psidev-ms-dev

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

[mayerg97 <ger...@ru...>]

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/>

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

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

Thank you, Gerhard!



*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Wednesday, October 07, 2015 1:31 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] New version 3.79.0 of psi-ms.obo



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

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

[mayerg97 <ger...@ru...>]

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/>

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

[Yasset Perez-R. <yp...@eb...>]

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

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

[Mathias W. <wa...@in...>]

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

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

[Chambers, M. <mat...@gm...>]

+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
>
>

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

[Yasset Perez-R. <yp...@eb...>]

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

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

[Qi, D. <D....@li...>]

I support Mathias’ suggestion. To further this, I remember Simon (current developer of ProteoSuite) have mentioned this before in here, would we consider merging the CV related Java classes (e.g. CvParam, UserParam) in jmzML, jmzIdentML, jmzQuantML into a united library instead of repeated in each API? The current Java implementation of them is not economic when dealing with mzML, mzIdentML, mzQuantML files in one piece of code.

Thanks,
Da


From: Yasset Perez-Riverol [mailto:yp...@eb...]
Sent: 15 October 2015 09:48
To: Mathias Walzer; psi...@li...; psi...@li...; psi...@li...
Subject: Re: [Psidev-ms-vocab] [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo

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...><mailto:yp...@eb...>

To: "mayerg97" <ger...@ru...><mailto:ger...@ru...>, psi...@li...<mailto:psi...@li...>, psi...@li...<mailto:psi...@li...>, psi...@li...<mailto: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...<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







--

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

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

[Julian U. <jul...@ru...>]

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 





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Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER 

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Medizinisches Proteom-Center 

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Yasset Perez-Riverol PhD.
Bioinformatician
Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
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Cambridge CB10 1SD
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Twitter: @ypriverol 
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Re: [Psidev-ms-dev] [Psidev-pi-dev] New version 3.79.0 of psi-ms.obo

[Steffen N. <sne...@ip...>]

Hi,

On Mi, 2015-10-14 at 11:09 -0500, Chambers, Matthew wrote:
> 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.

The awesome thing on github.com is the built-in editor, 
so someone could just hit the "Edit" button, and request 
a new term right away. git fork/branch/change/PR is done 
in the background :-). What's left is to accept the change. 

Yours,
Steffen

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IPB Halle                    AG Massenspektrometrie & Bioinformatik
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