psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

[jeleclai <jel...@un...>]

Hi Andy,

I am using the c++ libraries but lately, we tried  HDF5's dotnet 
framework with c# successfully to read and write HDF5 files. In case of 
Java and Python, I currently have little experience, but as far as I 
know most functionalities of HDF5 are supported in these languages, and 
some datatypes (such as compound and variable length datatypes), which 
were problematic some time ago are now supported by translation to 
alternative datatypes. Concerning the Java interface, there are some 
functions that are not supported, most of them connected to pointers. 
See 
(https://www.hdfgroup.org/products/java/JNI/jhi5/jhi5_unsupported_functions.html) 
for a complete list.

So far, we converted Waters HDMS data to our format without storing 
empty scans. I will attend the PSI, so it would be great to discuss with 
you about it.
Best,

Jenny


Am 26.01.2016 um 15:36 schrieb Jones, Andy:
> Hi Jenny,
>
> When we last evaluated mz5, one of the issues appeared to be lack of good libraries beyond C++ for HDF5, so I would be interested to see if Java and Python libraries have improved in the last few years - do you know if much has changed? My recollection was that the Java methods only worked by bridging into C++, and did not provide native support for all reading and writing tasks that would be needed. As such, unless we took on the job of building true HDF5 support into Java and other languages, it seemed that other developers would be locked out. In the PSI we need to be quite conservative about the technologies we build upon, and this was certainly a concern at that time.
>
> All that said, I think there is still interest in the PSI for exploring how data representations might evolve in the future. It is ultimately up to Eric Deutsch who leads the PSI-MS part, but I would be keen to hear about what you've been doing at the upcoming PSI meeting in Ghent (18-20th April) if you can come along?
>
> Eric - what do you think, is there room on the agenda for this?
>
> I also have a few projects going with Waters, and I'm far from convinced that mzML is the right solution for representing their HDMS (ion mobility) data sets, at least without very specialised compression for all the empty scans that result. Independently of progress within the PSI, I would be interested to see what you've been developing.
> best wishes
> Andy
>
>
>
>
>
> ________________________________________
> From: jeleclai [jel...@un...]
> Sent: 26 January 2016 14:14
> To: psi...@li...
> Subject: Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats
>
> Hi,
>
> thanks for your email.
>
> So far, the file format is implemented for ion mobility data but the
> design is applicable to non-IMS data as well. So the support for
> "regular" experiments is planned as well.
>
> We are aware of the mz5 implementation as it is a good example how mass
> spectrometry data can be transferred to a binary format in combination
> with the benefits from the mzML ontology. Nevertheless, it seems that
> mz5, although being available now for quite some time (2012),  it has
> not been extensively used. mz5 is more efficient in terms of file size
> and I/O compared to mzML. But this gain in performance alone didn't seem
> to convince the broad mass spectrometry community to change to a new
> file format.  I can see two reasons for that: First, never change a
> running system. Second, data was not "large enough" to push a change in
> using a different file format. But especially with the addition of ion
> mobility as an extra dimension of separation, data complexity is
> increasing and will continue to increase in the future with evolving
> techniques. Therefore, although it requires  the use of an additional
> library (HDF5) a binary format will become essential when working with
> large data. HDF5 is portable and has C, C++,  Java and python
> interfaces, so it should not be an obstacle.  In addition, it is
> well-established as scientific file format with many different tools
> including tools to inspect the file (HDF5View) and the hdf group offers
> good service ( detailed documentation, free email support, new release
> twice a year...).
>
> Numpress definitely sounds interesting and I will take a look at it. ;-)
>
> Best wishes,
>
> Jenny
>
>
>
> Am 25.01.2016 um 16:43 schrieb Johan Teleman:
>> Hi Jenny,
>>
>> Having access to a binary format could clearly benefit many applications. Will this format be solely intended for ion mobility experiments, or do you also aim to target "regular" experiment data?
>>
>> The HDF5 library was utilized once already for a MS data format: mz5 (http://www.mcponline.org/content/11/1/O111.011379.full.pdf+html), maybe something can be reused from there. Depending on how data will be stored locally, numerical compression through Numpress might be interesting? Further I would recommend to walk the extra mile and benchmark the file format using data-files from different vendors and on different samples. Your result will vary depending on data density.
>>
>> A last mention is that I've had great experience with Google protobuf based binary file format, if the HDF5 does not work out for you. Protobuf does NOT have any support for random access though, so that would require a custom solution.
>>
>> Just my few cents, good luck with the implementation!
>>
>> /J
>>
>> Johan Teleman
>> Ph.D. student
>> Dept. of Immunotechnology
>> Lund University
>>
>> ________________________________________
>> Från: jeleclai [jel...@un...]
>> Skickat: den 25 januari 2016 13:34
>> Till:psi...@li...
>> Kopia: Navarro, Pedro
>> Ämne: [Psidev-ms-dev] HDF5-based mass spectrometry formats
>>
>> Hi all,
>>
>> I am a Phd student in Stefan Tenzer's lab. We are currently working on a
>> new format for mass spectrometric data, based on HDF5.
>>
>> We started to develop this format because we struggled with ion mobility
>> data: random access data to vendor's raw files is, as everyone knows,
>> suboptimal, and especially in the case of including ion mobility, we
>> foresee better ways to organize MS data in order to improve random access.
>>
>> In this regard, the HDF5 library is of great advantage as it combines a
>> simple and flexible way to structure the data with several efficient
>> methods for I/O access.
>>
>> Additionally, HDF5 library offers a good support for developers. It is
>> already successfully implemented in many other scientific fields like
>> Astronomy, Climatology, Genetics... All of this makes it a good
>> candidate for future developing of standard formats of large data, which
>> are interrogated in a random access way.
>>
>> We would be very happy to bring this topic to discussion for the next
>> PSI meeting!
>>
>> Best wishes,
>>
>> Jenny
>>
>> --
>>
>> Jennifer Leclaire
>> M.Sc. Angewandte Bioinformatik
>>
>> --------------------------------------------------
>> Institut für Immunologie
>> Universitätsmedizin der
>> Johannes Gutenberg-Universität
>> Langenbeckstr.1
>> 55131 Mainz
>> www.immunologie.uni-mainz.de
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> --
>
> Jennifer Leclaire
> M.Sc. Angewandte Bioinformatik
>
> --------------------------------------------------
> Institut für Immunologie
> Universitätsmedizin der
> Johannes Gutenberg-Universität
> Langenbeckstr.1
> 55131 Mainz
> www.immunologie.uni-mainz.de
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

-- 

Jennifer Leclaire
M.Sc. Angewandte Bioinformatik

--------------------------------------------------
Institut für Immunologie
Universitätsmedizin der
Johannes Gutenberg-Universität
Langenbeckstr.1
55131 Mainz
www.immunologie.uni-mainz.de

Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

[Jones, A. <And...@li...>]

Hi Jenny,

When we last evaluated mz5, one of the issues appeared to be lack of good libraries beyond C++ for HDF5, so I would be interested to see if Java and Python libraries have improved in the last few years - do you know if much has changed? My recollection was that the Java methods only worked by bridging into C++, and did not provide native support for all reading and writing tasks that would be needed. As such, unless we took on the job of building true HDF5 support into Java and other languages, it seemed that other developers would be locked out. In the PSI we need to be quite conservative about the technologies we build upon, and this was certainly a concern at that time. 

All that said, I think there is still interest in the PSI for exploring how data representations might evolve in the future. It is ultimately up to Eric Deutsch who leads the PSI-MS part, but I would be keen to hear about what you've been doing at the upcoming PSI meeting in Ghent (18-20th April) if you can come along? 

Eric - what do you think, is there room on the agenda for this?

I also have a few projects going with Waters, and I'm far from convinced that mzML is the right solution for representing their HDMS (ion mobility) data sets, at least without very specialised compression for all the empty scans that result. Independently of progress within the PSI, I would be interested to see what you've been developing.
best wishes
Andy





________________________________________
From: jeleclai [jel...@un...]
Sent: 26 January 2016 14:14
To: psi...@li...
Subject: Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

Hi,

thanks for your email.

So far, the file format is implemented for ion mobility data but the
design is applicable to non-IMS data as well. So the support for
"regular" experiments is planned as well.

We are aware of the mz5 implementation as it is a good example how mass
spectrometry data can be transferred to a binary format in combination
with the benefits from the mzML ontology. Nevertheless, it seems that
mz5, although being available now for quite some time (2012),  it has
not been extensively used. mz5 is more efficient in terms of file size
and I/O compared to mzML. But this gain in performance alone didn't seem
to convince the broad mass spectrometry community to change to a new
file format.  I can see two reasons for that: First, never change a
running system. Second, data was not "large enough" to push a change in
using a different file format. But especially with the addition of ion
mobility as an extra dimension of separation, data complexity is
increasing and will continue to increase in the future with evolving
techniques. Therefore, although it requires  the use of an additional
library (HDF5) a binary format will become essential when working with
large data. HDF5 is portable and has C, C++,  Java and python
interfaces, so it should not be an obstacle.  In addition, it is
well-established as scientific file format with many different tools
including tools to inspect the file (HDF5View) and the hdf group offers
good service ( detailed documentation, free email support, new release
twice a year...).

Numpress definitely sounds interesting and I will take a look at it. ;-)

Best wishes,

Jenny



Am 25.01.2016 um 16:43 schrieb Johan Teleman:
> Hi Jenny,
>
> Having access to a binary format could clearly benefit many applications. Will this format be solely intended for ion mobility experiments, or do you also aim to target "regular" experiment data?
>
> The HDF5 library was utilized once already for a MS data format: mz5 (http://www.mcponline.org/content/11/1/O111.011379.full.pdf+html), maybe something can be reused from there. Depending on how data will be stored locally, numerical compression through Numpress might be interesting? Further I would recommend to walk the extra mile and benchmark the file format using data-files from different vendors and on different samples. Your result will vary depending on data density.
>
> A last mention is that I've had great experience with Google protobuf based binary file format, if the HDF5 does not work out for you. Protobuf does NOT have any support for random access though, so that would require a custom solution.
>
> Just my few cents, good luck with the implementation!
>
> /J
>
> Johan Teleman
> Ph.D. student
> Dept. of Immunotechnology
> Lund University
>
> ________________________________________
> Från: jeleclai [jel...@un...]
> Skickat: den 25 januari 2016 13:34
> Till:psi...@li...
> Kopia: Navarro, Pedro
> Ämne: [Psidev-ms-dev] HDF5-based mass spectrometry formats
>
> Hi all,
>
> I am a Phd student in Stefan Tenzer's lab. We are currently working on a
> new format for mass spectrometric data, based on HDF5.
>
> We started to develop this format because we struggled with ion mobility
> data: random access data to vendor's raw files is, as everyone knows,
> suboptimal, and especially in the case of including ion mobility, we
> foresee better ways to organize MS data in order to improve random access.
>
> In this regard, the HDF5 library is of great advantage as it combines a
> simple and flexible way to structure the data with several efficient
> methods for I/O access.
>
> Additionally, HDF5 library offers a good support for developers. It is
> already successfully implemented in many other scientific fields like
> Astronomy, Climatology, Genetics... All of this makes it a good
> candidate for future developing of standard formats of large data, which
> are interrogated in a random access way.
>
> We would be very happy to bring this topic to discussion for the next
> PSI meeting!
>
> Best wishes,
>
> Jenny
>
> --
>
> Jennifer Leclaire
> M.Sc. Angewandte Bioinformatik
>
> --------------------------------------------------
> Institut für Immunologie
> Universitätsmedizin der
> Johannes Gutenberg-Universität
> Langenbeckstr.1
> 55131 Mainz
> www.immunologie.uni-mainz.de
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

--

Jennifer Leclaire
M.Sc. Angewandte Bioinformatik

--------------------------------------------------
Institut für Immunologie
Universitätsmedizin der
Johannes Gutenberg-Universität
Langenbeckstr.1
55131 Mainz
www.immunologie.uni-mainz.de


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

[jeleclai <jel...@un...>]

Hi,

thanks for your email.

So far, the file format is implemented for ion mobility data but the 
design is applicable to non-IMS data as well. So the support for 
"regular" experiments is planned as well.

We are aware of the mz5 implementation as it is a good example how mass 
spectrometry data can be transferred to a binary format in combination 
with the benefits from the mzML ontology. Nevertheless, it seems that 
mz5, although being available now for quite some time (2012),  it has 
not been extensively used. mz5 is more efficient in terms of file size 
and I/O compared to mzML. But this gain in performance alone didn't seem 
to convince the broad mass spectrometry community to change to a new 
file format.  I can see two reasons for that: First, never change a 
running system. Second, data was not "large enough" to push a change in 
using a different file format. But especially with the addition of ion 
mobility as an extra dimension of separation, data complexity is 
increasing and will continue to increase in the future with evolving 
techniques. Therefore, although it requires  the use of an additional 
library (HDF5) a binary format will become essential when working with 
large data. HDF5 is portable and has C, C++,  Java and python 
interfaces, so it should not be an obstacle.  In addition, it is 
well-established as scientific file format with many different tools 
including tools to inspect the file (HDF5View) and the hdf group offers 
good service ( detailed documentation, free email support, new release 
twice a year...).

Numpress definitely sounds interesting and I will take a look at it. ;-)

Best wishes,

Jenny



Am 25.01.2016 um 16:43 schrieb Johan Teleman:
> Hi Jenny,
>
> Having access to a binary format could clearly benefit many applications. Will this format be solely intended for ion mobility experiments, or do you also aim to target "regular" experiment data?
>
> The HDF5 library was utilized once already for a MS data format: mz5 (http://www.mcponline.org/content/11/1/O111.011379.full.pdf+html), maybe something can be reused from there. Depending on how data will be stored locally, numerical compression through Numpress might be interesting? Further I would recommend to walk the extra mile and benchmark the file format using data-files from different vendors and on different samples. Your result will vary depending on data density.
>
> A last mention is that I've had great experience with Google protobuf based binary file format, if the HDF5 does not work out for you. Protobuf does NOT have any support for random access though, so that would require a custom solution.
>
> Just my few cents, good luck with the implementation!
>
> /J
>
> Johan Teleman
> Ph.D. student
> Dept. of Immunotechnology
> Lund University
>
> ________________________________________
> Från: jeleclai [jel...@un...]
> Skickat: den 25 januari 2016 13:34
> Till:psi...@li...
> Kopia: Navarro, Pedro
> Ämne: [Psidev-ms-dev] HDF5-based mass spectrometry formats
>
> Hi all,
>
> I am a Phd student in Stefan Tenzer's lab. We are currently working on a
> new format for mass spectrometric data, based on HDF5.
>
> We started to develop this format because we struggled with ion mobility
> data: random access data to vendor's raw files is, as everyone knows,
> suboptimal, and especially in the case of including ion mobility, we
> foresee better ways to organize MS data in order to improve random access.
>
> In this regard, the HDF5 library is of great advantage as it combines a
> simple and flexible way to structure the data with several efficient
> methods for I/O access.
>
> Additionally, HDF5 library offers a good support for developers. It is
> already successfully implemented in many other scientific fields like
> Astronomy, Climatology, Genetics... All of this makes it a good
> candidate for future developing of standard formats of large data, which
> are interrogated in a random access way.
>
> We would be very happy to bring this topic to discussion for the next
> PSI meeting!
>
> Best wishes,
>
> Jenny
>
> --
>
> Jennifer Leclaire
> M.Sc. Angewandte Bioinformatik
>
> --------------------------------------------------
> Institut für Immunologie
> Universitätsmedizin der
> Johannes Gutenberg-Universität
> Langenbeckstr.1
> 55131 Mainz
> www.immunologie.uni-mainz.de
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

-- 

Jennifer Leclaire
M.Sc. Angewandte Bioinformatik

--------------------------------------------------
Institut für Immunologie
Universitätsmedizin der
Johannes Gutenberg-Universität
Langenbeckstr.1
55131 Mainz
www.immunologie.uni-mainz.de

Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

[Johan T. <joh...@im...>]

Hi Jenny,

Having access to a binary format could clearly benefit many applications. Will this format be solely intended for ion mobility experiments, or do you also aim to target "regular" experiment data?

The HDF5 library was utilized once already for a MS data format: mz5 (http://www.mcponline.org/content/11/1/O111.011379.full.pdf+html), maybe something can be reused from there. Depending on how data will be stored locally, numerical compression through Numpress might be interesting? Further I would recommend to walk the extra mile and benchmark the file format using data-files from different vendors and on different samples. Your result will vary depending on data density.

A last mention is that I've had great experience with Google protobuf based binary file format, if the HDF5 does not work out for you. Protobuf does NOT have any support for random access though, so that would require a custom solution.

Just my few cents, good luck with the implementation!

/J

Johan Teleman
Ph.D. student
Dept. of Immunotechnology
Lund University

________________________________________
Från: jeleclai [jel...@un...]
Skickat: den 25 januari 2016 13:34
Till: psi...@li...
Kopia: Navarro, Pedro
Ämne: [Psidev-ms-dev] HDF5-based mass spectrometry formats

Hi all,

I am a Phd student in Stefan Tenzer's lab. We are currently working on a
new format for mass spectrometric data, based on HDF5.

We started to develop this format because we struggled with ion mobility
data: random access data to vendor's raw files is, as everyone knows,
suboptimal, and especially in the case of including ion mobility, we
foresee better ways to organize MS data in order to improve random access.

In this regard, the HDF5 library is of great advantage as it combines a
simple and flexible way to structure the data with several efficient
methods for I/O access.

Additionally, HDF5 library offers a good support for developers. It is
already successfully implemented in many other scientific fields like
Astronomy, Climatology, Genetics... All of this makes it a good
candidate for future developing of standard formats of large data, which
are interrogated in a random access way.

We would be very happy to bring this topic to discussion for the next
PSI meeting!

Best wishes,

Jenny

--

Jennifer Leclaire
M.Sc. Angewandte Bioinformatik

--------------------------------------------------
Institut für Immunologie
Universitätsmedizin der
Johannes Gutenberg-Universität
Langenbeckstr.1
55131 Mainz
www.immunologie.uni-mainz.de


------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] HDF5-based mass spectrometry formats

[jeleclai <jel...@un...>]

Hi all,

I am a Phd student in Stefan Tenzer's lab. We are currently working on a 
new format for mass spectrometric data, based on HDF5.

We started to develop this format because we struggled with ion mobility 
data: random access data to vendor's raw files is, as everyone knows, 
suboptimal, and especially in the case of including ion mobility, we 
foresee better ways to organize MS data in order to improve random access.

In this regard, the HDF5 library is of great advantage as it combines a 
simple and flexible way to structure the data with several efficient 
methods for I/O access.

Additionally, HDF5 library offers a good support for developers. It is 
already successfully implemented in many other scientific fields like 
Astronomy, Climatology, Genetics... All of this makes it a good 
candidate for future developing of standard formats of large data, which 
are interrogated in a random access way.

We would be very happy to bring this topic to discussion for the next 
PSI meeting!

Best wishes,

Jenny

-- 

Jennifer Leclaire
M.Sc. Angewandte Bioinformatik

--------------------------------------------------
Institut für Immunologie
Universitätsmedizin der
Johannes Gutenberg-Universität
Langenbeckstr.1
55131 Mainz
www.immunologie.uni-mainz.de

[Psidev-ms-dev] New version 3.82.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new version 3.82.0 of the psi-ms.obo file.

New CV terms in version 3.82.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002599
name: splash key
def: "The Splash, is an unique identifier for Spectra, as the InChI Key 
is an unique identifier for chemical compounds." 
[http://splash.fiehnlab.ucdavis.edu/]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details


Changed CV terms in version 3.82.0 of psi-ms.obo:
=================================================
************ No other changes

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-ms-dev] New version 3.81.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new version 3.81 of the psi-ms.obo file.

New CV terms in version 3.81.0 of psi-ms.obo:
=============================================
************ Terms for the MS1 format and DTASelect
[Term]
id: MS:1002597
name: MS1 format
def: "MS1 file format for MS1 spectral data." [PMID:15317041, 
DOI:10.1002/rcm.1603]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002598
name: DTASelect
def: "Analysis software designed to reassemble the SEQUEST peptide 
identifications and to highlight the most significant matches." 
[PMID:12643522, http://fields.scripps.edu/DTASelect/]
is_a: MS:1001456 ! analysis software


Changed CV terms in version 3.81.0 of psi-ms.obo:
=================================================
************ Changed the is_a relationship from
************ intermediate analysis format to
************ mass spectrometer file format
[Term]
id: MS:1001466
name: MS2 format
def: "MS2 file format for MS2 spectral data." [PMID:15317041, 
DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html]
is_a: MS:1000560 ! mass spectrometer file format

************ Added string value type
[Term]
id: MS:1001922
name: Digital Object Identifier (DOI)
def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
synonym: "doi" EXACT []
is_a: MS:1000878 ! external reference identifier
relationship: has_regexp MS:1002480 ! 
(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)

************ Changed the definition to be more descriptive
[Term]
id: MS:1002596
name: ProLuCID
def: "The SEQUEST-like sequence search engine ProLuCID, developed in the 
Yates Lab at the Scripps Research Institute." [PMID:26171723]
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/>

[Psidev-ms-dev] Release candidate 3.81.0_rc2 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.81_rc2 of the psi-ms.obo file.

New CV terms in version 3.81.0_rc2 of psi-ms.obo:
=================================================
************ Terms for the MS1 format and DTASelect
[Term]
id: MS:1002597
name: MS1 format
def: "MS1 file format for MS1 spectral data." [PMID:15317041, 
DOI:10.1002/rcm.1603]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002598
name: DTASelect
def: "Analysis software designed to reassemble the SEQUEST peptide 
identifications and to highlight the most significant matches." 
[PMID:12643522, http://fields.scripps.edu/DTASelect/]
is_a: MS:1001456 ! analysis software


Changed CV terms in version 3.81.0_rc2 of psi-ms.obo:
=====================================================
************ Changed the is_a relationship from
************ intermediate analysis format to
************ mass spectrometer file format
[Term]
id: MS:1001466
name: MS2 format
def: "MS2 file format for MS2 spectral data." [PMID:15317041, 
DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html]
is_a: MS:1000560 ! mass spectrometer file format

************ Added string value type
[Term]
id: MS:1001922
name: Digital Object Identifier (DOI)
def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
synonym: "doi" EXACT []
is_a: MS:1000878 ! external reference identifier
relationship: has_regexp MS:1002480 ! 
(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)

************ Changed the definition to be more descriptive
[Term]
id: MS:1002596
name: ProLuCID
def: "The SEQUEST-like sequence search engine ProLuCID, developed in the 
Yates Lab at the Scripps Research Institute." [PMID:26171723]
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/>

Re: [Psidev-ms-dev] Release candidate 3.81.0_rc1 of psi-ms.obo

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

Thanks, Gerhard!



*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Wednesday, December 09, 2015 3:10 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] Release candidate 3.81.0_rc1 of psi-ms.obo



Dear proteomics community,

attached you find the release candidate 3.81_rc1 of the psi-ms.obo file.

New CV terms in version 3.81.0_rc1 of psi-ms.obo:
=================================================
************ Term for the MS1 format
[Term]
id: MS:1002597
name: MS1 format
def: "MS1 file format for MS1 spectral data." [PMID:15317041,
DOI:10.1002/rcm.1603]
is_a: MS:1000560 ! mass spectrometer file format


Changed CV terms in version 3.81.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the is_a relationship from
************ intermediate analysis format to
************ mass spectrometer file format
[Term]
id: MS:1001466
name: MS2 format
def: "MS2 file format for MS2 spectral data." [PMID:15317041,
DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html]
is_a: MS:1000560 ! mass spectrometer file format

************ Added string value type
[Term]
id: MS:1001922
name: Digital Object Identifier (DOI)
def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
synonym: "doi" EXACT []
is_a: MS:1000878 ! external reference identifier
relationship: has_regexp MS:1002480 !
(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)

************ Changed the definition to be more descriptive
[Term]
id: MS:1002596
name: ProLuCID
def: "The SEQUEST-like sequence search engine ProLuCID, developed in the
Yates Lab at the Scripps Research Institute." [PMID:26171723]
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...

www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.81.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.81_rc1 of the psi-ms.obo file.

New CV terms in version 3.81.0_rc1 of psi-ms.obo:
=================================================
************ Term for the MS1 format
[Term]
id: MS:1002597
name: MS1 format
def: "MS1 file format for MS1 spectral data." [PMID:15317041, 
DOI:10.1002/rcm.1603]
is_a: MS:1000560 ! mass spectrometer file format


Changed CV terms in version 3.81.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the is_a relationship from
************ intermediate analysis format to
************ mass spectrometer file format
[Term]
id: MS:1001466
name: MS2 format
def: "MS2 file format for MS2 spectral data." [PMID:15317041, 
DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html]
is_a: MS:1000560 ! mass spectrometer file format

************ Added string value type
[Term]
id: MS:1001922
name: Digital Object Identifier (DOI)
def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
synonym: "doi" EXACT []
is_a: MS:1000878 ! external reference identifier
relationship: has_regexp MS:1002480 ! 
(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)

************ Changed the definition to be more descriptive
[Term]
id: MS:1002596
name: ProLuCID
def: "The SEQUEST-like sequence search engine ProLuCID, developed in the 
Yates Lab at the Scripps Research Institute." [PMID:26171723]
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/>

Re: [Psidev-ms-dev] New version 3.80.0 of psi-ms.obo

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

Hi Gerhard, thanks for setting up the new Github location. I have switched
my pointers to the new location and it seems to be working fine.

May I suggest an updated definition for ProLuCID? “The name of the…” isn’t
a great way to start a definition. How about something more like this:

def: "The SEQUEST-like sequence search engine ProLuCID, developed in the
Yates Lab at the Scripps Research Institute." [PMID:26171723]

Regards,

Eric



*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Tuesday, December 8, 2015 5:59 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] New version 3.80.0 of psi-ms.obo



Dear proteomics community,

attached you find the new version 3.80.0 of the psi-ms.obo file.

New CV terms in version 3.80.0 of psi-ms.obo:
=========================================
[Term]
id: MS:1002596
name: ProLuCID
def: "The name of the ProLuCID search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

Note that as discussed, I created now a *new own repository for the CV*,
so please update your links pointing to the new
    https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo
location.

Then I will delete the old cv from the mzML branch in a week or so.

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-ms-dev] New version 3.80.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new version 3.80.0 of the psi-ms.obo file.

New CV terms in version 3.80.0 of psi-ms.obo:
=========================================
[Term]
id: MS:1002596
name: ProLuCID
def: "The name of the ProLuCID search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

Note that as discussed, I created now a *new own repository for the CV*,
so please update your links pointing to the new
     https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo
location.

Then I will delete the old cv from the mzML branch in a week or so.

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] Notes from today's PEFF call

[Juan A. V. <ju...@eb...>]

Hi Eric,

Thanks for taking care of this. 

About the remaining issue related to modifications, for reading software (as usual I am biased in that direction) it would be definitely easier to deal with modifications encoded by CVparams (differentiate between the 2 options (PSI-MOD and/or UniMod) or not is secondary in my opinion, I can accommodate to Eric’s approach for differentiating between all of them) or "free text” (e.g. “phospho-") in a different way. For instance, for reading properly files with custom modifications, there must be extra custom file to know what the modifications really are.

The final decision here will be probably used as well for the proBAM format (for proteogenomics)  since it does not make sense to use different approaches for these text-based formats, so we are not only talking about this particular case (PEFF). 

But I understand that this is not the main priority for others. So, I don’t want to delay the discussion and if the majority thinks that it is better to go for the opposite approach, let’s do that instead of spending much more time discussing about it.

Cheers,

Juan



> On 20 Oct 2015, at 22:55, Eric Deutsch <ede...@sy...> wrote:
> 
> Hi everyone, due to vacations and HUPO and other things, PEFF progress ground to a halt over the last few months, but with renewed vigor from HUPO, let’s see if we can get this finished! So, where we left off: I sent around a Doodle poll and we voted on various implementation options:
> http://doodle.com/e37uwaa83mzgshtn <http://doodle.com/e37uwaa83mzgshtn>
>  
> There was a clear winner on most of the decisions and I have gone with these for the moment. This leaves only the decision on whether to combine or separate \ModResPsi, \ModResUnimod, and \ModRes. I thought that keeping them separate would quite simplify things for parsers, but I was in the minority. Combining them all got the most support, but just barely. Considering the small-number statistics, it is really more of a 3-way tie within the uncertainties.. a change of one vote could have changed things considerably. So it is difficult to find the clear winner. Perhaps Pierre-Alain, Juanan , and I will settle this via an arm-wrestling contest. Or if anyone else would like to add their thumb to the Doodle scale at this late time, go for it. Or perhaps the first person to actually create a full implementation takes the day.
>  
> Please find attached the latest PEFF specification. I have updated it based on the winning decisions. The 3 ModRes terms remain as they were, still separated for now. Let’s see if we can make a decision and create some sample files and validators/parsers/writers.
>  
> Thanks,
> Eric
>  
>  
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Thursday, July 02, 2015 10:22 AM
> To: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>
> Cc: Eric Deutsch
> Subject: Notes from today's PEFF call
>  
> 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
>  
>  
>  
> <PEFF.1.0.draft16.docx>------------------------------------------------------------------------------
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li... <mailto:Psi...@li...>
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev <https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev>

Re: [Psidev-ms-dev] Notes from today's PEFF call

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

Hi everyone, due to vacations and HUPO and other things, PEFF progress
ground to a halt over the last few months, but with renewed vigor from
HUPO, let’s see if we can get this finished! So, where we left off: I sent
around a Doodle poll and we voted on various implementation options:

http://doodle.com/e37uwaa83mzgshtn



There was a clear winner on most of the decisions and I have gone with
these for the moment. This leaves only the decision on whether to combine
or separate \ModResPsi, \ModResUnimod, and \ModRes. I thought that keeping
them separate would quite simplify things for parsers, but I was in the
minority. Combining them all got the most support, but just barely.
Considering the small-number statistics, it is really more of a 3-way tie
within the uncertainties.. a change of one vote could have changed things
considerably. So it is difficult to find the clear winner. Perhaps
Pierre-Alain, Juanan , and I will settle this via an arm-wrestling contest.
Or if anyone else would like to add their thumb to the Doodle scale at this
late time, go for it. Or perhaps the first person to actually create a full
implementation takes the day.



Please find attached the latest PEFF specification. I have updated it based
on the winning decisions. The 3 ModRes terms remain as they were, still
separated for now. Let’s see if we can make a decision and create some
sample files and validators/parsers/writers.



Thanks,

Eric









*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Thursday, July 02, 2015 10:22 AM
*To:* Mass spectrometry standard development;
psi...@li...
*Cc:* Eric Deutsch
*Subject:* Notes from today's PEFF call



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

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

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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

[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-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 





------------------------------------------------------------------------------ 

_______________________________________________
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

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

[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

[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

[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] 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

[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/>

[Psidev-ms-dev] Release candidate 3.79.0_rc1 of psi-ms.obo

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

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/>