psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] EuBIC 2018 developer’s meeting - Extended project submission deadline

[EuBIC developer's m. <eu...@gm...>]

*— EuBIC 2018 developer’s meeting —*



*Project proposal submission deadline extended!*



Project submission proposal is now open until *September 24, 2017*.



EuBIC members will be present at the HUPO conference in Dublin this week.
Find us there at the bioinformatics hub to get more information about the
developer’s meeting and discuss your project proposal.



To submit a project proposal please follow the instructions provided here:
http://uahost.uantwerpen.be/eubic18/submission.html



*EuBIC 2018 developer’s meeting*



Date: January 9-12, 2018

Venue: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium

For more details on the program, please check the website:
http://uahost.uantwerpen.be/eubic18/



*Key dates*



*September 24, 2017: Extended project proposal submission deadline*

October 2, 2017: Announcement of selected projects

October 2, 2017: Conference registration opens

January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent



*Topics*



Hackathon projects can cover all topics in proteomics bioinformatics,
including, but not limited to:

- Tools

    - Extension of existing bioinformatics tools under the guidance of
their original authors

    - Development of novel bioinformatics tools to solve open problems

- Benchmarking

    - Compilation of gold-truth datasets

    - Collection of reference algorithmic implementations

    - Specification of benchmarking criteria

- Workflows

    - Definition of formal protocols

    - Development of tutorials for bioinformatics software usage

- Data analysis

    - (Re)analysis of publicly available proteomics datasets



*More information*



- website: http://uahost.uantwerpen.be/eubic18/

- social media hashtag: #EuBIC18

- conference email: eu...@gm...



*Sponsorship *inquiries are welcome at eu...@gm...





We look forward to welcoming you in Ghent!



On behalf of the organizing committee,

Wout Bittremieux

[Psidev-ms-dev] Release candidate 4.0.15_rc3 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.15_rc3 of the psi-ms.obo file.

It contains new terms for the MetaMorpheus search engine,
new terms for the metabolomics software package XCMS,
a new term for 'alternating polarity mode' and two new
cleavage agent terms:


New CV terms in version 4.0.15_rc3 of psi-ms.obo:
=================================================
************ new terms for the MetaMorpheus search engine
[Term]
id: MS:1002826
name: MetaMorpheus
def: "MetaMorpheus search engine." 
[https://github.com/smith-chem-wisc/MetaMorpheus]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002827
name: MetaMorpheus:score
def: "MetaMorpheus score for PSMs." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002828
name: MetaMorpheus:protein score
def: "MetaMorpheus score for protein groups." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better

************ new terms for XCMS
[Term]
id: MS:1002829
name: XCMS:into
def: "Feature intensity produced by XCMS findPeaks() from integrated 
peak intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002830
name: XCMS:intf
def: "Feature intensity produced by XCMS findPeaks() from baseline 
corrected integrated peak intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002831
name: XCMS:maxo
def: "Feature intensity produced by XCMS findPeaks() from maximum peak 
intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002832
name: XCMS:area
def: "Feature intensity produced by XCMS findPeaks() from feature area 
that is not normalized by the scan rate." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

************ new term 'alternating polarity mode'
[Term]
id: MS:1002833
name: alternating polarity mode
def: "Polarities of the scans of a run are alternating, i.e. both 
positive and negative mode scans are acquired." [PSI:PI]
is_a: MS:1000857 ! run attribute

************ new cleavage agent terms
[Term]
id: MS:1002834
name: (?<=[K])(?\!P)
def: "Regular expression for Trypsin/K." [PSI:PI]
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1002835
name: Trypsin/K
def: "Cleavage agent Trypsin/K." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1002834 ! (?<=[K])(?\!P)

[Term]
id: MS:1002836
name: (?<=[R])(?\!P)
def: "Regular expression for Trypsin/R." [PSI:PI]
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1002837
name: Trypsin/R
def: "Cleavage agent Trypsin/R." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1002834 ! (?<=[R])(?\!P)


Changed CV terms in version 4.0.15_rc3 of psi-ms.obo:
=====================================================
************ Changed the definition
[Term]
id: MS:1000465
name: scan polarity
def: "Relative orientation of the electromagnetic field during the 
selection and detection of ions in the mass spectrometer." [PSI:MS]
relationship: part_of MS:1000441 ! scan


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 4.0.15_rc2 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.15_rc2 of the psi-ms.obo file.

It contains new terms for the MetaMorpheus search engine,
new terms for the metabolomics software package XCMS and
a new term for 'alternating polarity mode',


New CV terms in version 4.0.15_rc2 of psi-ms.obo:
=================================================
************ new terms for the MetaMorpheus search engine
[Term]
id: MS:1002826
name: MetaMorpheus
def: "MetaMorpheus search engine." 
[https://github.com/smith-chem-wisc/MetaMorpheus]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002827
name: MetaMorpheus:score
def: "MetaMorpheus score for PSMs." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002828
name: MetaMorpheus:protein score
def: "MetaMorpheus score for protein groups." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better

************ new terms for XCMS
[Term]
id: MS:1002829
name: XCMS:into
def: "Feature intensity produced by XCMS findPeaks() from integrated 
peak intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002830
name: XCMS:intf
def: "Feature intensity produced by XCMS findPeaks() from baseline 
corrected integrated peak intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002831
name: XCMS:maxo
def: "Feature intensity produced by XCMS findPeaks() from maximum peak 
intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002832
name: XCMS:area
def: "Feature intensity produced by XCMS findPeaks() from feature area 
that is not normalized by the scan rate." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

************ new term 'alternating polarity mode'
[Term]
id: MS:1002833
name: alternating polarity mode
def: "Polarities of the scans of a run are alternating, i.e. both 
positive and negative mode scans are acquired." [PSI:PI]
is_a: MS:1000857 ! run attribute


Changed CV terms in version 4.0.15_rc2 of psi-ms.obo:
=====================================================
************ Changed the definition
[Term]
id: MS:1000465
name: scan polarity
def: "Relative orientation of the electromagnetic field during the 
selection and detection of ions in the mass spectrometer." [PSI:MS]
relationship: part_of MS:1000441 ! scan


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] [HUPO-PSI/psi-ms-CV] Alternating polarity missing (#7)

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

Hello Steffen,

would it make sense to make 'alternating polarity scan' a child of 'run 
attribute'?

[Term]
id: MS:1002826
name: alternating polarity mode
def: "Polarities of the scans of a run are alternating, i.e. both 
positive and negative mode scans are acquired." [PSI:MS]
is_a: MS:1000857 ! run attribute

Cheers,
Gerhard


Am 24.08.2017 um 00:16 schrieb sneumann:
>
> Hi, the reason I brought this up was because ISA-Tab is describing the 
> content of an mzML file, i.e. an attribute of the |<run>| as such 
> being positive/negative/alternating.
> As indicated in my first comment, "alternating" can't be a scan 
> attribute, but when I searched our obo for "alternating" that parent 
> term came up. Maybe that was the reason why alternating was obsoleted:
> https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo#L3241
> So a better home for "alternating polarity" could be "MS:1001954 
> acquisition parameter" (which currently has no children at all ?!) and 
> which resides below the |<scanSettings>| of the mzML,
> which I think is the closest to describing the instrument method we 
> can find in mzML.
> The mapping file currently does not specify which CV terms can go 
> below |<scanSettings>|.
> I also realised we had obsoleted "ionization mode" 
> https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo#L111 , 
> which probably sounded a bad idea as scan attribute, but which might 
> have been good to keep among the |<scanSettings>|.
>
> So what about:
>
>  1. Grammar fix, plus removal of mentioning alternating as scan attribute:
>
> |[Term] id: MS:1000465 name: scan polarity def: "An acquisition mode to 
> which specifies whether polarity is negative or positive." [PSI:MS] 
> relationship: part_of MS:1000441 ! scan |
>
>  2. still add "alternating", but with different parent than proposed
>     above:
>
> |[Term] id: MS:1000XXX name: alternating polarity mode def: "Polarity 
> of the scans is alternating, i.e. both positive and negative mode 
> scans are acquired.[PSI:MS] is_a: MS:1000009 ! ionization mode |
>
>  3. Consider re-adding MS:1000009 ! ionization mode, but now as
>     acquisition parameter (not sure what it was before):
>
> |[Term] id: MS:1000009 name: ionization mode def: "Whether positive or 
> negative ions are selected for analysis by the spectrometer." [PSI:MS] 
> is_a: MS:1001954 ! acquisition parameter |
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub 
> <https://github.com/HUPO-PSI/psi-ms-CV/issues/7#issuecomment-324478232>, 
> or mute the thread 
> <https://github.com/notifications/unsubscribe-auth/ADJPfHFTaplW-9_kaetXCkqBJS5mRqHJks5sbKSrgaJpZM4O_syz>.
>

-- 

*--------------------------------------------------------------------*

*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] EuBIC 2018 developer's meeting – Save the date & call for project proposals

[David H. <hol...@gm...>]

Hi, I just had a look at the winterschool page on 
https://www.proteomics-academy.org/ws-2018 and I think it would be good to 
update the relevant links there to include this one 
http://uahost.uantwerpen.be/eubic18/ 
<http://www.google.com/url?q=http%3A%2F%2Fuahost.uantwerpen.be%2Feubic18%2F&sa=D&sntz=1&usg=AFQjCNG5OiG9mIsU0W4YUjVf08HIEvTU1w>. 
It might be a bit difficult to find the most up to date information from 
the current state of the website.

Best,
David

Am Mittwoch, 2. August 2017 11:36:29 UTC+2 schrieb EuBIC developer's 
meeting:
>
> *— EuBIC 2018 developer’s meeting – Save the date & call for project 
> proposals —*
>
>  
>
> We are pleased to announce that the upcoming EuBIC 2018 developer’s 
> meeting will be held in Ghent, Belgium, on January 9-12, 2018.
>
>  
>
> The EuBIC 2018 developer's meeting will bring together scientists active 
> in the field of bioinformatics and computational proteomics.
>
>  
>
> Date: January 9-12, 2018
>
> Venue: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium
>
> Website: http://uahost.uantwerpen.be/eubic18/ 
> <http://www.google.com/url?q=http%3A%2F%2Fuahost.uantwerpen.be%2Feubic18%2F&sa=D&sntz=1&usg=AFQjCNG5OiG9mIsU0W4YUjVf08HIEvTU1w>
>
>  
>
> *Key dates*
>
>  
>
> September 17, 2017: Project proposal submission deadline
>
> October 2, 2017: Announcement of selected projects
>
> October 2, 2017: Conference registration opens
>
> January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent
>
>  
>
> *Call for project proposals*
>
>  
>
> The call for topics for the hackathon sessions during the EuBIC 2018 
> developer's meeting is now open!
>
>  
>
> During the EuBIC 2018 developer’s meeting the participants will engage in 
> a hackathon where they will develop bioinformatics tools and resources. The 
> participants will break up into small groups to work together on these 
> topics in an open, constructive, and productive atmosphere.
>
>  
>
> You can now submit project proposals for inclusion into the EuBIC 2018 
> developer’s meeting program. Submit your project proposal before 17 
> September through the meeting website: 
> http://uahost.uantwerpen.be/eubic18/submission.html
>
>  
>
> *Topics*
>
>  
>
> Hackathon projects can cover all topics in proteomics bioinformatics, 
> including, but not limited to:
>
> - Tools
>
>     - Extension of existing bioinformatics tools under the guidance of 
> their original authors
>
>     - Development of novel bioinformatics tools to solve open problems
>
> - Benchmarking
>
>     - Compilation of gold-truth datasets
>
>     - Collection of reference algorithmic implementations
>
>     - Specification of benchmarking criteria
>
> - Workflows
>
>     - Definition of formal protocols
>
>     - Development of tutorials for bioinformatics software usage
>
> - Data analysis
>
>     - (Re)analysis of publicly available proteomics datasets
>
>  
>
> *More information*
>
>  
>
> - Website: http://uahost.uantwerpen.be/eubic18/
>
> - Social media hashtag: #EuBIC18
>
> - Conference email: *eub...@gmail.com <javascript:>*
>
>  
>
> *Sponsorship* inquiries are welcome at *eub...@gmail.com <javascript:>*
>
>  
>
>  
>
> We look forward to welcoming you in Ghent!
>
>  
>
> On behalf of the organizing committee,
>
>  
>
> Wout Bittremieux
>

[Psidev-ms-dev] mzTab developments

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

Here is copied a message I just posted on the mzTab for metabolomics google group. Copied here for information, since proteomics people may be interested in discussions around mzTab development.
Best wishes
Andy

*****

Hi all,

For those of you who were not at the EBI the last couple of days, here is a quick summary of what was discussed and decided at the workshop. Longer version of the minutes are here: https://docs.google.com/document/d/1d77BzfyZLCz-5TPiVEun-8G8VBOxGOjkD-HhaqWanz4/edit

Outcomes
We are working towards an mzTab-M 1.1 release over the next few months, and there is a spec doc in GitHub that is close to release candidate status. In this document, the proteomics aspects have been stripped out, and it has been separated into core and metabolomics parts.

At the moment, there is no impetus to move proteomics to 1.1 release, so for now mzTab 1.0 is the stable proteomics standard. When further implementations are developed, then it might be that there is a desire to develop an mzTab-P 1.1 or 1.2 version, to fix bugs etc.

Towards release candidate, then release:
- We will convert the spec doc to an ascii doc format, which can be rendered for viewing, but can also be picked up by software - Nils is going to work on this.
- Nils is going to develop jmzTab and validation
- Joel is going to update the Progenesis QI exporter
- Steffen has already implemented a draft XCMS to mzTab exporter

The overall plan is to produce a release candidate over the next month or so, then look to submit to a document process before the year end. A PSI-like document process will be run, probably under an MSI banner.

We will resume fortnightly calls later on in Sept, and will make active use of GitHub issues list. I will also update the existing issues, with things discussed and resolved in the meeting.

best wishes
Andy

Re: [Psidev-ms-dev] Preparations for the Bioinformatics Hub at HUPO 2017

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

Hi everyone, I just updated the Hub page with the latest information about
Sunday:



https://github.com/CompMS/Overview/wiki/HUPO-2017



Please update the Doodle poll with your availability so that we can plan
accordingly:



http://doodle.com/poll/runkh2uwb5ztnmry



We know people are going to be there, please put your name down! Yasset,
Yassene, Lennart, Yves, Sue, Sam, David, Nuno, Henry, Hannes, George,
Mohammed, Steffen, Sandra, Gerben, everyone else, please respond!



Thanks,

Eric





*From:* Juan Antonio Vizcaino [mailto:ju...@eb...]
*Sent:* Monday, August 21, 2017 8:50 AM
*To:* 'psi...@li...' (
psi...@li...) <Psi...@li...>;
Mass spectrometry standard development <psi...@li...>;
co...@go...
*Cc:* Lennart Martens <len...@UG...>; Yasset Perez-Riverol <
yp...@eb...>; Andy Jones <And...@li...>; Eric Deutsch <
ede...@sy...>; Henning Hermjakob <hh...@eb...>; Mathias
Walzer <wa...@eb...>
*Subject:* Preparations for the Bioinformatics Hub at HUPO 2017



Dear all,



In order to make some preparations for the “Bioinformatics Hub” during HUPO
2017 in Dublin, we would need to know who is planning to attend the event.



I have created a Doodle poll to record this information. Please select
those days where you are planning to go to the event. It does not mean that
you will not be there all the time, but at least you are planning to spend
some time there:



http://doodle.com/poll/runkh2uwb5ztnmry





It is important to highlight that for Sunday (September 17th), the event
will not take place in the convention center. It will take place in the
O’Brien Science Centre on the UCD Campus, as the other events planned for
Sunday morning/early afternoon. So, extra arrangements need to be done for
that day. We have been asked by the organisers to tell everyone that will
be attending the event on Sunday to get registered properly for the
"Bioinformatics Hub" (for planning the catering, among other reasons).  To
register, you need to send an e-mail to:



HU...@co...



I will also create an issue in the CompMS GitHub page, containing this
information. This is the wiki page for the event. The content at this point
is what we did in Taiwan last year:



https://github.com/CompMS/Overview/wiki/HUPO-2017





Best regards,



Juan



P.S. Please send this e-mail to anyone that you think would be interested
in attending.

Re: [Psidev-ms-dev] Release candidate 4.0.15_rc1 of psi-ms.obo

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

Hi Gerhard, thanks for this. I think we should consider and revise this a
bit more before committing.



Everyone, if you care about this topic, please see ongoing GitHub
conversation:



https://github.com/HUPO-PSI/psi-ms-CV/issues/7



thanks!

Eric







*From:* mayerg97 via Psidev-ms-dev [mailto:
psi...@li...]
*Sent:* Wednesday, August 23, 2017 4:58 AM
*To:* psi...@li...;
psi...@li...; Mass spectrometry standard development
<psi...@li...>
*Cc:* mayerg97 <ger...@ru...>
*Subject:* [Psidev-ms-dev] Release candidate 4.0.15_rc1 of psi-ms.obo



Dear proteomics community,

attached there's the release candidate 4.0.15_rc1 of the psi-ms.obo file.
It contains one new term for 'alternating polarity scans'.


New CV terms in version 4.0.15_rc1 of psi-ms.obo:
=================================================
************ new term 'alternating polarity scans'
[Term]
id: MS:1002826
name: alternating polarity scans
def: "Polarities of the scans are alternating." [PSI:PI]
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute


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 4.0.15_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.15_rc1 of the psi-ms.obo file.
It contains one new term for 'alternating polarity scans'.


New CV terms in version 4.0.15_rc1 of psi-ms.obo:
=================================================
************ new term 'alternating polarity scans'
[Term]
id: MS:1002826
name: alternating polarity scans
def: "Polarities of the scans are alternating." [PSI:PI]
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute


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] Preparations for the Bioinformatics Hub at HUPO 2017

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

Dear all,

In order to make some preparations for the “Bioinformatics Hub” during HUPO 2017 in Dublin, we would need to know who is planning to attend the event.

I have created a Doodle poll to record this information. Please select those days where you are planning to go to the event. It does not mean that you will not be there all the time, but at least you are planning to spend some time there:

http://doodle.com/poll/runkh2uwb5ztnmry <http://doodle.com/poll/runkh2uwb5ztnmry>


It is important to highlight that for Sunday (September 17th), the event will not take place in the convention center. It will take place in the O’Brien Science Centre on the UCD Campus, as the other events planned for Sunday morning/early afternoon. So, extra arrangements need to be done for that day. We have been asked by the organisers to tell everyone that will be attending the event on Sunday to get registered properly for the "Bioinformatics Hub" (for planning the catering, among other reasons).  To register, you need to send an e-mail to: 

HU...@co... <mailto:HU...@co...>

I will also create an issue in the CompMS GitHub page, containing this information. This is the wiki page for the event. The content at this point is what we did in Taiwan last year:

https://github.com/CompMS/Overview/wiki/HUPO-2017 <https://github.com/CompMS/Overview/wiki/HUPO-2017>


Best regards,

Juan 

P.S. Please send this e-mail to anyone that you think would be interested in attending.

Re: [Psidev-ms-dev] New version 4.0.14 of psi-ms.obo

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

Thank you, Gerhard!





*From:* mayerg97 via Psidev-ms-dev [mailto:
psi...@li...]
*Sent:* Tuesday, August 08, 2017 3:06 AM
*To:* psi...@li...;
psi...@li...; Mass spectrometry standard development
<psi...@li...>
*Cc:* mayerg97 <ger...@ru...>
*Subject:* [Psidev-ms-dev] New version 4.0.14 of psi-ms.obo



Dear proteomics community,

attached there's the new version 4.0.14 of the psi-ms.obo file.
It contains new terms for OpenMS file formats.


New CV terms in version 4.0.14 of psi-ms.obo:
=============================================
************ new terms for OpenMS file formats
[Term]
id: MS:1002822
name: OpenMS file format
def: "File format developed by the OpenMS team." [PMID: 27575624]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002823
name: idXML
def: "OpenMS intermediate identification format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format

[Term]
id: MS:1002824
name: featureXML
def: "OpenMS feature file format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format

[Term]
id: MS:1002825
name: consensusXML
def: "OpenMS consensus map format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format


Changed CV terms in version 4.0.14 of psi-ms.obo:
=================================================
************ Changed name from
************ Andromeda result file --> Andromeda result format
[Term]
id: MS:1002576
name: Andromeda result format
def: "Andromeda result file output format." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

************ Changed the definitions
[Term]
id: MS:1001421
name: pepXML format
def: "The XML-based pepXML file format for encoding PSM information,
created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001422
name: protXML format
def: "The XML-based protXML file format for encoding protein
identifications, created and maintained by the Trans-Proteomic Pipeline
developers." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

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 4.0.14 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 4.0.14 of the psi-ms.obo file.
It contains new terms for OpenMS file formats.


New CV terms in version 4.0.14 of psi-ms.obo:
=============================================
************ new terms for OpenMS file formats
[Term]
id: MS:1002822
name: OpenMS file format
def: "File format developed by the OpenMS team." [PMID: 27575624]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002823
name: idXML
def: "OpenMS intermediate identification format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format

[Term]
id: MS:1002824
name: featureXML
def: "OpenMS feature file format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format

[Term]
id: MS:1002825
name: consensusXML
def: "OpenMS consensus map format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format


Changed CV terms in version 4.0.14 of psi-ms.obo:
=================================================
************ Changed name from
************ Andromeda result file --> Andromeda result format
[Term]
id: MS:1002576
name: Andromeda result format
def: "Andromeda result file output format." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

************ Changed the definitions
[Term]
id: MS:1001421
name: pepXML format
def: "The XML-based pepXML file format for encoding PSM information, 
created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001422
name: protXML format
def: "The XML-based protXML file format for encoding protein 
identifications, created and maintained by the Trans-Proteomic Pipeline 
developers." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

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 4.0.14_rc1 of psi-ms.obo

[Walzer <wa...@eb...>]

Hi,

I agree with Steffen that mitigating the restriction to something more 
open (like a originating description) is a good idea.

best,

On 04/08/17 08:27, Neumann, Steffen wrote:
> Hi,
>
> I am a bit unsure about this description as OpenMS *specific* formats,
> what if xcms would read/write that one day ?
>
> While we have prior examples (MGF ...) a slight modification
> could be "File format developed by the OpenMS team."
>
> I know that this is nitpicking, just wanted to share my 2c,
> and it's the OpenMS team and/or Gerd to decide.
>
> Yours,
> Steffen
>
>
> On Fri, 2017-07-21 at 09:32 +0200, mayerg97 via Psidev-ms-dev wrote:
>> Dear proteomics community,
>>
>> attached there's the release candidate 4.0.14_rc1 of the psi-ms.obo
>> file.
>> It contains new terms for OpenMS file formats.
>>
>>
>> New CV terms in version 4.0.14_rc1 of psi-ms.obo:
>> =================================================
>> ************ new terms for OpenMS file formats
>> [Term]
>> id: MS:1002822
>> name: OpenMS file format
>> def: "A file format specific for the OpenMS software." [PMID:
>> 27575624]
>> is_a: MS:1001459 ! file format
>>
>> [Term]
>> id: MS:1002823
>> name: idXML
>> def: "OpenMS intermediate identification format." [PSI:PI]
>> is_a: MS:1002822 ! OpenMS file format
>>
>> [Term]
>> id: MS:1002824
>> name: featureXML
>> def: "OpenMS feature file format." [PSI:PI]
>> is_a: MS:1002822 ! OpenMS file format
>>
>> [Term]
>> id: MS:1002825
>> name: consensusXML
>> def: "OpenMS consensus map format." [PSI:PI]
>> is_a: MS:1002822 ! OpenMS file format
>>
>>
>> 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
>> -------------------------------------------------------------------
>> -----------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

Re: [Psidev-ms-dev] Release candidate 4.0.14_rc1 of psi-ms.obo

[Neumann, S. <sne...@ip...>]

Hi,

I am a bit unsure about this description as OpenMS *specific* formats, 
what if xcms would read/write that one day ? 

While we have prior examples (MGF ...) a slight modification 
could be "File format developed by the OpenMS team."

I know that this is nitpicking, just wanted to share my 2c,
and it's the OpenMS team and/or Gerd to decide.

Yours,
Steffen


On Fri, 2017-07-21 at 09:32 +0200, mayerg97 via Psidev-ms-dev wrote:
> Dear proteomics community,
> 
> attached there's the release candidate 4.0.14_rc1 of the psi-ms.obo
> file.
> It contains new terms for OpenMS file formats.
> 
> 
> New CV terms in version 4.0.14_rc1 of psi-ms.obo:
> =================================================
> ************ new terms for OpenMS file formats
> [Term]
> id: MS:1002822
> name: OpenMS file format
> def: "A file format specific for the OpenMS software." [PMID:
> 27575624]
> is_a: MS:1001459 ! file format
> 
> [Term]
> id: MS:1002823
> name: idXML
> def: "OpenMS intermediate identification format." [PSI:PI]
> is_a: MS:1002822 ! OpenMS file format
> 
> [Term]
> id: MS:1002824
> name: featureXML
> def: "OpenMS feature file format." [PSI:PI]
> is_a: MS:1002822 ! OpenMS file format
> 
> [Term]
> id: MS:1002825
> name: consensusXML
> def: "OpenMS consensus map format." [PSI:PI]
> is_a: MS:1002822 ! OpenMS file format
> 
> 
> 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
> -------------------------------------------------------------------
> -----------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
-- 

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

[Psidev-ms-dev] EuBIC 2018 developer's meeting – Save the date & call for project proposals

[EuBIC developer's m. <eu...@gm...>]

*— EuBIC 2018 developer’s meeting – Save the date & call for project
proposals —*



We are pleased to announce that the upcoming EuBIC 2018 developer’s meeting
will be held in Ghent, Belgium, on January 9-12, 2018.



The EuBIC 2018 developer's meeting will bring together scientists active in
the field of bioinformatics and computational proteomics.



Date: January 9-12, 2018

Venue: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium

Website: http://uahost.uantwerpen.be/eubic18/



*Key dates*



September 17, 2017: Project proposal submission deadline

October 2, 2017: Announcement of selected projects

October 2, 2017: Conference registration opens

January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent



*Call for project proposals*



The call for topics for the hackathon sessions during the EuBIC 2018
developer's meeting is now open!



During the EuBIC 2018 developer’s meeting the participants will engage in a
hackathon where they will develop bioinformatics tools and resources. The
participants will break up into small groups to work together on these
topics in an open, constructive, and productive atmosphere.



You can now submit project proposals for inclusion into the EuBIC 2018
developer’s meeting program. Submit your project proposal before 17
September through the meeting website:
http://uahost.uantwerpen.be/eubic18/submission.html



*Topics*



Hackathon projects can cover all topics in proteomics bioinformatics,
including, but not limited to:

- Tools

    - Extension of existing bioinformatics tools under the guidance of
their original authors

    - Development of novel bioinformatics tools to solve open problems

- Benchmarking

    - Compilation of gold-truth datasets

    - Collection of reference algorithmic implementations

    - Specification of benchmarking criteria

- Workflows

    - Definition of formal protocols

    - Development of tutorials for bioinformatics software usage

- Data analysis

    - (Re)analysis of publicly available proteomics datasets



*More information*



- Website: http://uahost.uantwerpen.be/eubic18/

- Social media hashtag: #EuBIC18

- Conference email: *eu...@gm... <eu...@gm...>*



*Sponsorship* inquiries are welcome at *eu...@gm...
<eu...@gm...>*





We look forward to welcoming you in Ghent!



On behalf of the organizing committee,



Wout Bittremieux

Re: [Psidev-ms-dev] mzTab 1.1

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

Just copying this message over from the mzTab for metabolomics Google group. Plan for mzTab workshop on 22nd and 23rd Aug at the EBI.

Best wishes
Andy


*************

Hi all,
It doesn't seem perfect but it seems that 22nd and 23rd August seems possible for most interested people. Can we hold those days everyone?

Ken, I think you're now signed up for this list - can you tell me if there is an EBI room available for I guess around 10 people max on those days. I don't have a budget I can easily spend on this, can everyone cover their own costs to get to EBI and for lunches/dinners?

I've started a google sheet for people to register at, where I will also add an agenda. Please put your name down and any notes about travel plans etc
https://docs.google.com/spreadsheets/d/1R2fINJ5aXfQyTa0s0pTiISh7kpUgeozyqkqfkMn8PSI/edit?usp=sharing

Any questions, drop me a mail or discuss here.
cheers
Andy


From: Jones, Andy [mailto:And...@li...]
Sent: 26 July 2017 10:42
To: psi...@li...
Subject: [Psidev-pi-dev] mzTab 1.1

Hi all,

I have started discussions with the EBI Metabolights team about possibly having a 1.5 or 2 day workshop there around 21st – 24th Aug to work on finishing mzTab 1.1, I have also posted this on the https://groups.google.com/forum/#!forum/mztab4metabolomics Google Group. Please reply through either list if you’re interested in joining, and which dates you’re free.
Best wishes
Andy

[Psidev-ms-dev] HUPO PSI recommendation document (file format PSI-MI XML 3.0.0), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

http://www.psidev.info for an overview of activities).

 

There has been a submission to the PSI Document Process 

by the Molecular Interactions workgroup updating the 

PSI-MI format to version 3.0.0 

(from long-time stable XML 2.5, released 2005).

 

The submission (incl. current version of the specification document) can

be found here:

http://www.psidev.info/PSI-MI-in-docproc

 

After having passed a review of the PSI steering group 

with minor changes, the proposed document version 3.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 29th September 2017).

 

Purpose of the format (excerpt from the spec. doc.):

“The existing XML standard (PSI-MI XML2.5) has proven to be, 

and will continue to be, capable of capturing the vast majority 

of molecular interaction data, which are generated by 

techniques such as protein complementation assays, 

affinity capture, biophysical measurements and enzyme assays. 

However, use cases have arisen which cannot be adequately 

described within this XML schema, for example allosteric 

interactions, abstracted interactions and dynamic interactions. 

In order to meet these specialist use cases, a new version of

the XML format has been developed, PSI-MI XML3.0.”

 

Specification document: attached and at

http://www.psidev.info/PSI-MI-in-docproc

Schema MIF300.xsd:
https://github.com/HUPO-PSI/miXML/blob/master/3.0/src/MIF300.xsd 

Schema documentation (Schema browser):
<https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html>
https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html

Schema documentation and use case examples (as Word docs.): 

See appendix documents

at https://github.com/HUPO-PSI/miXML/tree/master/3.0/pub 

or
<https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0>
https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0

(details of appendices in the spec. doc. and below).

 

 PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/PSI-MI-in-docproc) 

or send them directly to martin.eisenacher: at : rub.de for 

example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

 


1.      Appendices


Example files showing how the schema meets each of the use cases listed in
section 1.3. Note, all examples available in the IntAct database (
<http://www.ebi.ac.uk/intact> www.ebi.ac.uk/intact) unless otherwise stated


1.1         Appendix 1 Schema documentation for MIF300.xsd


1.2         Appendix 2 Example file showing the representation of all
molecular interaction data from a single publication (PMID: 26919541) in
PSI-MI XML3.0 – note, includes use case 1.3k, rewrite of bibliography
section


1.3         Appendix 3 Representation of a negative feature range (use case
1.3a)


1.4         Appendix 4 Representation of the sequence change caused by
introduction of a mutation (use case 1.3b)


1.5         Appendix 5 Representation of multiple feature detection methods
and feature roles (use cases 1.3c, 1.3d)


1.6         Appendix 6 Representation of kinetic parameters added at feature
level (use case 1.3e)


1.7         Appendix 7 Representation of variable conditions (dynamic
interactions) in an experiment (use case 1.3f)


1.8         Appendix 8 Representation of an abstracted interaction, a
manually curated protein complex, in PSI-MI XML3.0 (use case 1.3g)


1.9         Appendix 9 Representation of a cooperative interaction in PSI-MI
XML3.0 (Use case 1.3h)


1.10     Appendix 10 Representation of molecule sets i.e. cases where a
participant may be one of a list of molecules (use case 1.3i)


1.11     Appendix 11 Representation of the systematic capture of the
stoichiometry of molecules within an interaction (use case 1.3j)


 

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

 

[Psidev-ms-dev] Release candidate 4.0.14_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 4.0.14_rc1 of the psi-ms.obo file.
It contains new terms for OpenMS file formats.


New CV terms in version 4.0.14_rc1 of psi-ms.obo:
=================================================
************ new terms for OpenMS file formats
[Term]
id: MS:1002822
name: OpenMS file format
def: "A file format specific for the OpenMS software." [PMID: 27575624]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002823
name: idXML
def: "OpenMS intermediate identification format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format

[Term]
id: MS:1002824
name: featureXML
def: "OpenMS feature file format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format

[Term]
id: MS:1002825
name: consensusXML
def: "OpenMS consensus map format." [PSI:PI]
is_a: MS:1002822 ! OpenMS file format


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 1.1.0 of XLMOD.obo

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

Dear proteomics community,

attached there's the new version 1.1.0 of the XLMOD.obo file
for cross-linking reagents.

It contains many new terms for cross-linker reagents, PTM's derived from
them and new "cross-linking attribute"'s describing their properties, e.g.
property_value: spacerLength: "x.y" xsd:float
or information about their cleavability, labelling, handles used
for click chemistry or enrichment, ...

I used the following index ranges:
==================================
reactive groups and attributes have ID's below XLMOD:01000
(mono-functional) cross-linker related PTM's have ID's above XLMOD:01000
label transfer reagents have ID's above XLMOD:01800
analogues of amino acids have ID's above XLMOD:01900
bi-functional cross-linker have ID's above XLMOD:02000
tri-functional cross-linker have ID's above XLMOD:03000

Of course the ID's of our old version (releases/2016-07-13) were not 
changed.

Where available I added also cross-references to databases
like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ...

I removed the chemical reaction-specificities from the cross-linkers to the
reactive groups, which are now terms by their own, i.e. each 
cross-linker has now a
relationship: has_reactive_group XLMOD:0xxxx ! ...

Therefore the specificities have to be specified only once for each 
reactive group,
which avoids unnecessary redundancies.

I added also terms under the branch "label transfer reagents",
which are not yet contained in PSI-MOD.obo / unimod.obo

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 4.0.13 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 4.0.13 of the psi-ms.obo file.
It contains terms for defining adduct ions and for ion mobility mass 
spectrometry (IM-MS).


New CV terms in version 4.0.13 of psi-ms.obo:
=============================================
************ new terms for adduct ions
[Term]
id: MS:1002806
name: ion
def: "An atomic or molecular species having a net positive or negative 
electric charge." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Ontology

[Term]
id: MS:1002807
name: positive mode adduct ion
def: "Adduct ion with positive ionization." [PSI:MS]
is_a: MS:1000353 ! adduct ion

[Term]
id: MS:1002808
name: negative mode adduct ion
def: "Adduct ion with negative ionization." [PSI:MS]
is_a: MS:1000353 ! adduct ion

[Term]
id: MS:1002809
name: adduct ion attribute
def: "Attribute describing an adduct formation." [PSI:PI]
is_a: MS:1000547 ! object attribute

[Term]
id: MS:1002810
name: adduct ion mass
def: "Mass of an adduct formation specified by the given value." 
[DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute

[Term]
id: MS:1002811
name: adduct ion isotope
def: "Isotope of the matrix molecule M of an adduct formation." 
[PMID:18790129]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute

[Term]
id: MS:1002812
name: Regular expression for adduct ion formula
def: 
"(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." 
[PSI:PI]
is_a: MS:1002479 ! regular expression

[Term]
id: MS:1002813
name: adduct ion formula
def: "Adduct formation formula specified by the given value." 
[PMID:22111785, DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute
relationship: has_regexp MS:1002812 ! 
(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])


************ new terms for IM-MS
[Term]
id: MS:1002814
name: volt-second per square centimeter
def: "An electrical mobility unit that equals the speed [cm/s] an ion 
reaches when pulled through a gas by a Voltage[V] over a certain 
distance [cm]." [PSI:PI]
synonym: "Vs/cm^2" EXACT []
is_a: UO:0000000 ! unit

[Term]
id: MS:1002815
name: inverse reduced ion mobility
def: "Ion mobility measurement for an ion or spectrum of ions as 
measured in an ion mobility mass spectrometer. This might refer to the 
central value of a bin into which all ions within a narrow range of 
mobilities have been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1000503 ! scan attribute
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of drift times or inverse reduced ion mobilities, averaged 
from a matrix of binned m/z and ion mobility values, corresponding to a 
spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

[Term]
id: MS:1002817
name: Bruker TDF format
def: "Bruker TDF raw file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002818
name: Bruker TDF nativeID format
def: "Native format defined by frame=xsd:nonNegativeInteger 
scan=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1002819
name: Bruker TDF nativeID format, combined spectra
def: "Bruker TDF comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

************ some concrete ion species
************ are there other concrete ions species, which should be 
included here?
[Term]
id: MS:1002820
name: M+H ion
def: "M+H ion from positive ion mode (M in the property ionMass denotes 
the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
property_value: ionMass: "M + 1.007276" xsd:string
is_a: MS:1002807 ! positive mode adduct ion

[Term]
id: MS:1002821
name: M-H ion
def: "M-H ion from negative ion mode (M in the property ionMass denotes 
the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
property_value: ionMass: "M - 1.007276" xsd:string
is_a: MS:1002808 ! negative mode adduct ion


Changed CV terms in version 4.0.13 of psi-ms.obo:
=================================================
************ Reactivated the obsolete term 'adduct ion'
[Term]
id: MS:1000353
name: adduct ion
def: "Ion formed by the interaction of an ion with one or more atoms or 
molecules to form an ion containing all the constituent atoms of the 
precursor ion as well as the additional atoms from the associated atoms 
or molecules." [PSI:MS]
is_a: MS:1002806 ! ion

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] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 1.1.0_rc1 of XLMOD.obo

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

For example the current pride-mod library in PRIDE needs to handle three 
different providers: UNIMOD, PSI-MS and PSI-MOD.


On 27/06/2017 11:08, Yasset Perez-Riverol wrote:
>
> Why not adding this into PSI-MS as a section as you already did. It 
> would be great to have this only in one place. We have already 
> fragment neutral loss in the PSI-MS 
> http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001524 
> . I recommend to extend only this concept and do not create another 
> Obo file, for two main reasons:
>
>   - Is not recommended in any of our file formats.
>
>   - It is something will not growth more than a ~100 terms, then we 
> need to mantain another file just for a few number of terms.
>
>   - It will be in two files the same information in PSI-MS and XLMOD 
> obo, we will need to take care of sync, etc.
>
> Hope you understand my points.
>
> Regards
>
> Yasset
>
>
> On 27/06/2017 10:58, Jones, Andy wrote:
>>
>> It is stand-alone for the moment – for encoding cross-linking 
>> reagents that didn’t fit easily into other mod CVs (PSI-MOD or 
>> Unimod) for different reasons
>>
>> *From:*Yasset Perez-Riverol [mailto:yp...@eb...]
>> *Sent:* 27 June 2017 10:53
>> *To:* mayerg97 <ger...@ru...>; 
>> psi...@li...; 
>> psi...@li...; Mass spectrometry standard 
>> development <psi...@li...>; Lutz Fischer 
>> <lfi...@st...>; le...@im...
>> *Subject:* Re: [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 
>> 1.1.0_rc1 of XLMOD.obo
>>
>> Is this a new PTM ontology or this will be under PSI-MS?
>>
>> On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote:
>>
>>     Dear proteomics community,
>>
>>     attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo
>>     file
>>     for cross-linking reagents.
>>
>>     It contains many new terms for cross-linker reagents, PTM's
>>     derived from
>>     them and new "cross-linking attribute"'s describing their
>>     properties, e.g.
>>     property_value: spacerLength: "x.y" xsd:float
>>     or information about their cleavability, labelling, handles used
>>     for click chemistry or enrichment, ...
>>
>>     I used the following index ranges:
>>     ===========================
>>     reactive groups and attributes have ID's below XLMOD:01000
>>     (mono-functional) cross-linker related PTM's have ID's above
>>     XLMOD:01000
>>     label transfer reagents have ID's above XLMOD:01800
>>     analogues of amino acids have ID's above XLMOD:01900
>>     bi-functional cross-linker have ID's above XLMOD:02000
>>     tri-functional cross-linker have ID's above XLMOD:03000
>>
>>     Of course the ID's of our old version (releases/2016-07-13) were
>>     not changed.
>>
>>     Where available I added also cross-references to databases
>>     like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ...
>>
>>     I removed the chemical reaction-specificities from the
>>     cross-linkers to the
>>     reactive groups, which are now terms by their own, i.e. each
>>     cross-linker has now a
>>     relationship: has_reactive_group XLMOD:0xxxx ! ...
>>
>>     Therefore the specificities have to be specified only once for
>>     each reactive group,
>>     which avoids unnecessary redundancies.
>>
>>     I added also terms under the branch "label transfer reagents",
>>     which are not yet contained in PSI-MOD.obo / unimod.obo
>>
>>     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/>
>>
>>
>>
>>
>>     ------------------------------------------------------------------------------
>>
>>     Check out the vibrant tech community on one of the world's most
>>
>>     engaging tech sites, Slashdot.org!http://sdm.link/slashdot
>>
>>
>>
>>
>>     _______________________________________________
>>
>>     Psidev-pi-dev mailing list
>>
>>     Psi...@li...
>>     <mailto:Psi...@li...>
>>
>>     https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>>
>>
>>
>> -- 
>> Yasset Perez-Riverol PhD.
>> Project Leader: PRIDE Resources
>> Proteomics Services Team, PRIDE Group
>> European Bioinformatics Institute (EMBL-EBI)
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> United Kingdom
>> Twitter: @ypriverol
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org!http://sdm.link/slashdot
>>
>>
>> _______________________________________________
>> Psidev-pi-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
> -- 
> Yasset Perez-Riverol PhD.
> Project Leader: PRIDE Resources
> Proteomics Services Team, PRIDE Group
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Twitter: @ypriverol
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
Yasset Perez-Riverol PhD.
Project Leader: PRIDE Resources
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] [Psidev-ms-vocab] Release candidate 1.1.0_rc1 of XLMOD.obo

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

Why not adding this into PSI-MS as a section as you already did. It 
would be great to have this only in one place. We have already fragment 
neutral loss in the PSI-MS 
http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001524 
. I recommend to extend only this concept and do not create another Obo 
file, for two main reasons:

   - Is not recommended in any of our file formats.

   - It is something will not growth more than a ~100 terms, then we 
need to mantain another file just for a few number of terms.

   - It will be in two files the same information in PSI-MS and XLMOD 
obo, we will need to take care of sync, etc.

Hope you understand my points.

Regards

Yasset


On 27/06/2017 10:58, Jones, Andy wrote:
>
> It is stand-alone for the moment – for encoding cross-linking reagents 
> that didn’t fit easily into other mod CVs (PSI-MOD or Unimod) for 
> different reasons
>
> *From:*Yasset Perez-Riverol [mailto:yp...@eb...]
> *Sent:* 27 June 2017 10:53
> *To:* mayerg97 <ger...@ru...>; 
> psi...@li...; 
> psi...@li...; Mass spectrometry standard 
> development <psi...@li...>; Lutz Fischer 
> <lfi...@st...>; le...@im...
> *Subject:* Re: [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 
> 1.1.0_rc1 of XLMOD.obo
>
> Is this a new PTM ontology or this will be under PSI-MS?
>
> On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote:
>
>     Dear proteomics community,
>
>     attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file
>     for cross-linking reagents.
>
>     It contains many new terms for cross-linker reagents, PTM's
>     derived from
>     them and new "cross-linking attribute"'s describing their
>     properties, e.g.
>     property_value: spacerLength: "x.y" xsd:float
>     or information about their cleavability, labelling, handles used
>     for click chemistry or enrichment, ...
>
>     I used the following index ranges:
>     ===========================
>     reactive groups and attributes have ID's below XLMOD:01000
>     (mono-functional) cross-linker related PTM's have ID's above
>     XLMOD:01000
>     label transfer reagents have ID's above XLMOD:01800
>     analogues of amino acids have ID's above XLMOD:01900
>     bi-functional cross-linker have ID's above XLMOD:02000
>     tri-functional cross-linker have ID's above XLMOD:03000
>
>     Of course the ID's of our old version (releases/2016-07-13) were
>     not changed.
>
>     Where available I added also cross-references to databases
>     like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ...
>
>     I removed the chemical reaction-specificities from the
>     cross-linkers to the
>     reactive groups, which are now terms by their own, i.e. each
>     cross-linker has now a
>     relationship: has_reactive_group XLMOD:0xxxx ! ...
>
>     Therefore the specificities have to be specified only once for
>     each reactive group,
>     which avoids unnecessary redundancies.
>
>     I added also terms under the branch "label transfer reagents",
>     which are not yet contained in PSI-MOD.obo / unimod.obo
>
>     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/>
>
>
>
>
>     ------------------------------------------------------------------------------
>
>     Check out the vibrant tech community on one of the world's most
>
>     engaging tech sites, Slashdot.org!http://sdm.link/slashdot
>
>
>
>
>     _______________________________________________
>
>     Psidev-pi-dev mailing list
>
>     Psi...@li...
>     <mailto:Psi...@li...>
>
>     https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>
>
> -- 
> Yasset Perez-Riverol PhD.
> Project Leader: PRIDE Resources
> Proteomics Services Team, PRIDE Group
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Twitter: @ypriverol
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
Yasset Perez-Riverol PhD.
Project Leader: PRIDE Resources
Proteomics Services Team, PRIDE Group
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Twitter: @ypriverol

Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 1.1.0_rc1 of XLMOD.obo

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

It is stand-alone for the moment – for encoding cross-linking reagents that didn’t fit easily into other mod CVs (PSI-MOD or Unimod) for different reasons

From: Yasset Perez-Riverol [mailto:yp...@eb...]
Sent: 27 June 2017 10:53
To: mayerg97 <ger...@ru...>; psi...@li...; psi...@li...; Mass spectrometry standard development <psi...@li...>; Lutz Fischer <lfi...@st...>; le...@im...
Subject: Re: [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 1.1.0_rc1 of XLMOD.obo


Is this a new PTM ontology or this will be under PSI-MS?

On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote:

Dear proteomics community,

attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file
for cross-linking reagents.

It contains many new terms for cross-linker reagents, PTM's derived from
them and new "cross-linking attribute"'s describing their properties, e.g.
property_value: spacerLength: "x.y" xsd:float
or information about their cleavability, labelling, handles used
for click chemistry or enrichment, ...

I used the following index ranges:
===========================
reactive groups and attributes have ID's below XLMOD:01000
(mono-functional) cross-linker related PTM's have ID's above XLMOD:01000
label transfer reagents have ID's above XLMOD:01800
analogues of amino acids have ID's above XLMOD:01900
bi-functional cross-linker have ID's above XLMOD:02000
tri-functional cross-linker have ID's above XLMOD:03000

Of course the ID's of our old version (releases/2016-07-13) were not changed.

Where available I added also cross-references to databases
like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ...

I removed the chemical reaction-specificities from the cross-linkers to the
reactive groups, which are now terms by their own, i.e. each cross-linker has now a
relationship: has_reactive_group XLMOD:0xxxx ! ...

Therefore the specificities have to be specified only once for each reactive group,
which avoids unnecessary redundancies.

I added also terms under the branch "label transfer reagents",
which are not yet contained in PSI-MOD.obo / unimod.obo

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/>




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

Check out the vibrant tech community on one of the world's most

engaging tech sites, Slashdot.org! http://sdm.link/slashdot




_______________________________________________

Psidev-pi-dev mailing list

Psi...@li...<mailto:Psi...@li...>

https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev



--

Yasset Perez-Riverol PhD.

Project Leader: PRIDE Resources

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] Release candidate 1.1.0_rc1 of XLMOD.obo

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

Is this a new PTM ontology or this will be under PSI-MS?


On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote:
>
> Dear proteomics community,
>
> attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file
> for cross-linking reagents.
>
> It contains many new terms for cross-linker reagents, PTM's derived from
> them and new "cross-linking attribute"'s describing their properties, e.g.
> property_value: spacerLength: "x.y" xsd:float
> or information about their cleavability, labelling, handles used
> for click chemistry or enrichment, ...
>
> I used the following index ranges:
> ===========================
> reactive groups and attributes have ID's below XLMOD:01000
> (mono-functional) cross-linker related PTM's have ID's above XLMOD:01000
> label transfer reagents have ID's above XLMOD:01800
> analogues of amino acids have ID's above XLMOD:01900
> bi-functional cross-linker have ID's above XLMOD:02000
> tri-functional cross-linker have ID's above XLMOD:03000
>
> Of course the ID's of our old version (releases/2016-07-13) were not 
> changed.
>
> Where available I added also cross-references to databases
> like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ...
>
> I removed the chemical reaction-specificities from the cross-linkers 
> to the
> reactive groups, which are now terms by their own, i.e. each 
> cross-linker has now a
> relationship: has_reactive_group XLMOD:0xxxx ! ...
>
> Therefore the specificities have to be specified only once for each 
> reactive group,
> which avoids unnecessary redundancies.
>
> I added also terms under the branch "label transfer reagents",
> which are not yet contained in PSI-MOD.obo / unimod.obo
>
> 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/>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
Yasset Perez-Riverol PhD.
Project Leader: PRIDE Resources
Proteomics Services Team, PRIDE Group
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Twitter: @ypriverol

[Psidev-ms-dev] Release candidate 1.1.0_rc1 of XLMOD.obo

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

Dear proteomics community,

attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file
for cross-linking reagents.

It contains many new terms for cross-linker reagents, PTM's derived from
them and new "cross-linking attribute"'s describing their properties, e.g.
property_value: spacerLength: "x.y" xsd:float
or information about their cleavability, labelling, handles used
for click chemistry or enrichment, ...

I used the following index ranges:
===========================
reactive groups and attributes have ID's below XLMOD:01000
(mono-functional) cross-linker related PTM's have ID's above XLMOD:01000
label transfer reagents have ID's above XLMOD:01800
analogues of amino acids have ID's above XLMOD:01900
bi-functional cross-linker have ID's above XLMOD:02000
tri-functional cross-linker have ID's above XLMOD:03000

Of course the ID's of our old version (releases/2016-07-13) were not 
changed.

Where available I added also cross-references to databases
like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ...

I removed the chemical reaction-specificities from the cross-linkers to the
reactive groups, which are now terms by their own, i.e. each 
cross-linker has now a
relationship: has_reactive_group XLMOD:0xxxx ! ...

Therefore the specificities have to be specified only once for each 
reactive group,
which avoids unnecessary redundancies.

I added also terms under the branch "label transfer reagents",
which are not yet contained in PSI-MOD.obo / unimod.obo

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/>