Re: [Psidev-ms-dev] [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo

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+1 (even though I'd have to change my scripts again)

I think the git fork/branch/change/PR paradigm is a too heavy for 
anything other than major CV overhauls, but having it won't hurt. We can 
also add some continuous integration to validate CV changes (and PRs!) 
with an OBO validator. I'm not sure what the non-GUI validator would be. 
Do you use anything in particular Gerhard?

-Matt

On 10/14/2015 11:01 AM, 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
> -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
>
>