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From: Yasset Perez-R. <yp...@eb...> - 2015-10-15 08:48:00
|
My comments here: On 14/10/2015 17:01, Mathias Walzer wrote: > Hi all, > > One thing I'd like to bring up as an idea: > since there is migratory adaption to be made by most CV consumers due to the GitHub move anyway, > might it not also be good to create an own repository for the CV? > -It is not only used in the mzML domain (predominantly though), so it is not the most intuitive place to look for it. > -We may have a readme.md for the repository or even a github page *1- Agree with this, but only @Gerhard can say how difficult is to maintain this and actually make sense because will make more stable the mzML repo because most of the changes in the current structure are associated with CV terms. *2- My proposal is two start using the github channel for this topics, we can add an issue in the github about this idea and with the current notation +1, etc support this idea. @Mathias I will open the issue for you ;) > -And CV issues would not clog the mzML repository > -It would make it way easier to propose changes (fork & branch + change -> pullrequest: github shows the diff nicely rendered on the pullrequest page, where additional comments and discussion can be made.) > > furthermore, a small remark, if you want to use direct web file access via your programs > https://raw.githubusercontent.com/HUPO-PSI/mzML/master/cv/psi-ms.obo > might be the more robust choice. Or https://raw.githubusercontent.com/HUPO-PSI/ControlledVocabulary/master/... if we dare this additional step. Going in this direction we should try to move out of the repositories the validators, what I did at eh very beginning was to keep the previous SF/GC structure but now we can do some refinements like move the *official validators* to their own repositories making even more stable the file format repos. Also the validators should be integrated with github tools: *travis*, etc. > > In any case, thanks for the work on the CV, Gerhard! > > best, > Mathias > > ----- Original Message ----- > From: "Yasset Perez-Riverol" <yp...@eb...> > To: "mayerg97" <ger...@ru...>, psi...@li..., psi...@li..., psi...@li... > Sent: Monday, 12 October, 2015 4:37:47 PM > Subject: Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo > > > Thanks Gerhard: > Can you check if using the github issues you can trace and announce the changes in the new github repo!!! > Regards > Yasset > > On 12/10/2015 15:16, mayerg97 wrote: > > > Dear proteomics community, > > sorry for any inconveniencies about the last (3.79.0) psi-ms.obo update. > I updated it now for the last time at both the old SourceForge and the new GitHub location. > > In future I will only update the new location at GitHub. So change your links in case you > parse in the ps-ms.obo file by your programs. > > The new link is > https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo > > I also updated the links pointing tp psi-ms.obo at BioPortal and requested the OBOFoundry link update. > > In addition I updated the mzIdentML validator to version 1.4.14 (new Apache xerces library, so it runs now also under Java 8). > The link to the mzIdentML validator is: > https://github.com/HUPO-PSI/mzIdentML/blob/master/validator/trunk/mzIdentMLValidator/mzIdentMLValidator_GUI_v1.4.14-SNAPSHOT.zip > > Best Regards, > Gerhard > > > Am 09.10.2015 um 20:13 schrieb Eric Deutsch: > > > > > > Thanks for pointing this out, Matt. > > So I’m unsure of what the situation here is. There is a movement in progress to move everything to GitHub and this may already have been completed. I am unsure of where this new version went. Did it go into SourceForge CVS? Did it go into GitHub? What is our plan going forward here? It would be nice to be a little more explicit and noisy about that is happening. I have automated processes here at ISB that pull the latest CVs from various version controls automatically and I need to update these, but I’m wondering when to do this. I think nearly all PSI related materials are being or have moved to GitHub. > > So I expect there will be some forthcoming announcements very soon that will describe what has moved and what has not and what version control processes need to be changed. > > Thanks, > > Eric > > > > > > From: Chambers, Matthew [mailto: mat...@gm... ] > Sent: Friday, October 09, 2015 10:31 AM > To: psi...@li... > Subject: Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo > > > > Thanks Gerhard. Can you commit the update to CVS as well? > > Thanks, > -Matt > > > > > On 10/7/2015 3:31 AM, mayerg97 wrote: > > > > Dear proteomics community, > > attached you find the new version 3.79 of the psi-ms.obo file. > > > Changed CV terms in version 3.79 of psi-ms.obo: > =============================================== > ************ Replaced all "AB Sciex" terms by "SCIEX" > > ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF > [Term] > id: MS:1001482 > name: 5800 TOF/TOF > def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > > > New CV terms in version 3.79.0 of psi-ms.obo: > ============================================= > ************ New terms for Andromeda result file > [Term] > id: MS:1002576 > name: Andromeda result file > def: "Andromeda result file output format." [PSI:PI] > is_a: MS:1001040 ! intermediate analysis format > > ************ New terms for Sciex instruments > [Term] > id: MS:1002577 > name: 2000 QTRAP > def: "SCIEX 2000 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002578 > name: 2500 QTRAP > def: "SCIEX 2500 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002579 > name: 3500 QTRAP > def: "SCIEX 3500 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002580 > name: QTRAP 4500 > def: "SCIEX QTRAP 4500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002581 > name: QTRAP 6500 > def: "SCIEX QTRAP 6500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002582 > name: QTRAP 6500+ > def: "SCIEX QTRAP 6500+." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002583 > name: TripleTOF 4600 > def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002584 > name: TripleTOF 5600+ > def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002585 > name: API 100 > def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002586 > name: API 100LC > def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002587 > name: API 165 > def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002588 > name: API 300 > def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002589 > name: API 350 > def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002590 > name: API 365 > def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002591 > name: Triple Quad 3500 > def: "SCIEX Triple Quad 3500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002592 > name: Triple Quad 4500 > def: "SCIEX Triple Quad 4500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002593 > name: Triple Quad 5500 > def: "SCIEX Triple Quad 5500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002594 > name: Triple Quad 6500 > def: "SCIEX Triple Quad 6500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002595 > name: Triple Quad 6500+ > def: "SCIEX Triple Quad 6500+." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > Best Regards, > Gerhard > > -- Yasset Perez-Riverol PhD. Bioinformatician Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
|
From: Julian U. <jul...@ru...> - 2015-10-15 07:42:33
|
Hi, I support Mathias' suggestion of creating an own repository for the CV. Also the idea with the fork and pull-requests sound very promising. Gerhard usually answers mails fast and incorporates the changes, but using the pull-requests might make it even easier for him? As long, as they don't break the structure of the file, which could be nicely explained in an README.md Gerhard, what do you think of this? Regards, Julian -----Ursprüngliche Nachricht----- Von: Mathias Walzer [mailto:wa...@in...] Gesendet: 14 October 2015 18:02 An: psi...@li...; psi...@li...; psi...@li... Betreff: Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo Hi all, One thing I'd like to bring up as an idea: since there is migratory adaption to be made by most CV consumers due to the GitHub move anyway, might it not also be good to create an own repository for the CV? -It is not only used in the mzML domain (predominantly though), so it is not the most intuitive place to look for it. -We may have a readme.md for the repository or even a github page -And CV issues would not clog the mzML repository -It would make it way easier to propose changes (fork & branch + change -> pullrequest: github shows the diff nicely rendered on the pullrequest page, where additional comments and discussion can be made.) furthermore, a small remark, if you want to use direct web file access via your programs https://raw.githubusercontent.com/HUPO-PSI/mzML/master/cv/psi-ms.obo might be the more robust choice. Or https://raw.githubusercontent.com/HUPO-PSI/ControlledVocabulary/master/... if we dare this additional step. In any case, thanks for the work on the CV, Gerhard! best, Mathias ----- Original Message ----- From: "Yasset Perez-Riverol" <yp...@eb...> To: "mayerg97" <ger...@ru...>, psi...@li..., psi...@li..., psi...@li... Sent: Monday, 12 October, 2015 4:37:47 PM Subject: Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo Thanks Gerhard: Can you check if using the github issues you can trace and announce the changes in the new github repo!!! Regards Yasset On 12/10/2015 15:16, mayerg97 wrote: Dear proteomics community, sorry for any inconveniencies about the last (3.79.0) psi-ms.obo update. I updated it now for the last time at both the old SourceForge and the new GitHub location. In future I will only update the new location at GitHub. So change your links in case you parse in the ps-ms.obo file by your programs. The new link is https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo I also updated the links pointing tp psi-ms.obo at BioPortal and requested the OBOFoundry link update. In addition I updated the mzIdentML validator to version 1.4.14 (new Apache xerces library, so it runs now also under Java 8). The link to the mzIdentML validator is: https://github.com/HUPO-PSI/mzIdentML/blob/master/validator/trunk/mzIdentMLValidator/mzIdentMLValidator_GUI_v1.4.14-SNAPSHOT.zip Best Regards, Gerhard Am 09.10.2015 um 20:13 schrieb Eric Deutsch: Thanks for pointing this out, Matt. So I’m unsure of what the situation here is. There is a movement in progress to move everything to GitHub and this may already have been completed. I am unsure of where this new version went. Did it go into SourceForge CVS? Did it go into GitHub? What is our plan going forward here? It would be nice to be a little more explicit and noisy about that is happening. I have automated processes here at ISB that pull the latest CVs from various version controls automatically and I need to update these, but I’m wondering when to do this. I think nearly all PSI related materials are being or have moved to GitHub. So I expect there will be some forthcoming announcements very soon that will describe what has moved and what has not and what version control processes need to be changed. Thanks, Eric From: Chambers, Matthew [mailto: mat...@gm... ] Sent: Friday, October 09, 2015 10:31 AM To: psi...@li... Subject: Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo Thanks Gerhard. Can you commit the update to CVS as well? Thanks, -Matt On 10/7/2015 3:31 AM, mayerg97 wrote: Dear proteomics community, attached you find the new version 3.79 of the psi-ms.obo file. Changed CV terms in version 3.79 of psi-ms.obo: =============================================== ************ Replaced all "AB Sciex" terms by "SCIEX" ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF [Term] id: MS:1001482 name: 5800 TOF/TOF def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model New CV terms in version 3.79.0 of psi-ms.obo: ============================================= ************ New terms for Andromeda result file [Term] id: MS:1002576 name: Andromeda result file def: "Andromeda result file output format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format ************ New terms for Sciex instruments [Term] id: MS:1002577 name: 2000 QTRAP def: "SCIEX 2000 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002578 name: 2500 QTRAP def: "SCIEX 2500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002579 name: 3500 QTRAP def: "SCIEX 3500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002580 name: QTRAP 4500 def: "SCIEX QTRAP 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002581 name: QTRAP 6500 def: "SCIEX QTRAP 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002582 name: QTRAP 6500+ def: "SCIEX QTRAP 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002583 name: TripleTOF 4600 def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002584 name: TripleTOF 5600+ def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002585 name: API 100 def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002586 name: API 100LC def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002587 name: API 165 def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002588 name: API 300 def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002589 name: API 350 def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002590 name: API 365 def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002591 name: Triple Quad 3500 def: "SCIEX Triple Quad 3500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002592 name: Triple Quad 4500 def: "SCIEX Triple Quad 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002593 name: Triple Quad 5500 def: "SCIEX Triple Quad 5500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002594 name: Triple Quad 6500 def: "SCIEX Triple Quad 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002595 name: Triple Quad 6500+ def: "SCIEX Triple Quad 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model Best Regards, Gerhard -- -- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru... www.medizinisches-proteom-center.de ------------------------------------------------------------------------------ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- -- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru... www.medizinisches-proteom-center.de ------------------------------------------------------------------------------ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Bioinformatician Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol ------------------------------------------------------------------------------ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev ------------------------------------------------------------------------------ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Mathias W. <wa...@in...> - 2015-10-14 16:02:18
|
Hi all, One thing I'd like to bring up as an idea: since there is migratory adaption to be made by most CV consumers due to the GitHub move anyway, might it not also be good to create an own repository for the CV? -It is not only used in the mzML domain (predominantly though), so it is not the most intuitive place to look for it. -We may have a readme.md for the repository or even a github page -And CV issues would not clog the mzML repository -It would make it way easier to propose changes (fork & branch + change -> pullrequest: github shows the diff nicely rendered on the pullrequest page, where additional comments and discussion can be made.) furthermore, a small remark, if you want to use direct web file access via your programs https://raw.githubusercontent.com/HUPO-PSI/mzML/master/cv/psi-ms.obo might be the more robust choice. Or https://raw.githubusercontent.com/HUPO-PSI/ControlledVocabulary/master/... if we dare this additional step. In any case, thanks for the work on the CV, Gerhard! best, Mathias ----- Original Message ----- From: "Yasset Perez-Riverol" <yp...@eb...> To: "mayerg97" <ger...@ru...>, psi...@li..., psi...@li..., psi...@li... Sent: Monday, 12 October, 2015 4:37:47 PM Subject: Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo Thanks Gerhard: Can you check if using the github issues you can trace and announce the changes in the new github repo!!! Regards Yasset On 12/10/2015 15:16, mayerg97 wrote: Dear proteomics community, sorry for any inconveniencies about the last (3.79.0) psi-ms.obo update. I updated it now for the last time at both the old SourceForge and the new GitHub location. In future I will only update the new location at GitHub. So change your links in case you parse in the ps-ms.obo file by your programs. The new link is https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo I also updated the links pointing tp psi-ms.obo at BioPortal and requested the OBOFoundry link update. In addition I updated the mzIdentML validator to version 1.4.14 (new Apache xerces library, so it runs now also under Java 8). The link to the mzIdentML validator is: https://github.com/HUPO-PSI/mzIdentML/blob/master/validator/trunk/mzIdentMLValidator/mzIdentMLValidator_GUI_v1.4.14-SNAPSHOT.zip Best Regards, Gerhard Am 09.10.2015 um 20:13 schrieb Eric Deutsch: Thanks for pointing this out, Matt. So I’m unsure of what the situation here is. There is a movement in progress to move everything to GitHub and this may already have been completed. I am unsure of where this new version went. Did it go into SourceForge CVS? Did it go into GitHub? What is our plan going forward here? It would be nice to be a little more explicit and noisy about that is happening. I have automated processes here at ISB that pull the latest CVs from various version controls automatically and I need to update these, but I’m wondering when to do this. I think nearly all PSI related materials are being or have moved to GitHub. So I expect there will be some forthcoming announcements very soon that will describe what has moved and what has not and what version control processes need to be changed. Thanks, Eric From: Chambers, Matthew [mailto: mat...@gm... ] Sent: Friday, October 09, 2015 10:31 AM To: psi...@li... Subject: Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo Thanks Gerhard. Can you commit the update to CVS as well? Thanks, -Matt On 10/7/2015 3:31 AM, mayerg97 wrote: Dear proteomics community, attached you find the new version 3.79 of the psi-ms.obo file. Changed CV terms in version 3.79 of psi-ms.obo: =============================================== ************ Replaced all "AB Sciex" terms by "SCIEX" ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF [Term] id: MS:1001482 name: 5800 TOF/TOF def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model New CV terms in version 3.79.0 of psi-ms.obo: ============================================= ************ New terms for Andromeda result file [Term] id: MS:1002576 name: Andromeda result file def: "Andromeda result file output format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format ************ New terms for Sciex instruments [Term] id: MS:1002577 name: 2000 QTRAP def: "SCIEX 2000 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002578 name: 2500 QTRAP def: "SCIEX 2500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002579 name: 3500 QTRAP def: "SCIEX 3500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002580 name: QTRAP 4500 def: "SCIEX QTRAP 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002581 name: QTRAP 6500 def: "SCIEX QTRAP 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002582 name: QTRAP 6500+ def: "SCIEX QTRAP 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002583 name: TripleTOF 4600 def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002584 name: TripleTOF 5600+ def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002585 name: API 100 def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002586 name: API 100LC def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002587 name: API 165 def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002588 name: API 300 def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002589 name: API 350 def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002590 name: API 365 def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002591 name: Triple Quad 3500 def: "SCIEX Triple Quad 3500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002592 name: Triple Quad 4500 def: "SCIEX Triple Quad 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002593 name: Triple Quad 5500 def: "SCIEX Triple Quad 5500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002594 name: Triple Quad 6500 def: "SCIEX Triple Quad 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002595 name: Triple Quad 6500+ def: "SCIEX Triple Quad 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model Best Regards, Gerhard -- -- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru... www.medizinisches-proteom-center.de ------------------------------------------------------------------------------ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- -- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru... www.medizinisches-proteom-center.de ------------------------------------------------------------------------------ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Bioinformatician Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol ------------------------------------------------------------------------------ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Yasset Perez-R. <yp...@eb...> - 2015-10-12 14:38:01
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Thanks Gerhard: Can you check if using the github issues you can trace and announce the changes in the new github repo!!! Regards Yasset On 12/10/2015 15:16, mayerg97 wrote: > Dear proteomics community, > > sorry for any inconveniencies about the last (3.79.0) psi-ms.obo update. > I updated it now for the last time at both the old SourceForge and the > new GitHub location. > > In future I will only update the new location at GitHub. So change > your links in case you > parse in the ps-ms.obo file by your programs. > > The new link is > https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo > > I also updated the links pointing tp psi-ms.obo at BioPortal and > requested the OBOFoundry link update. > > In addition I updated the mzIdentML validator to version 1.4.14 (new > Apache xerces library, so it runs now also under Java 8). > The link to the mzIdentML validator is: > https://github.com/HUPO-PSI/mzIdentML/blob/master/validator/trunk/mzIdentMLValidator/mzIdentMLValidator_GUI_v1.4.14-SNAPSHOT.zip > > Best Regards, > Gerhard > > Am 09.10.2015 um 20:13 schrieb Eric Deutsch: >> >> Thanks for pointing this out, Matt. >> >> So I'm unsure of what the situation here is. There is a movement in >> progress to move everything to GitHub and this may already have been >> completed. I am unsure of where this new version went. Did it go into >> SourceForge CVS? Did it go into GitHub? What is our plan going >> forward here? It would be nice to be a little more explicit and noisy >> about that is happening. I have automated processes here at ISB that >> pull the latest CVs from various version controls automatically and I >> need to update these, but I'm wondering when to do this. I think >> nearly all PSI related materials are being or have moved to GitHub. >> >> So I expect there will be some forthcoming announcements very soon >> that will describe what has moved and what has not and what version >> control processes need to be changed. >> >> Thanks, >> >> Eric >> >> *From:*Chambers, Matthew [mailto:mat...@gm... >> <mailto:mat...@gm...>] >> *Sent:* Friday, October 09, 2015 10:31 AM >> *To:* psi...@li... >> <mailto:psi...@li...> >> *Subject:* Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo >> >> Thanks Gerhard. Can you commit the update to CVS as well? >> >> Thanks, >> -Matt >> >> On 10/7/2015 3:31 AM, mayerg97 wrote: >> >> Dear proteomics community, >> >> attached you find the new version 3.79 of the psi-ms.obo file. >> >> >> Changed CV terms in version 3.79 of psi-ms.obo: >> =============================================== >> ************ Replaced all "AB Sciex" terms by "SCIEX" >> >> ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF >> [Term] >> id: MS:1001482 >> name: 5800 TOF/TOF >> def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> >> >> New CV terms in version 3.79.0 of psi-ms.obo: >> ============================================= >> ************ New terms for Andromeda result file >> [Term] >> id: MS:1002576 >> name: Andromeda result file >> def: "Andromeda result file output format." [PSI:PI] >> is_a: MS:1001040 ! intermediate analysis format >> >> ************ New terms for Sciex instruments >> [Term] >> id: MS:1002577 >> name: 2000 QTRAP >> def: "SCIEX 2000 QTRAP." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002578 >> name: 2500 QTRAP >> def: "SCIEX 2500 QTRAP." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002579 >> name: 3500 QTRAP >> def: "SCIEX 3500 QTRAP." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002580 >> name: QTRAP 4500 >> def: "SCIEX QTRAP 4500." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002581 >> name: QTRAP 6500 >> def: "SCIEX QTRAP 6500." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002582 >> name: QTRAP 6500+ >> def: "SCIEX QTRAP 6500+." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002583 >> name: TripleTOF 4600 >> def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." >> [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002584 >> name: TripleTOF 5600+ >> def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." >> [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002585 >> name: API 100 >> def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002586 >> name: API 100LC >> def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002587 >> name: API 165 >> def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002588 >> name: API 300 >> def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002589 >> name: API 350 >> def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002590 >> name: API 365 >> def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002591 >> name: Triple Quad 3500 >> def: "SCIEX Triple Quad 3500." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002592 >> name: Triple Quad 4500 >> def: "SCIEX Triple Quad 4500." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002593 >> name: Triple Quad 5500 >> def: "SCIEX Triple Quad 5500." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002594 >> name: Triple Quad 6500 >> def: "SCIEX Triple Quad 6500." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> [Term] >> id: MS:1002595 >> name: Triple Quad 6500+ >> def: "SCIEX Triple Quad 6500+." [PSI:MS] >> is_a: MS:1000121 ! SCIEX instrument model >> >> Best Regards, >> Gerhard >> >> -- >> >> *--* >> >> *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* >> >> *PhD student* >> >> *Medizinisches Proteom-Center* >> >> *DEPARTMENT Medical Bioinformatics* >> >> *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum >> >> *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 >> >> *E-mail *ger...@ru... >> >> www.medizinisches-proteom-center.de >> >> >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- > > *--* > > *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum > > *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 > > *E-mail***ger...@ru... > > www.medizinisches-proteom-center.de > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Bioinformatician Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: mayerg97 <ger...@ru...> - 2015-10-12 14:17:16
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Dear proteomics community, sorry for any inconveniencies about the last (3.79.0) psi-ms.obo update. I updated it now for the last time at both the old SourceForge and the new GitHub location. In future I will only update the new location at GitHub. So change your links in case you parse in the ps-ms.obo file by your programs. The new link is https://github.com/HUPO-PSI/mzML/blob/master/cv/psi-ms.obo I also updated the links pointing tp psi-ms.obo at BioPortal and requested the OBOFoundry link update. In addition I updated the mzIdentML validator to version 1.4.14 (new Apache xerces library, so it runs now also under Java 8). The link to the mzIdentML validator is: https://github.com/HUPO-PSI/mzIdentML/blob/master/validator/trunk/mzIdentMLValidator/mzIdentMLValidator_GUI_v1.4.14-SNAPSHOT.zip Best Regards, Gerhard Am 09.10.2015 um 20:13 schrieb Eric Deutsch: > > Thanks for pointing this out, Matt. > > So I’m unsure of what the situation here is. There is a movement in > progress to move everything to GitHub and this may already have been > completed. I am unsure of where this new version went. Did it go into > SourceForge CVS? Did it go into GitHub? What is our plan going forward > here? It would be nice to be a little more explicit and noisy about > that is happening. I have automated processes here at ISB that pull > the latest CVs from various version controls automatically and I need > to update these, but I’m wondering when to do this. I think nearly all > PSI related materials are being or have moved to GitHub. > > So I expect there will be some forthcoming announcements very soon > that will describe what has moved and what has not and what version > control processes need to be changed. > > Thanks, > > Eric > > *From:*Chambers, Matthew [mailto:mat...@gm... > <mailto:mat...@gm...>] > *Sent:* Friday, October 09, 2015 10:31 AM > *To:* psi...@li... > <mailto:psi...@li...> > *Subject:* Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo > > Thanks Gerhard. Can you commit the update to CVS as well? > > Thanks, > -Matt > > On 10/7/2015 3:31 AM, mayerg97 wrote: > > Dear proteomics community, > > attached you find the new version 3.79 of the psi-ms.obo file. > > > Changed CV terms in version 3.79 of psi-ms.obo: > =============================================== > ************ Replaced all "AB Sciex" terms by "SCIEX" > > ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF > [Term] > id: MS:1001482 > name: 5800 TOF/TOF > def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > > > New CV terms in version 3.79.0 of psi-ms.obo: > ============================================= > ************ New terms for Andromeda result file > [Term] > id: MS:1002576 > name: Andromeda result file > def: "Andromeda result file output format." [PSI:PI] > is_a: MS:1001040 ! intermediate analysis format > > ************ New terms for Sciex instruments > [Term] > id: MS:1002577 > name: 2000 QTRAP > def: "SCIEX 2000 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002578 > name: 2500 QTRAP > def: "SCIEX 2500 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002579 > name: 3500 QTRAP > def: "SCIEX 3500 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002580 > name: QTRAP 4500 > def: "SCIEX QTRAP 4500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002581 > name: QTRAP 6500 > def: "SCIEX QTRAP 6500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002582 > name: QTRAP 6500+ > def: "SCIEX QTRAP 6500+." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002583 > name: TripleTOF 4600 > def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002584 > name: TripleTOF 5600+ > def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." > [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002585 > name: API 100 > def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002586 > name: API 100LC > def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002587 > name: API 165 > def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002588 > name: API 300 > def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002589 > name: API 350 > def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002590 > name: API 365 > def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002591 > name: Triple Quad 3500 > def: "SCIEX Triple Quad 3500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002592 > name: Triple Quad 4500 > def: "SCIEX Triple Quad 4500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002593 > name: Triple Quad 5500 > def: "SCIEX Triple Quad 5500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002594 > name: Triple Quad 6500 > def: "SCIEX Triple Quad 6500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002595 > name: Triple Quad 6500+ > def: "SCIEX Triple Quad 6500+." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > Best Regards, > Gerhard > > -- > > *--* > > *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum > > *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 > > *E-mail *ger...@ru... <mailto:ger...@ru...> > > www.medizinisches-proteom-center.de > <http://www.medizinisches-proteom-center.de> > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- *--* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Chambers, M. <mat...@gm...> - 2015-10-09 18:15:07
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Good to know, Eric. I too have scripts that need to be updated when the new location is known. :) On 10/9/2015 1:13 PM, Eric Deutsch wrote: > > Thanks for pointing this out, Matt. > > So I’m unsure of what the situation here is. There is a movement in > progress to move everything to GitHub and this may already have been > completed. I am unsure of where this new version went. Did it go into > SourceForge CVS? Did it go into GitHub? What is our plan going forward > here? It would be nice to be a little more explicit and noisy about > that is happening. I have automated processes here at ISB that pull > the latest CVs from various version controls automatically and I need > to update these, but I’m wondering when to do this. I think nearly all > PSI related materials are being or have moved to GitHub. > > So I expect there will be some forthcoming announcements very soon > that will describe what has moved and what has not and what version > control processes need to be changed. > > Thanks, > > Eric > > *From:*Chambers, Matthew [mailto:mat...@gm... > <mailto:mat...@gm...>] > *Sent:* Friday, October 09, 2015 10:31 AM > *To:* psi...@li... > <mailto:psi...@li...> > *Subject:* Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo > > Thanks Gerhard. Can you commit the update to CVS as well? > > Thanks, > -Matt > > On 10/7/2015 3:31 AM, mayerg97 wrote: > > Dear proteomics community, > > attached you find the new version 3.79 of the psi-ms.obo file. > > > Changed CV terms in version 3.79 of psi-ms.obo: > =============================================== > ************ Replaced all "AB Sciex" terms by "SCIEX" > > ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF > [Term] > id: MS:1001482 > name: 5800 TOF/TOF > def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > > > New CV terms in version 3.79.0 of psi-ms.obo: > ============================================= > ************ New terms for Andromeda result file > [Term] > id: MS:1002576 > name: Andromeda result file > def: "Andromeda result file output format." [PSI:PI] > is_a: MS:1001040 ! intermediate analysis format > > ************ New terms for Sciex instruments > [Term] > id: MS:1002577 > name: 2000 QTRAP > def: "SCIEX 2000 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002578 > name: 2500 QTRAP > def: "SCIEX 2500 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002579 > name: 3500 QTRAP > def: "SCIEX 3500 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002580 > name: QTRAP 4500 > def: "SCIEX QTRAP 4500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002581 > name: QTRAP 6500 > def: "SCIEX QTRAP 6500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002582 > name: QTRAP 6500+ > def: "SCIEX QTRAP 6500+." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002583 > name: TripleTOF 4600 > def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002584 > name: TripleTOF 5600+ > def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." > [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002585 > name: API 100 > def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002586 > name: API 100LC > def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002587 > name: API 165 > def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002588 > name: API 300 > def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002589 > name: API 350 > def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002590 > name: API 365 > def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002591 > name: Triple Quad 3500 > def: "SCIEX Triple Quad 3500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002592 > name: Triple Quad 4500 > def: "SCIEX Triple Quad 4500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002593 > name: Triple Quad 5500 > def: "SCIEX Triple Quad 5500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002594 > name: Triple Quad 6500 > def: "SCIEX Triple Quad 6500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002595 > name: Triple Quad 6500+ > def: "SCIEX Triple Quad 6500+." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > Best Regards, > Gerhard > > -- > > *--* > > *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum > > *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 > > *E-mail *ger...@ru... <mailto:ger...@ru...> > > www.medizinisches-proteom-center.de > <http://www.medizinisches-proteom-center.de> > |
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From: Eric D. <ede...@sy...> - 2015-10-09 18:13:46
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Thanks for pointing this out, Matt. So I’m unsure of what the situation here is. There is a movement in progress to move everything to GitHub and this may already have been completed. I am unsure of where this new version went. Did it go into SourceForge CVS? Did it go into GitHub? What is our plan going forward here? It would be nice to be a little more explicit and noisy about that is happening. I have automated processes here at ISB that pull the latest CVs from various version controls automatically and I need to update these, but I’m wondering when to do this. I think nearly all PSI related materials are being or have moved to GitHub. So I expect there will be some forthcoming announcements very soon that will describe what has moved and what has not and what version control processes need to be changed. Thanks, Eric *From:* Chambers, Matthew [mailto:mat...@gm...] *Sent:* Friday, October 09, 2015 10:31 AM *To:* psi...@li... *Subject:* Re: [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo Thanks Gerhard. Can you commit the update to CVS as well? Thanks, -Matt On 10/7/2015 3:31 AM, mayerg97 wrote: Dear proteomics community, attached you find the new version 3.79 of the psi-ms.obo file. Changed CV terms in version 3.79 of psi-ms.obo: =============================================== ************ Replaced all "AB Sciex" terms by "SCIEX" ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF [Term] id: MS:1001482 name: 5800 TOF/TOF def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model New CV terms in version 3.79.0 of psi-ms.obo: ============================================= ************ New terms for Andromeda result file [Term] id: MS:1002576 name: Andromeda result file def: "Andromeda result file output format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format ************ New terms for Sciex instruments [Term] id: MS:1002577 name: 2000 QTRAP def: "SCIEX 2000 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002578 name: 2500 QTRAP def: "SCIEX 2500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002579 name: 3500 QTRAP def: "SCIEX 3500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002580 name: QTRAP 4500 def: "SCIEX QTRAP 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002581 name: QTRAP 6500 def: "SCIEX QTRAP 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002582 name: QTRAP 6500+ def: "SCIEX QTRAP 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002583 name: TripleTOF 4600 def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002584 name: TripleTOF 5600+ def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002585 name: API 100 def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002586 name: API 100LC def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002587 name: API 165 def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002588 name: API 300 def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002589 name: API 350 def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002590 name: API 365 def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002591 name: Triple Quad 3500 def: "SCIEX Triple Quad 3500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002592 name: Triple Quad 4500 def: "SCIEX Triple Quad 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002593 name: Triple Quad 5500 def: "SCIEX Triple Quad 5500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002594 name: Triple Quad 6500 def: "SCIEX Triple Quad 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002595 name: Triple Quad 6500+ def: "SCIEX Triple Quad 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model Best Regards, Gerhard -- *--* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail *ger...@ru... www.medizinisches-proteom-center.de |
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From: Chambers, M. <mat...@gm...> - 2015-10-09 17:31:24
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Thanks Gerhard. Can you commit the update to CVS as well? Thanks, -Matt On 10/7/2015 3:31 AM, mayerg97 wrote: > Dear proteomics community, > > attached you find the new version 3.79 of the psi-ms.obo file. > > > Changed CV terms in version 3.79 of psi-ms.obo: > =============================================== > ************ Replaced all "AB Sciex" terms by "SCIEX" > > ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF > [Term] > id: MS:1001482 > name: 5800 TOF/TOF > def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > > > New CV terms in version 3.79.0 of psi-ms.obo: > ============================================= > ************ New terms for Andromeda result file > [Term] > id: MS:1002576 > name: Andromeda result file > def: "Andromeda result file output format." [PSI:PI] > is_a: MS:1001040 ! intermediate analysis format > > ************ New terms for Sciex instruments > [Term] > id: MS:1002577 > name: 2000 QTRAP > def: "SCIEX 2000 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002578 > name: 2500 QTRAP > def: "SCIEX 2500 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002579 > name: 3500 QTRAP > def: "SCIEX 3500 QTRAP." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002580 > name: QTRAP 4500 > def: "SCIEX QTRAP 4500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002581 > name: QTRAP 6500 > def: "SCIEX QTRAP 6500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002582 > name: QTRAP 6500+ > def: "SCIEX QTRAP 6500+." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002583 > name: TripleTOF 4600 > def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002584 > name: TripleTOF 5600+ > def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002585 > name: API 100 > def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002586 > name: API 100LC > def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002587 > name: API 165 > def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002588 > name: API 300 > def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002589 > name: API 350 > def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002590 > name: API 365 > def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002591 > name: Triple Quad 3500 > def: "SCIEX Triple Quad 3500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002592 > name: Triple Quad 4500 > def: "SCIEX Triple Quad 4500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002593 > name: Triple Quad 5500 > def: "SCIEX Triple Quad 5500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002594 > name: Triple Quad 6500 > def: "SCIEX Triple Quad 6500." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > [Term] > id: MS:1002595 > name: Triple Quad 6500+ > def: "SCIEX Triple Quad 6500+." [PSI:MS] > is_a: MS:1000121 ! SCIEX instrument model > > Best Regards, > Gerhard > -- > > *--* > > *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum > > *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 > > *E-mail***ger...@ru... > > www.medizinisches-proteom-center.de > |
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From: mayerg97 <ger...@ru...> - 2015-10-07 08:45:44
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Dear proteomics community, attached you find the new version 3.79 of the psi-ms.obo file. Changed CV terms in version 3.79 of psi-ms.obo: =============================================== ************ Replaced all "AB Sciex" terms by "SCIEX" ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF [Term] id: MS:1001482 name: 5800 TOF/TOF def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model New CV terms in version 3.79.0 of psi-ms.obo: ============================================= ************ New terms for Andromeda result file [Term] id: MS:1002576 name: Andromeda result file def: "Andromeda result file output format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format ************ New terms for Sciex instruments [Term] id: MS:1002577 name: 2000 QTRAP def: "SCIEX 2000 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002578 name: 2500 QTRAP def: "SCIEX 2500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002579 name: 3500 QTRAP def: "SCIEX 3500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002580 name: QTRAP 4500 def: "SCIEX QTRAP 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002581 name: QTRAP 6500 def: "SCIEX QTRAP 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002582 name: QTRAP 6500+ def: "SCIEX QTRAP 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002583 name: TripleTOF 4600 def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002584 name: TripleTOF 5600+ def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002585 name: API 100 def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002586 name: API 100LC def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002587 name: API 165 def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002588 name: API 300 def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002589 name: API 350 def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002590 name: API 365 def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002591 name: Triple Quad 3500 def: "SCIEX Triple Quad 3500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002592 name: Triple Quad 4500 def: "SCIEX Triple Quad 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002593 name: Triple Quad 5500 def: "SCIEX Triple Quad 5500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002594 name: Triple Quad 6500 def: "SCIEX Triple Quad 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002595 name: Triple Quad 6500+ def: "SCIEX Triple Quad 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model Best Regards, Gerhard -- *--* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2015-10-01 10:26:48
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Dear proteomics community, attached you find the new version 3.79.0_rc1 of the psi-ms.obo file. Changed CV terms in version 3.79.0_rc1 of psi-ms.obo: ===================================================== ************ Replaced all "AB Sciex" terms by "SCIEX" ************ Renamed TOF/TOF 5800 --> 5800 TOF/TOF [Term] id: MS:1001482 name: 5800 TOF/TOF def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model New CV terms in version 3.79.0_rc1 of psi-ms.obo: ================================================= ************ New terms for Andromeda result file [Term] id: MS:1002576 name: Andromeda result file def: "Andromeda result file output format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format ************ New terms for Sciex instruments [Term] id: MS:1002577 name: 2000 QTRAP def: "SCIEX 2000 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002578 name: 2500 QTRAP def: "SCIEX 2500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002579 name: 3500 QTRAP def: "SCIEX 3500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002580 name: QTRAP 4500 def: "SCIEX QTRAP 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002581 name: QTRAP 6500 def: "SCIEX QTRAP 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002582 name: QTRAP 6500+ def: "SCIEX QTRAP 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002583 name: TripleTOF 4600 def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002584 name: TripleTOF 5600+ def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002585 name: API 100 def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002586 name: API 100LC def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002587 name: API 165 def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002588 name: API 300 def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002589 name: API 350 def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002590 name: API 365 def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002591 name: Triple Quad 3500 def: "SCIEX Triple Quad 3500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002592 name: Triple Quad 4500 def: "SCIEX Triple Quad 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002593 name: Triple Quad 5500 def: "SCIEX Triple Quad 5500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002594 name: Triple Quad 6500 def: "SCIEX Triple Quad 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002595 name: Triple Quad 6500+ def: "SCIEX Triple Quad 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model Best Regards, Gerhard -- *--* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2015-09-15 12:26:48
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Dear proteomics community, attached you find the new version 3.78.0 of the psi-ms.obo file. Changed CV terms in version 3.78.0 of psi-ms.obo: ================================================= ************ Added is_a: MS:1000808 ! chromatogram attribute ************ to the follwong two terms [Term] id: MS:1000129 name: negative scan def: "Polarity of the scan is negative." [PSI:MS] is_a: PATO:0002186 ! polarity is_a: MS:1000465 ! scan polarity is_a: MS:1000808 ! chromatogram attribute [Term] id: MS:1000130 name: positive scan def: "Polarity of the scan is positive." [PSI:MS] is_a: PATO:0002186 ! polarity is_a: MS:1000465 ! scan polarity is_a: MS:1000808 ! chromatogram attribute Best regards, Gerhard -- *--* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2015-08-06 07:02:01
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Dear proteomics community, attached you find the new release 3.77.0 of the psi-ms.obo file. Changed CV terms in version 3.77.0 of psi-ms.obo: ================================================= ************ Added string value type [Term] id: MS:1002487 name: MassIVE dataset identifier def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier New CV terms in version 3.77.0 of psi-ms.obo: ============================================= ************ Term for Tide search engine [Term] id: MS:1002575 name: Tide def: "Tide open-source sequence search program developed at the University of Washington." [PMID:21761931] is_a: MS:1001456 ! analysis software Best Regards, Gerhard -- *--* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Perkins, S. <Sim...@li...> - 2015-08-04 12:09:59
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Hello, Following on from this discussion about the small change to the mzid 1.1 schema and specification document (to mzid 1.1.1), changes have been made to the google code repository; the schema and specification document for 1.1.1 have been created. I will be updating the website imminently. Kind regards, Simon From: Perkins, Simon Sent: 14 July 2015 22:40 To: 'Chambers, Matthew'; psi...@li... Subject: RE: [Psidev-pi-dev] Mzid Specification For sure the version number will be bumped for this small update (1.1.1). I’m not sure how a reader that expects a float would react to a double. There’s no precise number of decimal places that a value of either type is guaranteed to be, so I imagine a reader wouldn’t notice, it’s just with a float less of the read number will be preserved if there are lots of decimal places. 1234.567899123456778 could be parsed as a float, just less of the number would be preserved than if it were parsed as a double – I think. Simon From: Chambers, Matthew [mailto:mat...@gm...] Sent: 14 July 2015 18:55 To: psi...@li...<mailto:psi...@li...> Subject: Re: [Psidev-pi-dev] Mzid Specification If someone wrote a double-length number to mzid, like 1234.567899123456778, how would that behave on a reader which expected a float? If it would crash/break any existing parser you have to consider making it a version bump (1.1.1). -Matt On 7/14/2015 12:51 PM, Perkins, Simon wrote: Hi Yasset, When version 1.2 is released, v1.1 will still exist. It will be up to developers to move to version 1.2 - if they want to, which we would recommend. The only dispute is over v1.1.1 which as far as I have seen was only ever a draft. There is only a draft specification document in the repository, there is no other reference to it anywhere else that I have seen. The small change being discussed (‘float’ -> ‘double’) would be released as a minor version update. The v1.1. xsd and documentation would not change – there would be an additional xsd and specification document for the minor version update. Thanks, Simon From: Yasset Perez-Riverol [mailto:yp...@eb...] Sent: 14 July 2015 00:19 To: Perkins, Simon; psi...@li...<mailto:psi...@li...> Subject: Re: [Psidev-pi-dev] Mzid Specification Hi: Agree, but please try to keep a version 1.1 because most of the search-engines and tools export to this version and we need to forward them to this documentation, and not to 1.2. Regards Yasset On 14/07/2015 00:14, Perkins, Simon wrote: Hello psi-pi list members, We are considering making a minor version update to mzIdentML. This is to change a single datatype from ‘float’ to ‘double’ for consistency with another place in the specification/schema, and has been requested by a member of the community. The change in question will be on the ‘massDelta’ attribute of ‘SearchModificationType’. The datatype is currently ‘float’, we would like to change it to ‘double’. The ‘ModificationType’ has attributes ‘avgMassDelta’ and ‘monoisotopicMassDelta’, which are both already of type ‘double’, so the change would only need to be on the ‘SearchModificationType’ attribute for consistency. There is an old draft minor version specification document in the repository, version 1.1.1, which contains changes, all of which have become part of the proposal for mzIdentML version 1.2 instead. It seems version 1.1.1 as it stands is a dead and unnecessary version in its current state. I propose that the draft specification version 1.1.1 is removed (as the original proposed changes are now part of the 1.2 proposal), and is replaced with a new 1.1.1 version, where the only change will be as described above. If you have any thoughts on this, please let me know ASAP. Kind regards, Simon ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Bioinformatician Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: mayerg97 <ger...@ru...> - 2015-08-03 11:30:03
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Dear proteomics community, attached you find the release candidate 3.77.0_rc1 of the psi-ms.obo file. Changed CV terms in version 3.77.0_rc1 of psi-ms.obo: ===================================================== ************ Added string value type [Term] id: MS:1002487 name: MassIVE dataset identifier def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier New CV terms in version 3.77.0_rc1 of psi-ms.obo: ================================================= ************ Term for Tide search engine [Term] id: MS:1002575 name: Tide def: "Tide open-source sequence search program developed at the University of Washington." [PMID:21761931] is_a: MS:1001456 ! analysis software Best Regards, Gerhard -- *--* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: <mzq...@go...> - 2015-07-27 15:02:42
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Revision: 396 Author: uk...@gm... Date: Mon Jul 27 15:02:18 2015 UTC Log: - moved SRM folder to under examples folder https://code.google.com/p/mzquantml/source/detail?r=396 Added: /trunk/examples/version1.0/SRM /trunk/examples/version1.0/SRM/Light_heavy_pairs_mzquantml_report.csv /trunk/examples/version1.0/SRM/Light_heavy_pairs_mzquantml_report.mzq /trunk/examples/version1.0/SRM/SRM_dev_notes.txt /trunk/examples/version1.0/SRM/Waters_QC_standard-mzquantml-report.csv /trunk/examples/version1.0/SRM/Waters_QC_standard-mzquantml-report.mzq /trunk/examples/version1.0/SRM/anubis_result.mzq Deleted: /trunk/examples/version1.0/files_under_development/SRM |
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From: Perkins, S. <Sim...@li...> - 2015-07-14 21:39:57
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For sure the version number will be bumped for this small update (1.1.1). I’m not sure how a reader that expects a float would react to a double. There’s no precise number of decimal places that a value of either type is guaranteed to be, so I imagine a reader wouldn’t notice, it’s just with a float less of the read number will be preserved if there are lots of decimal places. 1234.567899123456778 could be parsed as a float, just less of the number would be preserved than if it were parsed as a double – I think. Simon From: Chambers, Matthew [mailto:mat...@gm...] Sent: 14 July 2015 18:55 To: psi...@li... Subject: Re: [Psidev-pi-dev] Mzid Specification If someone wrote a double-length number to mzid, like 1234.567899123456778, how would that behave on a reader which expected a float? If it would crash/break any existing parser you have to consider making it a version bump (1.1.1). -Matt On 7/14/2015 12:51 PM, Perkins, Simon wrote: Hi Yasset, When version 1.2 is released, v1.1 will still exist. It will be up to developers to move to version 1.2 - if they want to, which we would recommend. The only dispute is over v1.1.1 which as far as I have seen was only ever a draft. There is only a draft specification document in the repository, there is no other reference to it anywhere else that I have seen. The small change being discussed (‘float’ -> ‘double’) would be released as a minor version update. The v1.1. xsd and documentation would not change – there would be an additional xsd and specification document for the minor version update. Thanks, Simon From: Yasset Perez-Riverol [mailto:yp...@eb...] Sent: 14 July 2015 00:19 To: Perkins, Simon; psi...@li...<mailto:psi...@li...> Subject: Re: [Psidev-pi-dev] Mzid Specification Hi: Agree, but please try to keep a version 1.1 because most of the search-engines and tools export to this version and we need to forward them to this documentation, and not to 1.2. Regards Yasset On 14/07/2015 00:14, Perkins, Simon wrote: Hello psi-pi list members, We are considering making a minor version update to mzIdentML. This is to change a single datatype from ‘float’ to ‘double’ for consistency with another place in the specification/schema, and has been requested by a member of the community. The change in question will be on the ‘massDelta’ attribute of ‘SearchModificationType’. The datatype is currently ‘float’, we would like to change it to ‘double’. The ‘ModificationType’ has attributes ‘avgMassDelta’ and ‘monoisotopicMassDelta’, which are both already of type ‘double’, so the change would only need to be on the ‘SearchModificationType’ attribute for consistency. There is an old draft minor version specification document in the repository, version 1.1.1, which contains changes, all of which have become part of the proposal for mzIdentML version 1.2 instead. It seems version 1.1.1 as it stands is a dead and unnecessary version in its current state. I propose that the draft specification version 1.1.1 is removed (as the original proposed changes are now part of the 1.2 proposal), and is replaced with a new 1.1.1 version, where the only change will be as described above. If you have any thoughts on this, please let me know ASAP. Kind regards, Simon ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Bioinformatician Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: Chambers, M. <mat...@gm...> - 2015-07-14 17:55:21
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If someone wrote a double-length number to mzid, like 1234.567899123456778, how would that behave on a reader which expected a float? If it would crash/break any existing parser you have to consider making it a version bump (1.1.1). -Matt On 7/14/2015 12:51 PM, Perkins, Simon wrote: > > Hi Yasset, > > When version 1.2 is released, v1.1 will still exist. It will be up to > developers to move to version 1.2 - if they want to, which we would > recommend. > > The only dispute is over v1.1.1 which as far as I have seen was only > ever a draft. There is only a draft specification document in the > repository, there is no other reference to it anywhere else that I > have seen. > > The small change being discussed (‘float’ -> ‘double’) would be > released as a minor version update. The v1.1. xsd and documentation > would not change – there would be an additional xsd and specification > document for the minor version update. > > Thanks, > > Simon > > *From:*Yasset Perez-Riverol [mailto:yp...@eb...] > *Sent:* 14 July 2015 00:19 > *To:* Perkins, Simon; psi...@li... > *Subject:* Re: [Psidev-pi-dev] Mzid Specification > > Hi: > Agree, but please try to keep a version 1.1 because most of the > search-engines and tools export to this version and we need to forward > them to this documentation, and > not to 1.2. > Regards > Yasset > > On 14/07/2015 00:14, Perkins, Simon wrote: > > Hello psi-pi list members, > > We are considering making a minor version update to mzIdentML. > This is to change a single datatype from ‘float’ to ‘double’ for > consistency with another place in the specification/schema, and > has been requested by a member of the community. > > The change in question will be on the ‘massDelta’ attribute of > ‘SearchModificationType’. The datatype is currently ‘float’, we > would like to change it to ‘double’. > > The ‘ModificationType’ has attributes ‘avgMassDelta’ and > ‘monoisotopicMassDelta’, which are both already of type ‘double’, > so the change would only need to be on the > ‘SearchModificationType’ attribute for consistency. > > There is an old draft minor version specification document in the > repository, version 1.1.1, which contains changes, all of which > have become part of the proposal for mzIdentML version 1.2 > instead. It seems version 1.1.1 as it stands is a dead and > unnecessary version in its current state. > > I propose that the draft specification version 1.1.1 is removed > (as the original proposed changes are now part of the 1.2 > proposal), and is replaced with a new 1.1.1 version, where the > only change will be as described above. > > If you have any thoughts on this, please let me know ASAP. > > Kind regards, > > Simon > > > > > ------------------------------------------------------------------------------ > > Don't Limit Your Business. Reach for the Cloud. > > GigeNET's Cloud Solutions provide you with the tools and support that > > you need to offload your IT needs and focus on growing your business. > > Configured For All Businesses. Start Your Cloud Today. > > https://www.gigenetcloud.com/ > > > > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > -- > Yasset Perez-Riverol PhD. > Bioinformatician > Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Twitter: @ypriverol |
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From: Perkins, S. <Sim...@li...> - 2015-07-14 17:51:50
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Hi Yasset, When version 1.2 is released, v1.1 will still exist. It will be up to developers to move to version 1.2 - if they want to, which we would recommend. The only dispute is over v1.1.1 which as far as I have seen was only ever a draft. There is only a draft specification document in the repository, there is no other reference to it anywhere else that I have seen. The small change being discussed (‘float’ -> ‘double’) would be released as a minor version update. The v1.1. xsd and documentation would not change – there would be an additional xsd and specification document for the minor version update. Thanks, Simon From: Yasset Perez-Riverol [mailto:yp...@eb...] Sent: 14 July 2015 00:19 To: Perkins, Simon; psi...@li... Subject: Re: [Psidev-pi-dev] Mzid Specification Hi: Agree, but please try to keep a version 1.1 because most of the search-engines and tools export to this version and we need to forward them to this documentation, and not to 1.2. Regards Yasset On 14/07/2015 00:14, Perkins, Simon wrote: Hello psi-pi list members, We are considering making a minor version update to mzIdentML. This is to change a single datatype from ‘float’ to ‘double’ for consistency with another place in the specification/schema, and has been requested by a member of the community. The change in question will be on the ‘massDelta’ attribute of ‘SearchModificationType’. The datatype is currently ‘float’, we would like to change it to ‘double’. The ‘ModificationType’ has attributes ‘avgMassDelta’ and ‘monoisotopicMassDelta’, which are both already of type ‘double’, so the change would only need to be on the ‘SearchModificationType’ attribute for consistency. There is an old draft minor version specification document in the repository, version 1.1.1, which contains changes, all of which have become part of the proposal for mzIdentML version 1.2 instead. It seems version 1.1.1 as it stands is a dead and unnecessary version in its current state. I propose that the draft specification version 1.1.1 is removed (as the original proposed changes are now part of the 1.2 proposal), and is replaced with a new 1.1.1 version, where the only change will be as described above. If you have any thoughts on this, please let me know ASAP. Kind regards, Simon ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Bioinformatician Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: Yasset Perez-R. <yp...@eb...> - 2015-07-13 23:19:25
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Hi: Agree, but please try to keep a version 1.1 because most of the search-engines and tools export to this version and we need to forward them to this documentation, and not to 1.2. Regards Yasset On 14/07/2015 00:14, Perkins, Simon wrote: > > Hello psi-pi list members, > > We are considering making a minor version update to mzIdentML. This is > to change a single datatype from 'float' to 'double' for consistency > with another place in the specification/schema, and has been requested > by a member of the community. > > The change in question will be on the 'massDelta' attribute of > 'SearchModificationType'. The datatype is currently 'float', we would > like to change it to 'double'. > > The 'ModificationType' has attributes 'avgMassDelta' and > 'monoisotopicMassDelta', which are both already of type 'double', so > the change would only need to be on the 'SearchModificationType' > attribute for consistency. > > There is an old draft minor version specification document in the > repository, version 1.1.1, which contains changes, all of which have > become part of the proposal for mzIdentML version 1.2 instead. It > seems version 1.1.1 as it stands is a dead and unnecessary version in > its current state. > > I propose that the draft specification version 1.1.1 is removed (as > the original proposed changes are now part of the 1.2 proposal), and > is replaced with a new 1.1.1 version, where the only change will be as > described above. > > If you have any thoughts on this, please let me know ASAP. > > Kind regards, > > Simon > > > > ------------------------------------------------------------------------------ > Don't Limit Your Business. Reach for the Cloud. > GigeNET's Cloud Solutions provide you with the tools and support that > you need to offload your IT needs and focus on growing your business. > Configured For All Businesses. Start Your Cloud Today. > https://www.gigenetcloud.com/ > > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Bioinformatician Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: Perkins, S. <Sim...@li...> - 2015-07-13 23:14:31
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Hello psi-pi list members, We are considering making a minor version update to mzIdentML. This is to change a single datatype from 'float' to 'double' for consistency with another place in the specification/schema, and has been requested by a member of the community. The change in question will be on the 'massDelta' attribute of 'SearchModificationType'. The datatype is currently 'float', we would like to change it to 'double'. The 'ModificationType' has attributes 'avgMassDelta' and 'monoisotopicMassDelta', which are both already of type 'double', so the change would only need to be on the 'SearchModificationType' attribute for consistency. There is an old draft minor version specification document in the repository, version 1.1.1, which contains changes, all of which have become part of the proposal for mzIdentML version 1.2 instead. It seems version 1.1.1 as it stands is a dead and unnecessary version in its current state. I propose that the draft specification version 1.1.1 is removed (as the original proposed changes are now part of the 1.2 proposal), and is replaced with a new 1.1.1 version, where the only change will be as described above. If you have any thoughts on this, please let me know ASAP. Kind regards, Simon |
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From: Eric D. <ede...@sy...> - 2015-07-06 21:03:39
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Hi everyone, for anyone interested in weighing in on some of the decisions we’re trying to make with respect to the final design of PEFF, whether or not you’ve been able to make the calls, please make your opinion known. The votes are not necessarily binding, but will hopefully serve to determine which issues have strong majority opinion and which are still divided and may need some more thinking and debate. http://doodle.com/e37uwaa83mzgshtn Dilemma 1: To go along with \VariantComplex, the we name the simple form \Variant or \VariantSimple? D1A1 Variant D1A2 VariantSimple Dilemma 2: Do we allow tagging of Variants? D2A1: No tagging explicitly (custom keywords still possible but not mainstream) D2A2: Support \VariantSimple_TAG= D2A3: Allow optional extra tag for each: \VariantSimple=(100|A)(105|C|TAG) Dilemma 3: Do we combine or separate the \ModRed terms? D3A1: Separate \ModResPsi, \ModResUnimod, \ModRes D3A2: Combine \ModResPsi & \ModResUnimod, but keep separate \ModRes D3A3: Combine them all into \ModRes Dilemma 4: Do we note deletion with empty or with a - ? D4A1: Empty D4A2: - (dash) The poll allows you to put a Yes, IfNeedBe, and No for each option. Feel free to use IfNeedBe to show half-hearted support. Feel free to only answer some of the dilemmas and not others if you do not have an opinion. Let’s see if this works. Ready. Set. Participate! Regards, Eric |
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From: Eric D. <ede...@sy...> - 2015-07-02 17:22:14
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Hi everyone, here are my notes from today’s PEFF call: Present: Juanan, Pierre-Alain, Karl, Eric, Lydie, Harald, Simon, Agenda: - Dilemma 1: \Variant or \VariantSimple + No strong feeling. Try a Doodle vote - Dilemma 2: Modify \Variant* keys with a further category + Opposing views on whether this should be here. Keep it simple, or allow some added tags + Lydie says they would rather have two PEFF files, one for gold level data, one for silver level, for example + Suggest that maybe each item could have an optional tag, e.g. instead of (223|A), allow (223|A|dbSNP) + Something like this implicitly already exists: the ability to create another key that allows, e.g., a free-text label + i.e. someone can create (using existing infrastructure) \VariantSimpleTagged=(223|A|neXtProt_dbSNP)(225|T|Specimen1)… + Try a poll - Dilemma 3: + Juanan advocates combining them + General agreement of combination + But then reconsidered later after discussing next - What about \ModRes? Okay as implemented? Combine with the previous as well? + Many opinions both ways and more + Also a suggestion of \ModRes for both PSI-MOD and Unimod and then \ModResCustom for other things + Would we save space by putting the names in the header? + Eric advocates that keeping them all separate as currently done makes it easier for readers. Explicit keys makes it easier for reader to know what to expect, rather than expending code trying to determine what kind of information is present + Easy consensus did not come. Try a vote and pick a way + For voting: yes, no, doesn’t matter - Custom key definitions + Did not have time to discuss this + Request that Pierre-Alain (and anyone else) follow up on the email Eric sent, and insert it into the spec doc + And then hold a slot for discussion on this on the next call Eugene's comments: 1) Bigger picture and longevity - will the current format stand the test of time - proteoforms come to mind and future advances in MS etc. + Full proteoforms seems easily supported with the current structure with separate entries. Variants would be the actual PTMs for a given proteoform. + May require a few additional terms, but the structure seems fine + If there are some specific use cases, this would be helpful 2) Do we have anyone representing NCBI/Refseq - if not what can we do about it. What about Ensembl, Eupathdb etc. - these are all well utilised resources especially EupathDB for those folks working with pathogens and mass spec. + We should make an effort. If they don’t participate now, they will be targeted as reviewers ;-) 3) Has anyone approached Juergen Cox or someone on his team to become involved considering Maxquant usage in the proteomics community? + Emanuele has shown him the specification + Ended here. + Eric will send out a Doodle poll to try voting on some items + Eric will send a poll to pick a date for the next call - Review examples of PEFF files - Review PEFF-supporting software - Central location for all supporting documentation |
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From: Eric D. <ede...@sy...> - 2015-07-02 14:04:55
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Hi everyone, this is just a reminder about the PEFF call in 1 hr. Dial in details: Dial-in information: Dial in numbers: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + Generic international: +44 2083222500 (UK number) + US: 877-420-0272 access code: 297427 # |
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From: Perkins, S. <Sim...@li...> - 2015-07-02 09:45:57
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Hi, Perhaps we could propose a ‘VariantCustom’ or ‘VariantSimpleCustom’, where something like ‘Germline_Somatic_UniProtKB_Cosmic’ would actually be in one of the data fields, as opposed to part of the key itself. That may make it cleaner and easier to parse for parsers which don’t recognise a specific ‘Variant*’ as currently proposed. Simon From: Lydie Lane [mailto:lyd...@is...] Sent: 01 July 2015 18:02 To: psi...@li... Subject: Re: [Psidev-pi-dev] Ideas for PEFF \Variant* construct hi everyone, We discussed the "Dilemma 2" internally at neXtProt. We feel that the proposed "suffix" solution is a bit simplistic. Indeed, many variants are both somatic and genomic, and present in different resources. Should they look like that : VariantSimple_Germline_Somatic_UniProtKB_Cosmic_etc? In our opinion, the Peff format should stay simple. If a user needs the evidence/source/reference for a variant, then he should use the XML files instead. I will be glad to be part of the discussion tomorrow. Best regards, Lydie On 30.06.2015 23:21, Eric Deutsch wrote: Hi everyone, here is a summary of the proposed PEFF \Variant* construct. There has been quite a bit of discussion. I think we still need some more discussion on this to come to a conclusion. The current perhaps minimum safe level is this: \VariantSimple=(223|A) (allows just single amino acid substitutions. *=nonsense allowed) \VariantComplex=(100|100|AP) (everything else including indels and more) Dilemma 1 is whether the keyword should be just \Variant or \VariantSimple - In favor \VariantSimple if a) starker contrast to VariantComplex, b) value will be different from current \Variant already in the wild - In favor of \Variant is x) it is shorter, y) very few files exist in the wild so reusing keyword with different format not an issue Dilemma 2 is whether we should support some form of tagging of variant lists (either suffixes or an alternate implementation). This topic is beyond the scope of the original PEFF, and so one possible decision is not to get fancy and stand with the current state. However, a very reasonable suggestion was made about considering the use cases. There is a very strong use case where a user will want to search a dataset with a PEFF file, finding variants, and then examine the variants to determine which are interesting. A basic categorization system would allow each set of variants to be tagged with their category, which may or may not be used. Consider the case where someone has an RNA-seq experiment that finds several SNPs for the sample at hand. Suppose the person begins with a PEFF file from neXtProt that already has SNPs in it, and the user wishes to add some unique to the sample. The PEFF format could potentially support a “_suffix” tag that could be interpreted by software. Suppose the PEFF file from neXtProt came with some of these: \VariantSimple_dbSNP= \VariantSimple_COSMIC= \VariantSimple_UniProtKB= \VarantSimple_Germline= \VariantSimple_Somatic= Then the user could potentially add: \VariantSimple_RNAseq= via a script that would edit the PEFF file. It would then be relatively simple to write software where perhaps the search engine would look for them all (or could allow a user to only search a subset), but then analysis software could easily differentiate between classes, showing the user that the search turned up 683 SNPs corresponding to UniProtKB, 125 SNPs corresponding to COSMIC, and 256 SNPs corresponding to RNAseq. - In favor of this approach: a) it allows selective searching against subsets of varants, b) it allows easy filtering of PEFF files for subsets of variants, c) It is quite flexible in terms of future use, d) It allow easy categorization of discovered variants; e) ? - Against this approach: x) it is beyond the scope of what we set out to do; y) it is clunky and requires parsing of partial keywords; z) ? - First, can anyone think of a more elegant way to do it? - Second, do we even want to do something like this? Please consider this for the next call on Thursday. Thanks, Eric ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Lydie Lane, Ph. D CALIPHO group co-director SIB-Swiss Institute of Bioinformatics Department of Human Protein Sciences, University of Geneva CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland + 41 (0) 22 379 58 41 |
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From: Eric D. <ede...@sy...> - 2015-07-01 21:32:02
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Hi everyone, another intended feature that is not in the current specification that Pierre-Alain mentions is the ability to define custom key-value pairs. Maybe Pierre-Alain can flesh this out, but from what I gather, the documentation should go something like the below. Please consider this and let’s discuss at the call tomorrow. In order to use a custom key-value pair (i.e. the key is not in the CV) in the sequence header blocks, it MUST be predefined in the file header. The definition MUST be of the form: # SpecificKey=KEYNAME:”KEYDEFINITION”:VALUEREGEXP For example, to define a SecondaryStructure term: # SpecificKey=SecondaryStructure:"Secondary structure element and position":\([0-9]+\|[0-9]+\|[\w:]*\|\S+?\) And then use: \SecondaryStructure=(617|673|ncithesaurus:C47937|Helix) Pierre-Alain, did I capture this correctly? The regexp part will be tricky.. Thanks, Eric |
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