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

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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 

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-- 

-- 

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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-- 
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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