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
>>
>>
>>
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>>
>>
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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