - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. If you have received this message in error, please notify us immediately by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. |
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From: Eric D. <ede...@sy...> - 2008-02-07 17:21:15
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The simple Perl XML validator that is distributed in the kit does check to see if the cv param names match the id's. It would be nice if this functionality could be added to the main validator. > -----Original Message----- > From: psi...@li... [mailto:psidev-ms-dev- > bo...@li...] On Behalf Of jtasman > Sent: Thursday, February 07, 2008 7:51 AM > To: len...@eb...; Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] CV param readability > > Great, thanks for clearing that up. I must have been remembering a > previous version of the validator. > > Josh > > Lennart Martens wrote: > > Hi Josh, > > > > > > > >> Yes, but the official validator will complain if the 'name' string > doesn't exactly match the CV, capitalization included. > >> > > > > This is incorrect (I actually tested it with version 0.99.1 of the > > semantic mzML validator we wrote and distributed in the kit). > > > > The tool validates solely on the CV accession numbers, because this is > > the only 'fixed quantity' (names have exact synonyms for instance), and > > the 'name' attribute is mainly in the standard format for readability > > reasons. > > > > So I think it's acceptable if people use acronyms instead of full > > versions, especially if they are present as exact synonyms in the CV. > > If the correct CV accession number is used for a term, there should > > never be a problem, since it has been decided throughout the PSI a long > > time ago (and I think we can all agree on this as well) that the > > accession number takes precedence over the name at all times. > > > > > > > >> Kessner, Darren E. wrote: > >> > >>> I wasn't thinking about validation, since I'm ignoring the 'name' > >>> attribute. > >>> > >>> This is solely a readability issue, for the mzML and for MSData client > >>> code. > >>> > >>> > >>> Darren > >>> > >>> > >>> -----Original Message----- > >>> From: psi...@li... > >>> [mailto:psi...@li...] On Behalf Of > Joshua > >>> Tasman > >>> Sent: Wednesday, February 06, 2008 12:00 PM > >>> To: Mass spectrometry standard development > >>> Subject: Re: [Psidev-ms-dev] CV param readability > >>> > >>> Hi Darren, > >>> > >>> Speaking only for myself, I think that the "name" attribute should be > >>> optional in the file and not interfere with validation. I've never > >>> understood why the text string needs to exactly match the CV for > >>> validation; someone one the list had brought up other languages, etc. > >>> But I think it came up on the list before, and requiring strict > mapping > >>> between accession numbers and text string seemed to be important for > the > >>> format. > >>> > >>> At the least, acronyms would require additional 'mapping files' or > >>> something similar to be added to the specification, and the validator > to > >>> be updated. Maybe someone more familiar with these tasks could step > in. > >>> Maybe the CV could be expanded so that every entry had an additional > >>> "acronym" field. This brings up other questions, like would > uniqueness > >>> be enforced, etc? > >>> > >>> Josh > >>> > >>> > >>> Kessner, Darren E. wrote: > >>> > >>>> I would like to propose using standard acronyms in the CV term names > >>>> when it is clear what they mean. > >>>> > >>>> > >>>> > >>>> We currently have: > >>>> > >>>> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted > >>>> > >>> laser > >>> > >>>> desorption ionization" value=""/> > >>>> > >>>> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform > >>>> > >>> ion > >>> > >>>> cyclotron resonance mass spectrometer" value=""/> > >>>> > >>>> > >>>> > >>>> I think this is more readable: > >>>> > >>>> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> > >>>> > >>>> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" > >>>> > >>> value=""/> > >>> > >>>> > >>>> > >>>> The full name can still be available in the term description field. > >>>> > >>>> > >>>> > >>>> I have an ulterior motive for this -- in the code generation of the > >>>> MSData library, the above terms become constants: > >>>> > >>>> MS_matrix_assisted_laser_desorption_ionization = 1000075, > >>>> > >>>> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = > >>>> 1000079, > >>>> > >>>> > >>>> > >>>> But I think the following is more programmer-friendly: > >>>> > >>>> MS_MALDI = 1000075, > >>>> > >>>> MS_FT_ICR_MS = 1000079, > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> Darren > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> Darren Kessner > >>>> > >>>> Scientific Programmer > >>>> > >>>> Dar...@cs... <mailto:Dar...@cs...> > >>>> > >>>> 310-423-9538 > >>>> > >>>> > >>>> > >>>> Spielberg Family Center for Applied Proteomics > >>>> > >>>> Cedars-Sinai Medical Center > >>>> > >>>> http://www.sfcap.cshs.org/ > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> IMPORTANT WARNING: This message is intended for the use of the person > >>>> > >>> or > >>> > >>>> entity to which it is addressed and may contain information that is > >>>> privileged and confidential, the disclosure of which is governed by > >>>> applicable law. If the reader of this message is not the intended > >>>> recipient, or the employee or agent responsible for delivering it to > >>>> > >>> the > >>> > >>>> intended recipient, you are hereby notified that any dissemination, > >>>> distribution or copying of this information is STRICTLY PROHIBITED. > >>>> > >>>> If you have received this message in error, please notify us > >>>> > >>> immediately > >>> > >>>> by calling (310) 423-6428 and destroy the related message. Thank You > >>>> > >>> for > >>> > >>>> your cooperation. > >>>> > >>>> > >>>> > >>>> > >>> ---------------------------------------------------------------------- > -- > >>> ---------------------------------------------------------------------- > -- > >>> - > >>> > >>>> This SF.net email is sponsored by: Microsoft > >>>> Defy all challenges. Microsoft(R) Visual Studio 2008. > >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>>> > >>>> > >>>> > >>>> > >>> ---------------------------------------------------------------------- > -- > >>> > >>>> _______________________________________________ > >>>> Psidev-ms-dev mailing list > >>>> Psi...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > >>>> > >>> ---------------------------------------------------------------------- > -- > >>> - > >>> This SF.net email is sponsored by: Microsoft > >>> Defy all challenges. Microsoft(R) Visual Studio 2008. > >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>> _______________________________________________ > >>> Psidev-ms-dev mailing list > >>> Psi...@li... > >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > >>> IMPORTANT WARNING: This message is intended for the use of the person > or entity to which it is addressed and may contain information that is > privileged and confidential, the disclosure of which is governed by > >>> applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivering it to the > intended recipient, you are hereby notified that any dissemination, > distribution or copying of this information is STRICTLY PROHIBITED. > >>> > >>> If you have received this message in error, please notify us > immediately > >>> by calling (310) 423-6428 and destroy the related message. Thank You > for your cooperation. > >>> > >>> ---------------------------------------------------------------------- > --- > >>> This SF.net email is sponsored by: Microsoft > >>> Defy all challenges. Microsoft(R) Visual Studio 2008. > >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>> _______________________________________________ > >>> Psidev-ms-dev mailing list > >>> Psi...@li... > >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > >>> > >> ----------------------------------------------------------------------- > -- > >> This SF.net email is sponsored by: Microsoft > >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> _______________________________________________ > >> Psidev-ms-dev mailing list > >> Psi...@li... > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > >> > >> > > > > ------------------------------------------------------------------------ > - > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > Psidev-ms-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > > > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Fredrik L. <Fre...@im...> - 2008-02-07 18:09:42
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Yes, consider the following examples: <cvParam cvLabel="MS" accession="MS:1000079" name="q-tof micro" value=""/> <cvParam cvLabel="MS" accession="MS:1000079" name="customized FT-ICR" value=""/> In my view these are not valid, since the accession numbers and names are not matching. If the mzML definition allows anything to be written into the name field it has to be clearly specified. I would guess that most people that inspect the file manually would only look at the name field, while software should use the accession field, this could clearly lead to errors. Could a possible definition of a valid cvParam be that the name field must match any of the exact synonyms in the CV version that it was made from? Fredrik Eric Deutsch skrev: > The simple Perl XML validator that is distributed in the kit does check > to see if the cv param names match the id's. It would be nice if this > functionality could be added to the main validator. > > > >> -----Original Message----- >> From: psi...@li... >> > [mailto:psidev-ms-dev- > >> bo...@li...] On Behalf Of jtasman >> Sent: Thursday, February 07, 2008 7:51 AM >> To: len...@eb...; Mass spectrometry standard development >> Subject: Re: [Psidev-ms-dev] CV param readability >> >> Great, thanks for clearing that up. I must have been remembering a >> previous version of the validator. >> >> Josh >> >> Lennart Martens wrote: >> >>> Hi Josh, >>> >>> >>> >>> >>>> Yes, but the official validator will complain if the 'name' string >>>> >> doesn't exactly match the CV, capitalization included. >> >>> This is incorrect (I actually tested it with version 0.99.1 of the >>> semantic mzML validator we wrote and distributed in the kit). >>> >>> The tool validates solely on the CV accession numbers, because this >>> > is > >>> the only 'fixed quantity' (names have exact synonyms for instance), >>> > and > >>> the 'name' attribute is mainly in the standard format for >>> > readability > >>> reasons. >>> >>> So I think it's acceptable if people use acronyms instead of full >>> versions, especially if they are present as exact synonyms in the >>> > CV. > >>> If the correct CV accession number is used for a term, there should >>> never be a problem, since it has been decided throughout the PSI a >>> > long > >>> time ago (and I think we can all agree on this as well) that the >>> accession number takes precedence over the name at all times. >>> >>> >>> >>> >>>> Kessner, Darren E. wrote: >>>> >>>> >>>>> I wasn't thinking about validation, since I'm ignoring the 'name' >>>>> attribute. >>>>> >>>>> This is solely a readability issue, for the mzML and for MSData >>>>> > client > >>>>> code. >>>>> >>>>> >>>>> Darren >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: psi...@li... >>>>> [mailto:psi...@li...] On Behalf Of >>>>> >> Joshua >> >>>>> Tasman >>>>> Sent: Wednesday, February 06, 2008 12:00 PM >>>>> To: Mass spectrometry standard development >>>>> Subject: Re: [Psidev-ms-dev] CV param readability >>>>> >>>>> Hi Darren, >>>>> >>>>> Speaking only for myself, I think that the "name" attribute should >>>>> > be > >>>>> optional in the file and not interfere with validation. I've >>>>> > never > >>>>> understood why the text string needs to exactly match the CV for >>>>> validation; someone one the list had brought up other languages, >>>>> > etc. > >>>>> But I think it came up on the list before, and requiring strict >>>>> >> mapping >> >>>>> between accession numbers and text string seemed to be important >>>>> > for > >> the >> >>>>> format. >>>>> >>>>> At the least, acronyms would require additional 'mapping files' or >>>>> something similar to be added to the specification, and the >>>>> > validator > >> to >> >>>>> be updated. Maybe someone more familiar with these tasks could >>>>> > step > >> in. >> >>>>> Maybe the CV could be expanded so that every entry had an >>>>> > additional > >>>>> "acronym" field. This brings up other questions, like would >>>>> >> uniqueness >> >>>>> be enforced, etc? >>>>> >>>>> Josh >>>>> >>>>> >>>>> Kessner, Darren E. wrote: >>>>> >>>>> >>>>>> I would like to propose using standard acronyms in the CV term >>>>>> > names > >>>>>> when it is clear what they mean. >>>>>> >>>>>> >>>>>> >>>>>> We currently have: >>>>>> >>>>>> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix >>>>>> > assisted > >>>>> laser >>>>> >>>>> >>>>>> desorption ionization" value=""/> >>>>>> >>>>>> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier >>>>>> > transform > >>>>> ion >>>>> >>>>> >>>>>> cyclotron resonance mass spectrometer" value=""/> >>>>>> >>>>>> >>>>>> >>>>>> I think this is more readable: >>>>>> >>>>>> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" >>>>>> > value=""/> > >>>>>> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" >>>>>> >>>>>> >>>>> value=""/> >>>>> >>>>> >>>>>> The full name can still be available in the term description >>>>>> > field. > >>>>>> >>>>>> I have an ulterior motive for this -- in the code generation of >>>>>> > the > >>>>>> MSData library, the above terms become constants: >>>>>> >>>>>> MS_matrix_assisted_laser_desorption_ionization = 1000075, >>>>>> >>>>>> >>>>>> > MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = > >>>>>> 1000079, >>>>>> >>>>>> >>>>>> >>>>>> But I think the following is more programmer-friendly: >>>>>> >>>>>> MS_MALDI = 1000075, >>>>>> >>>>>> MS_FT_ICR_MS = 1000079, >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Darren >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Darren Kessner >>>>>> >>>>>> Scientific Programmer >>>>>> >>>>>> Dar...@cs... <mailto:Dar...@cs...> >>>>>> >>>>>> 310-423-9538 >>>>>> >>>>>> >>>>>> >>>>>> Spielberg Family Center for Applied Proteomics >>>>>> >>>>>> Cedars-Sinai Medical Center >>>>>> >>>>>> http://www.sfcap.cshs.org/ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> IMPORTANT WARNING: This message is intended for the use of the >>>>>> > person > >>>>> or >>>>> >>>>> >>>>>> entity to which it is addressed and may contain information that >>>>>> > is > >>>>>> privileged and confidential, the disclosure of which is governed >>>>>> > by > >>>>>> applicable law. If the reader of this message is not the intended >>>>>> recipient, or the employee or agent responsible for delivering it >>>>>> > to > >>>>> the >>>>> >>>>> >>>>>> intended recipient, you are hereby notified that any >>>>>> > dissemination, > >>>>>> distribution or copying of this information is STRICTLY >>>>>> > PROHIBITED. > >>>>>> If you have received this message in error, please notify us >>>>>> >>>>>> >>>>> immediately >>>>> >>>>> >>>>>> by calling (310) 423-6428 and destroy the related message. Thank >>>>>> > You > >>>>> for >>>>> >>>>> >>>>>> your cooperation. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> > ---------------------------------------------------------------------- > >> -- >> > ---------------------------------------------------------------------- > >> -- >> >>>>> - >>>>> >>>>> >>>>>> This SF.net email is sponsored by: Microsoft >>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> > ---------------------------------------------------------------------- > >> -- >> >>>>>> _______________________________________________ >>>>>> Psidev-ms-dev mailing list >>>>>> Psi...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>>>>> >>>>>> > ---------------------------------------------------------------------- > >> -- >> >>>>> - >>>>> This SF.net email is sponsored by: Microsoft >>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>> _______________________________________________ >>>>> Psidev-ms-dev mailing list >>>>> Psi...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>>>> IMPORTANT WARNING: This message is intended for the use of the >>>>> > person > >> or entity to which it is addressed and may contain information that is >> privileged and confidential, the disclosure of which is governed by >> >>>>> applicable law. If the reader of this message is not the intended >>>>> >> recipient, or the employee or agent responsible for delivering it to >> > the > >> intended recipient, you are hereby notified that any dissemination, >> distribution or copying of this information is STRICTLY PROHIBITED. >> >>>>> If you have received this message in error, please notify us >>>>> >> immediately >> >>>>> by calling (310) 423-6428 and destroy the related message. Thank >>>>> > You > >> for your cooperation. >> >>>>> > ---------------------------------------------------------------------- > >> --- >> >>>>> This SF.net email is sponsored by: Microsoft >>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>> _______________________________________________ >>>>> Psidev-ms-dev mailing list >>>>> Psi...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>>>> >>>>> > ----------------------------------------------------------------------- > >> -- >> >>>> This SF.net email is sponsored by: Microsoft >>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>> _______________________________________________ >>>> Psidev-ms-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>>> >>>> >>>> >>> > ------------------------------------------------------------------------ > >> - >> >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>> >>> >> >> > ------------------------------------------------------------------------ > - > >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > |
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From: Rune S. P. <mai...@ph...> - 2008-02-06 20:02:27
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Kessner, Darren E. skrev: > > I would like to propose using standard acronyms in the CV term names > when it is clear what they mean. > Aren't there already support for synonyms in the CV. So shouldn't this already be allowed? -- Regards Rune |
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