psidev-pi-dev Mailing List for Proteomics Standards Initiative (Page 23)

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Hi all:
  This is the list of the psi-dev subscribers:
Arnaud CEOL 	aceol <https://sourceforge.net/u/aceol/> 	Admin
Bruno Aranda 	baranda <https://sourceforge.net/u/baranda/> 	Admin
Colin Combe 	cccolinc <https://sourceforge.net/u/cccolinc/> 	Admin
Chris Taylor 	chrisftaylor <https://sourceforge.net/u/chrisftaylor/> 	Admin
Angel Pizarro 	delagoya <https://sourceforge.net/u/delagoya/> 	Admin
Eric Deutsch 	edeutsch <https://sourceforge.net/u/edeutsch/> 	Admin
florian 	f_reisinger <https://sourceforge.net/u/userid-1867337/> 	Admin
Gary Bader 	gbader <https://sourceforge.net/u/gbader/> 	Admin
Henning Hermjakob 	hhe <https://sourceforge.net/u/hhe/> 	Admin
AndyJones 	jonesa21 <https://sourceforge.net/u/jonesa21/> 	Admin
Kai Runte 	krunte <https://sourceforge.net/u/krunte/> 	Admin
Oscar Forner Martinez 	maitesin <https://sourceforge.net/u/maitesin/> 
Admin
Marc Sturm 	marc_sturm <https://sourceforge.net/u/userid-923561/> 	Admin
Marine Dumousseau 	marine3 <https://sourceforge.net/u/marine3/> 	Admin
Lennart Martens 	martlenn <https://sourceforge.net/u/martlenn/> 	Admin
*Noemi del Toro Ayllón* 	*ntoro-ebi 
<https://sourceforge.net/u/ntoro-ebi/>* 	*Admin*
Sandra Orchard 	orchard <https://sourceforge.net/u/orchard/> 	Admin, 
Developer
Pierre-Alain Binz 	pabinz <https://sourceforge.net/u/pabinz/> 	Admin
Phil Jones (EBI) 	philip_jones 
<https://sourceforge.net/u/userid-1156700/> 	Admin
Pablo Porras 	pporras <https://sourceforge.net/u/pporras/> 	Admin
rajido 	rajido <https://sourceforge.net/u/rajido/> 	Admin
Randy Julian 	rkjulian <https://sourceforge.net/u/rkjulian/> 	Admin
*Simon Jupp* 	*simonjupp <https://sourceforge.net/u/simonjupp/>* 	*Admin*
Maximilian Koch 	tschaka1904 <https://sourceforge.net/u/tschaka1904/> 
Admin, Developer
Weimin Zhu 	weimin <https://sourceforge.net/u/weimin/> 	Admin
Antony Quinn 	aquinn <https://sourceforge.net/u/aquinn/> 	Developer
Matt Chambers 	chambm <https://sourceforge.net/u/chambm/> 	Developer
choogland 	choogland <https://sourceforge.net/u/choogland/> 	Developer
David Gloriam 	davidgloriam <https://sourceforge.net/u/davidgloriam/> 
Developer
Darren Kessner 	dkessner <https://sourceforge.net/u/dkessner/> 	Developer
david ovelleiro 	dovelleiro <https://sourceforge.net/u/dovelleiro/> 
Developer
Martin Eisenacher 	eisenach <https://sourceforge.net/u/eisenach/> 
Developer
Frank Gibson 	fgibson_sf <https://sourceforge.net/u/userid-1430184/> 
Developer
Fredrik Levander 	flevander <https://sourceforge.net/u/flevander/> 
Developer
Frank Potthast 	frank_ethz <https://sourceforge.net/u/userid-1029234/> 
Developer
gabbyreeves 	gabbyreeves <https://sourceforge.net/u/gabbyreeves/> 
Developer
*Gerhard Mayer* 	*gerhard64mayer 
<https://sourceforge.net/u/gerhard64mayer/>* 	*Developer*
Henning Mersch 	hmersch <https://sourceforge.net/u/hmersch/> 	Developer
John S. Garavelli 	jsgaravelli 
<https://sourceforge.net/u/jsgaravelli/> 	Developer
Lawrence Bower 	lbower <https://sourceforge.net/u/lbower/> 	Developer
luisa montecchi 	luisa_montecchi 
<https://sourceforge.net/u/userid-653048/> 	Developer
Lukasz Salwinski 	lukasz99 <https://sourceforge.net/u/lukasz99/> 	Developer
Matthias Oesterheld 	oesterheld 
<https://sourceforge.net/u/oesterheld/> 	Developer
Premanand Achuthan 	prem_intact 
<https://sourceforge.net/u/userid-2077443/> 	Developer
Puneet Souda 	psouda <https://sourceforge.net/u/psouda/> 	Developer
Peter Stockwell 	pstockwell <https://sourceforge.net/u/pstockwell/> 
Developer
Ruth McNally 	ruthmcnally <https://sourceforge.net/u/ruthmcnally/> 
Developer
Sara Abbani 	sara_1234 <https://sourceforge.net/u/userid-1577216/> 
Developer
*Salvador* 	*smartinez21 <https://sourceforge.net/u/smartinez21/>* 
*Developer*
Steffen Möller 	smoe <https://sourceforge.net/u/smoe/> 	Developer
volker 	stuempflen <https://sourceforge.net/u/stuempflen/> 	Developer
Susan Moore 	susanjmoore <https://sourceforge.net/u/susanjmoore/> 
Developer
Trish Whetzel 	whetzel <https://sourceforge.net/u/whetzel/> 	Developer

Would be important if all of you send the github account to add you to 
the github repos. If you are not interested to be part you can follow 
individual projects here:
    https://github.com/HUPO-PSI

Regards
Yasset

-- 
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

Hi all,

Various items from the sessions this morning in Gent:

1. mzid 1.2 validator not easy to locate on GitHub - Gerhard, are you able to make this prominently available as a build under a "Downloads" webpage on Githut. Apparently, it is fairly easy to build end user web-pages on GitHub - Tobias has experience of this.

2. There are various bugs in the validator - if you have identified one, please make sure to email it to Gerhard to fix

3. Eric has taken an action item to do some CV tidying, particularly around scores for PSMs, PTM, peptides, proteins and protein groups

4. We need ~11 new CV terms, as detailed in Table 2 of the spec doc (just pushed to GitHub) for combined spectra as input to searches

5. Term MS:102499 peptide level score should be deprecated as this was never intended to go in the CV - Gerhard, can you do this please

6. Terms starting "group PSMs by..." are under the wrong parent. They should be under a new parent term called "identification parameters", and a new link added to the mapping file for "AdditionalSearchParameters" allowing the child terms of this term to be used i.e. these terms are intended to be used in this part of the Protocol.

7. These terms: de novo, proteogenomics spectral  need an extra parent term: special processing (MS:1002489), so they trigger special behaviour of the validator.

Please add to this list with things I missed,
best wishes
Andy

Dear all

In attachment is the summary of the session on crosslinking.

Elien

Elien Vandermarliere, Dr
VIB Medical Biotechnology Center, Ugent
UGent faculteit Geneeskunde en Gezondheidswetenschappen
Albert Baertsoenkaai 3
B-9000 Gent
BELGIUM

Tel. +32 9 264 9359
Fax +32 9 264 9490
www.ugent.be
www.vib.be

From: Jones, Andy [mailto:And...@li...]
Sent: dinsdag 19 april 2016 16:56
To: tobias
Cc: eug...@tu...; le...@im...; Sule Yilmaz; ju...@ed...; Elien Vandermarliere; Lutz Fischer; Robert Chalkley; Juan Antonio Vizcaino; Yasset Perez-Riverol; psi...@li...
Subject: Cross-linking discussions at PSI meeting

Hi all,

This email is addressed to those who participated in the XL session at PSI today, plus Lutz and Robert (and plus Yasset for GitHub issues). Please forward this on to others who should be consulted. I have also copied to the PSI-PI list.

The major outcomes from today are as follows:

1. General agreement that we are nearly there with the mzid 1.2 encoding of XL info.
2. Plan for Lutz to maintain (via mzIdentML GitHub for example), a separate CV of crosslinker reagents, based off the attached sheet (converted to CSV format, with unique IDs per row e.g. XL:0001, XL:0002, more discussion needed to finalise format)
3. Some additions to mzid 1.2 to cover:
- cases of combined evidence from multiple input spectra (L v H isotopes; ETD+HCD; MS3 etc) to make an identification (not post-processing but intrinsic to the ID mechanism)
- Adding protein-level interaction evidence
- Re-using additions already proposed in mzid 1.2 for mod or XL localization ambiguity
4. No major interest at this stage to encode XL info in mztab, we may do this at our side following same model as mzid 1.2
5. Plan for wider project over medium to long term to write a cross-linking standards paper, including mzid 1.2 plus a minimum reporting guidelines doc (Juri / Alexander to progress this), with wider authorship
6. We will role these changes into mzid 1.2 specifications, and publish that paper separately (submitted in the short term). For those that contribute example files or major input of the specs, I will invite to join the author list of that paper.

I have started to write this up in the mzid 1.2 specification document (attached here and committed to our GitHub) - see pages 20-23), and an XML snippet for how the protein interaction part will look.

ACTION items:

- We discussed Lutz updating the xi export examples to include protein interaction scores, following our proposed spec
- Alexander and Eugen to update the examples exported from OpenMS and add to the mzid GitHub (please email Yasset - cc'd to get write access to the GitHub)
- Ideally, would be great if the Edinburgh visualisation software could read the mzid 1.2 files to see if all info is really covered
- Andy to continue cleaning and updating specification document

I would like to propose a conference call to progress this for 4pm UK/5pm Europe on Thurs 28th April - please reply to let me know if you can make it.

best wishes
Andy

Hi all,

This email is addressed to those who participated in the XL session at PSI today, plus Lutz and Robert (and plus Yasset for GitHub issues). Please forward this on to others who should be consulted. I have also copied to the PSI-PI list.

The major outcomes from today are as follows:

1. General agreement that we are nearly there with the mzid 1.2 encoding of XL info.
2. Plan for Lutz to maintain (via mzIdentML GitHub for example), a separate CV of crosslinker reagents, based off the attached sheet (converted to CSV format, with unique IDs per row e.g. XL:0001, XL:0002, more discussion needed to finalise format)
3. Some additions to mzid 1.2 to cover:
- cases of combined evidence from multiple input spectra (L v H isotopes; ETD+HCD; MS3 etc) to make an identification (not post-processing but intrinsic to the ID mechanism)
- Adding protein-level interaction evidence
- Re-using additions already proposed in mzid 1.2 for mod or XL localization ambiguity
4. No major interest at this stage to encode XL info in mztab, we may do this at our side following same model as mzid 1.2
5. Plan for wider project over medium to long term to write a cross-linking standards paper, including mzid 1.2 plus a minimum reporting guidelines doc (Juri / Alexander to progress this), with wider authorship
6. We will role these changes into mzid 1.2 specifications, and publish that paper separately (submitted in the short term). For those that contribute example files or major input of the specs, I will invite to join the author list of that paper.

I have started to write this up in the mzid 1.2 specification document (attached here and committed to our GitHub) - see pages 20-23), and an XML snippet for how the protein interaction part will look.

ACTION items:

- We discussed Lutz updating the xi export examples to include protein interaction scores, following our proposed spec
- Alexander and Eugen to update the examples exported from OpenMS and add to the mzid GitHub (please email Yasset - cc'd to get write access to the GitHub)
- Ideally, would be great if the Edinburgh visualisation software could read the mzid 1.2 files to see if all info is really covered
- Andy to continue cleaning and updating specification document

I would like to propose a conference call to progress this for 4pm UK/5pm Europe on Thurs 28th April - please reply to let me know if you can make it.

best wishes
Andy

Dear persons active in the PSI,

in 2014 a minor update of the PSI DocProc document has been agreed to 
by the steering committee.
It includes minor clarifications and DocProc document updates as well as a 
specification of version numbering.

It has not gone through a 14-day public review yet, after which its status
could
change to FINAL.
I attached version 1.1.1 PREFINAL with changes marked, so please add 
or comment until May 2nd!

  Thank you
    Bye
    Martin

--
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 mar...@ru...
www.medizinisches-proteom-center.de

Hi everyone,

the latest version 1.4.15 of the mzIdentML validator is available at
https://github.com/HUPO-PSI/mzIdentML/tree/master/validator/trunk/mzIdentMLValidator

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/>

Hi everyone, I have pulled the latest from github and refreshed the on-line
spec docs:

http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html

Note that the embedded images may not be updated from long ago, I have not
checked to see if they need to be updated.

This was generated using the PeptideShaker file as the only example,
because it seems that other examples still have CV errors in them. The
PeptideShaker files seems to be all up to date, except for the one CV value
issue under discussion in another thread.

One anomaly in the docs, under AnalysisParams:

http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html#AnalysisParams

the mapping file seems to say that a child of MS:1001194 is permitted.
Should that perhaps be a child of MS:1001060 instead?

Some CV errors and warnings from my validator on two other files I checked:

combined_fdr_1.2.mzid

+++++

ERROR: cvParam distinct peptide-level q-value should have units, but it
does not!

WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot MGF
file'

WARNING: MS:1001400 should be 'OMSSA xml format' instead of 'OMSSA xml file'

WARNING: MS:1002439 should be 'final PSM list' instead of 'final PSM list
UNDER DISCUSSION'

ERROR: cv PSI-MS still points to SourceForge

ERROR: cv UO still points to SourceForge

xiFDR-CrossLinkExample.mzid

+++++

ERROR: cvParam contact address should have a value, but it does not!

ERROR: cvParam contact name should have a value, but it does not!

ERROR: cvParam product ion intensity should have a value, but it does not!

ERROR: cvParam unknown modification should have a value, but it does not!

WARNING: cvParam product ion intensity has a legal unit MS:1000131 but its
name 'MS:1000131' should be 'number of detector counts'!

WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot MGF
file'

WARNING: MS:1001401 should be 'X!Tandem xml format' instead of 'X\!Tandem
xml file'

WARNING: MS:1002511 should be 'cross-link spectrum identification item'
instead of 'Cross-linked spectrum identification item.'

WARNING: MS:1002543 should be 'xiFDR' instead of 'XiFDR'

ERROR: cv PSI-MS still points to SourceForge

ERROR: cv UO still points to SourceForge

*From:* Jones, Andy [mailto:And...@li...]
*Sent:* Tuesday, April 05, 2016 4:21 AM
*To:* psi...@li...
*Subject:* Re: [Psidev-pi-dev] mzid 1.2 updates

Thanks Yasset, I’m in now, and pushed my updates.

Best wishes

Andy

*From:* Yasset Perez-Riverol [mailto:yp...@eb... <yp...@eb...>]
*Sent:* 05 April 2016 10:44
*To:* Jones, Andy <jo...@li...>;
psi...@li...
*Subject:* Re: [Psidev-pi-dev] mzid 1.2 updates

Invitation sent

On 05/04/2016 10:38, Jones, Andy wrote:

In fact, I didn’t manage to push this yet to the repository, looks like I
don’t have access. I will hopefully upload this later on today, if/when
someone can give me access!

Thanks

Andy

*From:* Jones, Andy [mailto:And...@li...
<And...@li...>]
*Sent:* 05 April 2016 10:10
*To:* psi...@li...
*Subject:* [Psidev-pi-dev] mzid 1.2 updates

Hi all,

I have linked up to GitHub now (at last), so I will start using that
location for all updates. If you would like to update your example files,
the schema, spec doc or anything else – please do so via GIT (
https://github.com/HUPO-PSI/mzIdentML).

I have just updated the spec doc and XSD with minor changes that are being
discussed on the list.

If you need access, send a mail to the list, and someone will do this for
you. I’m quite new to GitHub, so perhaps someone else can help with this!

Also, anyone know how to get GitHub to send the commit messages to this
list?

Cheers

Andy

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

_______________________________________________

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

Hi all,

A couple of informatics posts going at Liverpool - please forward on to any colleagues who might be interested.
Best wishes
Andy

Data Analyst
https://www.liverpool.ac.uk/working/jobvacancies/currentvacancies/research/r-590620/

Software Engineer
https://www.liverpool.ac.uk/working/jobvacancies/currentvacancies/research/r-590617/

Dear PSI and PX colleagues—
    My best wishes for another productive HUPO-PSI leadership meeting in the beautiful city of Ghent.
    I remain keenly interested personally in your agenda and your important work.  We have major ties through the HUPO Human Proteome Project.
    I’m sure Eric will share the Guidelines for MS/MS data interpretation and the Checklist adopted by the HPP and the Journal of Proteome Research for the current Call for Papers for the 2016 C-HPP special issue.  See http://www.thehpp.org/guidelines/.  We welcome comments and queries from you, as we aim to stimulate consideration of adoption of these guidelines much more widely in the proteomics community and with additional journals.   There is an explicit process for amendment and updating of these Guidelines.
    Best wishes
       Gil

From: <psi...@eb...<mailto:psi...@eb...>> on behalf of "ede...@sy...<mailto:ede...@sy...>" <ede...@sy...<mailto:ede...@sy...>>
Date: Friday, March 25, 2016 at 2:11 PM
To: "psi...@eb...<mailto:psi...@eb...>" <psi...@eb...<mailto:psi...@eb...>>, Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>, "psi...@li...<mailto:psi...@li...>" <psi...@li...<mailto:psi...@li...>>
Subject: Re: [Psi-announce] Registration is open for PSI workshop April 18-20

Hi everyone, I just wanted to remind everyone that the PSI Spring Workshop is less than a month away! We have good registration numbers already, but if you’re planning on participating and have not yet registered, please do so right away so that we can have an accurate count for planning.

I look forward to seeing you in Ghent!

Regards,
Eric

From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Friday, February 05, 2016 8:21 AM
To: psi...@eb...<mailto:psi...@eb...>; Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>
Cc: Eric Deutsch
Subject: Registration is open for PSI workshop April 18-20

Hi everyone, I am pleased to announce that registration is now open for the PSI annual spring workshop in Ghent April 18-20.

The success of the PSI standards is only achieved through wide participation from the broader community, so please consider participating and contributing to this important effort. Registration is free as the workshop is supported by several grants.

You will find a link to the registration page, a draft workshop agenda, accommodation information, and additional details at:

http://www.psidev.info/content/hupo-psi-meeting-2016

Please let me know if you have any questions.

I look forward to seeing you in Ghent!

Regards,
Eric

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

Thanks Yasset, I’m in now, and pushed my updates.

Best wishes
Andy

From: Yasset Perez-Riverol [mailto:yp...@eb...]
Sent: 05 April 2016 10:44
To: Jones, Andy <jo...@li...>; psi...@li...
Subject: Re: [Psidev-pi-dev] mzid 1.2 updates

Invitation sent
On 05/04/2016 10:38, Jones, Andy wrote:
In fact, I didn’t manage to push this yet to the repository, looks like I don’t have access. I will hopefully upload this later on today, if/when someone can give me access!
Thanks
Andy

From: Jones, Andy [mailto:And...@li...]
Sent: 05 April 2016 10:10
To: psi...@li...<mailto:psi...@li...>
Subject: [Psidev-pi-dev] mzid 1.2 updates

Hi all,

I have linked up to GitHub now (at last), so I will start using that location for all updates. If you would like to update your example files, the schema, spec doc or anything else – please do so via GIT (https://github.com/HUPO-PSI/mzIdentML).

I have just updated the spec doc and XSD with minor changes that are being discussed on the list.

If you need access, send a mail to the list, and someone will do this for you. I’m quite new to GitHub, so perhaps someone else can help with this!

Also, anyone know how to get GitHub to send the commit messages to this list?

Cheers
Andy

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

_______________________________________________

Psidev-pi-dev mailing list

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

Invitation sent
On 05/04/2016 10:38, Jones, Andy wrote:
>
> In fact, I didn’t manage to push this yet to the repository, looks 
> like I don’t have access. I will hopefully upload this later on today, 
> if/when someone can give me access!
>
> Thanks
>
> Andy
>
> *From:*Jones, Andy [mailto:And...@li...]
> *Sent:* 05 April 2016 10:10
> *To:* psi...@li...
> *Subject:* [Psidev-pi-dev] mzid 1.2 updates
>
> Hi all,
>
> I have linked up to GitHub now (at last), so I will start using that 
> location for all updates. If you would like to update your example 
> files, the schema, spec doc or anything else – please do so via GIT 
> (https://github.com/HUPO-PSI/mzIdentML).
>
> I have just updated the spec doc and XSD with minor changes that are 
> being discussed on the list.
>
> If you need access, send a mail to the list, and someone will do this 
> for you. I’m quite new to GitHub, so perhaps someone else can help 
> with this!
>
> Also, anyone know how to get GitHub to send the commit messages to 
> this list?
>
> Cheers
>
> Andy
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> 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

In fact, I didn’t manage to push this yet to the repository, looks like I don’t have access. I will hopefully upload this later on today, if/when someone can give me access!
Thanks
Andy

From: Jones, Andy [mailto:And...@li...]
Sent: 05 April 2016 10:10
To: psi...@li...
Subject: [Psidev-pi-dev] mzid 1.2 updates

Hi all,

I have linked up to GitHub now (at last), so I will start using that location for all updates. If you would like to update your example files, the schema, spec doc or anything else – please do so via GIT (https://github.com/HUPO-PSI/mzIdentML).

I have just updated the spec doc and XSD with minor changes that are being discussed on the list.

If you need access, send a mail to the list, and someone will do this for you. I’m quite new to GitHub, so perhaps someone else can help with this!

Also, anyone know how to get GitHub to send the commit messages to this list?

Cheers
Andy

Andy:
  Probably the best way would be to avoid using Sourforge. You can use 
GitHub issues for the communication ans that will complete our move to 
github.
Regards
Yasset
On 05/04/2016 10:09, Jones, Andy wrote:
>
> Hi all,
>
> I have linked up to GitHub now (at last), so I will start using that 
> location for all updates. If you would like to update your example 
> files, the schema, spec doc or anything else – please do so via GIT 
> (https://github.com/HUPO-PSI/mzIdentML).
>
> I have just updated the spec doc and XSD with minor changes that are 
> being discussed on the list.
>
> If you need access, send a mail to the list, and someone will do this 
> for you. I’m quite new to GitHub, so perhaps someone else can help 
> with this!
>
> Also, anyone know how to get GitHub to send the commit messages to 
> this list?
>
> Cheers
>
> Andy
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> 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

Hi all,

I have linked up to GitHub now (at last), so I will start using that location for all updates. If you would like to update your example files, the schema, spec doc or anything else - please do so via GIT (https://github.com/HUPO-PSI/mzIdentML).

I have just updated the spec doc and XSD with minor changes that are being discussed on the list.

If you need access, send a mail to the list, and someone will do this for you. I'm quite new to GitHub, so perhaps someone else can help with this!

Also, anyone know how to get GitHub to send the commit messages to this list?

Cheers
Andy

Dear proteomics community,

here's the new version 3.84.0 of the psi-ms.obo file.
It contains mainly new terms for proteogenomics searches.

New CV terms in version 3.84.0 of psi-ms.obo:
=============================================
************
[Term]
id: MS:1002631
name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def: "A dissociation process combining electron-transfer and 
higher-energy collision dissociation (EThcD). It combines ETD (reaction 
time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1002632
name: jPOST dataset identifier
def: "Dataset identifier issued by the jPOST repository. A dataset can 
refer to either a single sample as part of a study, or all samples that 
are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002633
name: jPOST dataset URI
def: "URI that allows the access to one dataset in the jPOST repository. 
A dataset can refer to either a single sample as part of a study, or all 
samples that are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002634
name: Q Exactive Plus
def: "Thermo Scientific Q Exactive Plus." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002635
name: proteogenomics search
def: "Proteogenomics search performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002636
name: proteogenomics attribute
def: "Proteogenomics attribute." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002637
name: chromosome name
def: "The name or number of the chromosome to which a given peptide has 
been mapped." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002638
name: chromosome strand
def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002639
name: peptide start on chromosome
def: "The overall start position on the chromosome to which a peptide 
has been mapped i.e. the position of the first base of the first codon, 
using a zero-based counting system." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002640
name: peptide end on chromosome
def: "The overall end position on the chromosome to which a peptide has 
been mapped i.e. the position of the third base of the last codon, using 
a zero-based counting system." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002641
name: peptide exon count
def: "The number of exons to which the peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002642
name: peptide exon nucleotide sizes
def: "A comma separated list of the number of DNA bases within each exon 
to which a peptide has been mapped. Assuming standard operation of a 
search engine, the peptide exon sizes should sum to exactly three times 
the peptide length." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which 
the peptide has been mapped, relative to peptide-chromosome start." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002644
name: genome reference version
def: "The reference genome and versioning string as used for mapping. 
All coordinates are within this frame of reference." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002645
name: MSDK
def: "Mass Spectrometry Development Kit (MSDK) is a Java library of 
algorithms for processing of mass spectrometry data." [PSI:PI, 
http://msdk.github.io/]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

Changed CV terms in version 3.84.0 of psi-ms.obo:
=================================================
************ added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001031
name: spectral library search
def: "A search using a library of spectra." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ added relationship: has_units UO:0000169 ! parts per million
[Term]
id: MS:1001412
name: search tolerance plus value
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

************ added relationship: has_units UO:0000169 ! parts per million
[Term]
id: MS:1001413
name: search tolerance minus value
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

************ added value-type:xsd\:float to the following six 
PeptideShaker terms
[Term]
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002358 ! search engine specific score for distinct peptides
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." 
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

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/>

Hi Matthias,

Thanks for your comments, answers in line:

-----Original Message-----
From: Mathias Walzer [mailto:wa...@in...] 
Sent: 31 March 2016 16:57
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2

Hi all,

I feel a little silly, seems I was not able to dial in (enter access code does not work) - the institute's telephone system was switched, I guess it does not support this kind of function anymore. 
Anyways, maybe just some points in brief.

mzid schema general issues: why is experimental m/z in not in SpectrumIdentificationResult but (repeatedly) in SpectrumIdentificationItem? Why is peptide_ref in SpectrumIdentificationItem optional? As are the PeptideEvidence elements. Because of the potential small molecule usecase?

>> You are correct that "experimental m/z" should be an attribute of SpectrumIdentificationResult - this was an error in mzid 1.1. I hadn't considered changing it, since we are trying to make mzid 1.2 as near as backwards compatible as possible. Any opinions as to whether this is worth changing?

Why is peptide_ref in SpectrumIdentificationItem optional?

>>I don't know why we ever did this in mzid 1.1, possibly a mistake or a use case we never fully explored. I would vote for making it mandatory now in mzid 1.2, as we are revisiting cardinality and optionality of elements/attributes. Opinions all?

>> As are the PeptideEvidence elements.

This is to account for de novo sequencing and spectral library approaches, where peptides may not be linked to a parent protein. In a regular sequence database search, the validator checks that they are always present.

mzid ppxl issues: we will need many more CV entries. E.g. the types of cross-link. Be it a mono-link, loop-link or cross-link.

>> Please suggest terms needed and we will add them. 

And there are only mono-link definitions in unimod (and only for DSS), so I guess we need more reagents used for crosslinking in one of the ontologies that define the pairs, 

>> Lutz is working on a list of reagent CV terms to be added to PSI-MS CV, please coordinate with him.

Also, to my understanding, isotope labeling is often used as a measure of reassurance of the identified cross-links. I suppose that kind of detected pairing information would go in the SpectrumIdentificationResult?

>> Good point, although we haven't got a formal way of doing this. Scores can obviously be added but we don't have a way of formally linking differentially labelled pairs (nor for regular SILAC either though). This might be considered out of scope in mzIdentML, but please send a suggestion for how the data looks from a search engine.

And there seems to be ambiguous definition available on the pairing of the different SpectrumIdentificationItem elements in one SpectrumIdentificationResult as linked peptides. It is the value of cv term 'cross-link spectrum identification item', isn't it - so we can use rank for sorting?

>> The value of 'cross-link spectrum identification item' is a local unique identifier tying together the crosslinked peptides. Do you think this is still ambiguous?

Best wishes
Andy 

best,
 Mathias

----- Original Message -----
From: "Andy Jones" <And...@li...>
To: psi...@li...
Cc: psi...@li...
Sent: Thursday, 31 March, 2016 4:45:07 PM
Subject: Re: [Psidev-ms-dev]	[Psidev-pi-dev]	[Psidev-ms-vocab]		Proteogenomics update in mzid 1.2

Dial-in details, call in 15 mins: 

Numbers: 

+ UK: 0808 109 5644

+ US: 877-420-0272

+ Belgium: 0800 509 80

+ Germany: 0800 101 2079

+ Switzerland: 0800 000 860

+ Generic international: +44 (0) 20 8322 2500 (UK number)

Access code: 297427 # 

From: Jones, Andy [mailto:And...@li...] 
Sent: 29 March 2016 16:10 
To: psi...@li... 
Cc: psi...@li... 
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 

Hi all, 

Just confirming we will have a call to discuss mzid 1.2 this coming Thurs at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301 

Agenda: 

1. Discussion of encoding proteogenomics results in mzid 1.2 (review of docs sent previously) 

2. General review of mzid 1.2 specifications (attached here) – please take a look in advance if you can. We will probably not have time for a full review on the call, but we will see how far we get 

3. Any other business 

Juan – are you okay to start the call, and if so, can you circulate dial-in details? 

Thanks 

Andy 

From: Binz Pierre-Alain [ mailto:Pie...@ch... ] 
Sent: 22 March 2016 15:45 
To: psi...@li... 
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 

Fine for me too 

Pierre-Alain 

De : Eric Deutsch [ mailto:ede...@sy... ] 
Envoyé : mardi 22 mars 2016 14:53 
À : psi...@li... ; Mass spectrometry standard development; psi...@li... 
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 

That works fine for me! 

From: Jones, Andy [mailto: And...@li... ] 
Sent: Tuesday, March 22, 2016 2:49 AM 
To: Mass spectrometry standard development; psi...@li... ; psi...@li... 
Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 

Hi all, 

I think the 24 th is out for various people as an Easter-related holiday in some countries. Eric is correct, that time zones will be changing. 

On the 31 st , my preferred slot is actually 4pm British summer time: 

http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301 

This would be 8am in Seattle; 5pm Germany; 5pm Norway; (and 4pm in the independent nation state of the EBI) 

Does this work for everyone? 

Best wishes 

Andy 

From: Eric Deutsch [ mailto:ede...@sy... ] 
Sent: 22 March 2016 03:32 
To: Mass spectrometry standard development < psi...@li... >; psi...@li... ; psi...@li... 
Cc: Eric Deutsch < ede...@sy... > 
Subject: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2 

Thanks, Andy, I like this idea. The times are not good for me, however. Normally 4pm London time is 8am Seattle time, but for these few weeks, 4pm London time is 9am Seattle time and I have a standing meeting I cannot change. 

http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440 

An hour earlier would be fine for the 24 th . 

I hope I’m not getting confused between 4pm GMT and London local time? I think on the 24 th 16:00 GMT = 4pm local London, but on the 31 st , 16:00 GMT is 5pm London time? 

Thanks, 

Eric 

From: Jones, Andy [mailto: And...@li... ] 
Sent: Monday, March 21, 2016 4:21 AM 
To: psi...@li... ; psi...@li... ; psi...@li... 
Subject: [Psidev-ms-dev] Proteogenomics update in mzid 1.2 

Hi all, 

Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list. 

One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches. There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides). 

Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion. 

It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit: 

- This Thurs (24 th March) at 4pm GMT 

- Next Thurs (31 st March) at 4pm GMT 

Best wishes 

Andy 

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Hi Harald, excellent, thanks. I hope someone can give you push access to
mzIdentML, I don't think I can.

I think the new home for the Unit Ontology is here:
https://github.com/bio-ontology-research-group/unit-ontology

thanks!
Eric

-----Original Message-----
From: Harald Barsnes [mailto:Har...@ui...]
Sent: Friday, April 01, 2016 8:55 AM
To: Eric Deutsch
Cc: Jones, Andy; psi...@li...;
psi...@li...
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
Proteogenomics update in mzid 1.2

Hi Eric,

I've updated the PRIDE and PSI-MS obo URLs for the PeptideShaker example. Do
you have the new URL for the UO obo file?

As for the other PeptideShaker issues:

> ERROR: cvParam software vendor has a value, but it should not!

Fixed.

> WARNING: MS:1000588 should be 'contact URL' instead of 'contact url'

Fixed.

> ERROR: cvParam Phospho has a value, but it should not!
> ERROR: cvParam Oxidation has a value, but it should not!
> ERROR: cvParam Glu->pyro-Glu has a value, but it should not!
> ERROR: cvParam Carbamidomethyl has a value, but it should not!

Fixed.

Seems like I don't have push access to the new GitHub HUPO-PSI/mzIdentML
repository, so I've put the updated PeptideShaker example file on Dropbox in
the meantime:
https://www.dropbox.com/s/pucr2arc2tknp15/PeptideShaker_mzid_1_2_example.mzid.gz?dl=0

Let me now if you come across other issues with the PeptideShaker export.

Best regards,
Harald

Den 2016-04-01 00:40, skrev Eric Deutsch:
> Hi Andy, I fired up the schema generation script and refreshed
> everything based on what’s in github now. You can see the current
> result here:
>
> http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.h
> tml
> [3]
>
> The schema seems pretty fine, but the example files have some issues.
> Here are a few observations of things to fix:
>
> - Examples files still have older CV URLS like:
>
> <cv id="PSI-MS"
> uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/ps
> i-ms/mzML/controlledVocabulary/psi-ms.obo
> [4]" version="3.73.0" fullName="PSI-MS"/>
>
> <cv id="UO"
> uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenot
> ype/unit.obo
> [1]" fullName="UNIT-ONTOLOGY"/>
>
>     <cv id="PRIDE"
> uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core
> /schema/pride_cv.obo
> [2]" fullName="PRIDE"/>
>
> I ran a few of the files through my validator and have the following
> things:
>
> PeptideShaker_mzid_1_2_example.mzid
>
> ERROR: cvParam software vendor has a value, but it should not!
>
> WARNING: MS:1000588 should be 'contact URL' instead of 'contact url'
>
> ERROR: cvParam Phospho has a value, but it should not!
>
> ERROR: cvParam Oxidation has a value, but it should not!
>
> ERROR: cvParam Glu->pyro-Glu has a value, but it should not!
>
> ERROR: cvParam Carbamidomethyl has a value, but it should not!
>
> combined_fdr_1.2.mzid
>
> WARNING: MS:1001400 should be 'OMSSA xml format' instead of 'OMSSA xml
> file'
>
> WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot
> MGF file'
>
> ERROR: cvParam distinct peptide-level q-value should have units, but
> it does not!
>
> xiFDR-CrossLinkExample.mzid
>
> WARNING: MS:1002543 should be 'xiFDR' instead of 'XiFDR'
>
> ERROR: cvParam contact address should have a value, but it does not!
>
> ERROR: cvParam contact name should have a value, but it does not!
>
> ERROR: cvParam unknown modification should have a value, but it does
> not!
>
> This is not exhaustive, but just some results from a first foray into
> this.
>
> If someone is interested in fixing these things and checking them it,
> I can push further and report other problems.
>
> Regards,
>
> Eric
>
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Tuesday, March 29, 2016 8:10 AM
> TO: psi...@li...
> CC: psi...@li...
> SUBJECT: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
>
> Hi all,
>
> Just confirming we will have a call to discuss mzid 1.2 this coming
> Thurs at 4pm UK time:
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call
> &iso=20160331T16&p1=301
> [5]
>
> Agenda:
>
> 1.       Discussion of encoding proteogenomics results in mzid 1.2
> (review of docs sent previously)
>
> 2.       General review of mzid 1.2 specifications (attached here) –
> please take a look in advance if you can. We will probably not have
> time for a full review on the call, but we will see how far we get
>
> 3.       Any other business
>
> Juan – are you okay to start the call, and if so, can you circulate
> dial-in details?
>
> Thanks
>
> Andy
>
> FROM: Binz Pierre-Alain [mailto:Pie...@ch...]
> SENT: 22 March 2016 15:45
> TO: psi...@li...
> SUBJECT: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
>
> Fine for me too
>
> Pierre-Alain
>
> DE : Eric Deutsch [mailto:ede...@sy...]
> ENVOYÉ : mardi 22 mars 2016 14:53
> À : psi...@li...; Mass spectrometry standard
> development; psi...@li...
> OBJET : Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
>
> That works fine for me!
>
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Tuesday, March 22, 2016 2:49 AM
> TO: Mass spectrometry standard development;
> psi...@li...;
> psi...@li...
> SUBJECT: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update
> in mzid 1.2
>
> Hi all,
>
> I think the 24th is out for various people as an Easter-related
> holiday in some countries. Eric is correct, that time zones will be
> changing.
>
> On the 31st, my preferred slot is actually 4pm British summer time:
>
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call
> &iso=20160331T16&p1=301
> [5]
>
> This would be 8am in Seattle; 5pm Germany;  5pm Norway; (and 4pm in
> the independent nation state of the EBI)
>
> Does this work for everyone?
>
> Best wishes
>
> Andy
>
> FROM: Eric Deutsch [mailto:ede...@sy...]
> SENT: 22 March 2016 03:32
> TO: Mass spectrometry standard development
> <psi...@li...>;
> psi...@li...;
> psi...@li...
> CC: Eric Deutsch <ede...@sy...>
> SUBJECT: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
>
> Thanks, Andy, I like this idea. The times are not good for me,
> however. Normally 4pm London time is 8am Seattle time, but for these
> few weeks, 4pm London time is 9am Seattle time and I have a standing
> meeting I cannot change.
>
> http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p
> 1=1440
> [6]
>
> An hour earlier would be fine for the 24th.
>
> I hope I’m not getting confused between 4pm GMT and London local time?
> I think on the 24th 16:00 GMT = 4pm local London, but on the 31st,
> 16:00 GMT is 5pm London time?
>
> Thanks,
>
> Eric
>
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Monday, March 21, 2016 4:21 AM
> TO: psi...@li...;
> psi...@li...;
> psi...@li...
> SUBJECT: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
>
> Hi all,
>
> Over the coming weeks, I will be trying to get mzid 1.2 largely tied
> up for a final review in Ghent, before we submit the spec doc and
> associated manuscript. I have cross-posted this message (since PSI-PI
> has not been active lately), but probably will drop PSI-MS from the
> list in future. If you’re interested in mzid 1.2, please make sure to
> follow the PSI-PI list.
>
> One feature I would like to add into mzid 1.2 is better support for
> proteogenomics approaches.  There are some parallel efforts to adapt
> genome formats BED and BAM for proteomics (and updates will be
> presented in Ghent I think). It would be nice if the info needed for
> proBed and proBAM was consistently expressed in mzid 1.2 files (mainly
> genome coordinates for peptides).
>
> Along with Juan et al., we have come up with a proposal for how this
> might be done in mzid 1.2. Please see attached. Feel free to annotate
> any comments on the document, or email back to the list any parts you
> feel need adapting or comments for discussion.
>
> It might be useful to have one or two conference calls on mzid 1.2
> before Ghent. How would following dates suit:
>
> -          This Thurs (24th March) at 4pm GMT
>
> -          Next Thurs (31st March) at 4pm GMT
>
> Best wishes
>
> Andy
>
>
>
> Links:
> ------
> [1]
> http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/u
> nit.obo
> [2]
> http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/sche
> ma/pride_cv.obo
> [3]
> http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.h
> tml
> [4]
> http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/
> mzML/controlledVocabulary/psi-ms.obo
> [5]
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call
> &amp;iso=20160331T16&amp;p1=301
> [6]
> http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&a
> mp;p1=1440
>
> ----------------------------------------------------------------------
> --------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with Intel Data
> Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Hi Eric,

I've updated the PRIDE and PSI-MS obo URLs for the PeptideShaker 
example. Do you have the new URL for the UO obo file?

As for the other PeptideShaker issues:

> ERROR: cvParam software vendor has a value, but it should not!

Fixed.

> WARNING: MS:1000588 should be 'contact URL' instead of 'contact url'

Fixed.

> ERROR: cvParam Phospho has a value, but it should not!
> ERROR: cvParam Oxidation has a value, but it should not!
> ERROR: cvParam Glu->pyro-Glu has a value, but it should not!
> ERROR: cvParam Carbamidomethyl has a value, but it should not!

Fixed.

Seems like I don't have push access to the new GitHub HUPO-PSI/mzIdentML 
repository, so I've put the updated PeptideShaker example file on 
Dropbox in the meantime: 
https://www.dropbox.com/s/pucr2arc2tknp15/PeptideShaker_mzid_1_2_example.mzid.gz?dl=0

Let me now if you come across other issues with the PeptideShaker 
export.

Best regards,
Harald

Den 2016-04-01 00:40, skrev Eric Deutsch:
> Hi Andy, I fired up the schema generation script and refreshed
> everything based on what’s in github now. You can see the current
> result here:
> 
> http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html
> [3]
> 
> The schema seems pretty fine, but the example files have some issues.
> Here are a few observations of things to fix:
> 
> - Examples files still have older CV URLS like:
> 
> <cv id="PSI-MS"
> uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
> [4]" version="3.73.0" fullName="PSI-MS"/>
> 
> <cv id="UO"
> uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo
> [1]" fullName="UNIT-ONTOLOGY"/>
> 
>     <cv id="PRIDE"
> uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo
> [2]" fullName="PRIDE"/>
> 
> I ran a few of the files through my validator and have the following
> things:
> 
> PeptideShaker_mzid_1_2_example.mzid
> 
> ERROR: cvParam software vendor has a value, but it should not!
> 
> WARNING: MS:1000588 should be 'contact URL' instead of 'contact url'
> 
> ERROR: cvParam Phospho has a value, but it should not!
> 
> ERROR: cvParam Oxidation has a value, but it should not!
> 
> ERROR: cvParam Glu->pyro-Glu has a value, but it should not!
> 
> ERROR: cvParam Carbamidomethyl has a value, but it should not!
> 
> combined_fdr_1.2.mzid
> 
> WARNING: MS:1001400 should be 'OMSSA xml format' instead of 'OMSSA xml
> file'
> 
> WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot
> MGF file'
> 
> ERROR: cvParam distinct peptide-level q-value should have units, but
> it does not!
> 
> xiFDR-CrossLinkExample.mzid
> 
> WARNING: MS:1002543 should be 'xiFDR' instead of 'XiFDR'
> 
> ERROR: cvParam contact address should have a value, but it does not!
> 
> ERROR: cvParam contact name should have a value, but it does not!
> 
> ERROR: cvParam unknown modification should have a value, but it does
> not!
> 
> This is not exhaustive, but just some results from a first foray into
> this.
> 
> If someone is interested in fixing these things and checking them it,
> I can push further and report other problems.
> 
> Regards,
> 
> Eric
> 
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Tuesday, March 29, 2016 8:10 AM
> TO: psi...@li...
> CC: psi...@li...
> SUBJECT: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
> 
> Hi all,
> 
> Just confirming we will have a call to discuss mzid 1.2 this coming
> Thurs at 4pm UK time:
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
> [5]
> 
> Agenda:
> 
> 1.       Discussion of encoding proteogenomics results in mzid 1.2
> (review of docs sent previously)
> 
> 2.       General review of mzid 1.2 specifications (attached here) –
> please take a look in advance if you can. We will probably not have
> time for a full review on the call, but we will see how far we get
> 
> 3.       Any other business
> 
> Juan – are you okay to start the call, and if so, can you circulate
> dial-in details?
> 
> Thanks
> 
> Andy
> 
> FROM: Binz Pierre-Alain [mailto:Pie...@ch...]
> SENT: 22 March 2016 15:45
> TO: psi...@li...
> SUBJECT: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
> 
> Fine for me too
> 
> Pierre-Alain
> 
> DE : Eric Deutsch [mailto:ede...@sy...]
> ENVOYÉ : mardi 22 mars 2016 14:53
> À : psi...@li...; Mass spectrometry standard
> development; psi...@li...
> OBJET : Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
> 
> That works fine for me!
> 
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Tuesday, March 22, 2016 2:49 AM
> TO: Mass spectrometry standard development;
> psi...@li...;
> psi...@li...
> SUBJECT: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update
> in mzid 1.2
> 
> Hi all,
> 
> I think the 24th is out for various people as an Easter-related
> holiday in some countries. Eric is correct, that time zones will be
> changing.
> 
> On the 31st, my preferred slot is actually 4pm British summer time:
> 
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
> [5]
> 
> This would be 8am in Seattle; 5pm Germany;  5pm Norway; (and 4pm in
> the independent nation state of the EBI)
> 
> Does this work for everyone?
> 
> Best wishes
> 
> Andy
> 
> FROM: Eric Deutsch [mailto:ede...@sy...]
> SENT: 22 March 2016 03:32
> TO: Mass spectrometry standard development
> <psi...@li...>;
> psi...@li...;
> psi...@li...
> CC: Eric Deutsch <ede...@sy...>
> SUBJECT: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
> 
> Thanks, Andy, I like this idea. The times are not good for me,
> however. Normally 4pm London time is 8am Seattle time, but for these
> few weeks, 4pm London time is 9am Seattle time and I have a standing
> meeting I cannot change.
> 
> http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440
> [6]
> 
> An hour earlier would be fine for the 24th.
> 
> I hope I’m not getting confused between 4pm GMT and London local
> time? I think on the 24th 16:00 GMT = 4pm local London, but on the
> 31st, 16:00 GMT is 5pm London time?
> 
> Thanks,
> 
> Eric
> 
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Monday, March 21, 2016 4:21 AM
> TO: psi...@li...;
> psi...@li...;
> psi...@li...
> SUBJECT: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
> 
> Hi all,
> 
> Over the coming weeks, I will be trying to get mzid 1.2 largely tied
> up for a final review in Ghent, before we submit the spec doc and
> associated manuscript. I have cross-posted this message (since PSI-PI
> has not been active lately), but probably will drop PSI-MS from the
> list in future. If you’re interested in mzid 1.2, please make sure
> to follow the PSI-PI list.
> 
> One feature I would like to add into mzid 1.2 is better support for
> proteogenomics approaches.  There are some parallel efforts to adapt
> genome formats BED and BAM for proteomics (and updates will be
> presented in Ghent I think). It would be nice if the info needed for
> proBed and proBAM was consistently expressed in mzid 1.2 files (mainly
> genome coordinates for peptides).
> 
> Along with Juan et al., we have come up with a proposal for how this
> might be done in mzid 1.2. Please see attached. Feel free to annotate
> any comments on the document, or email back to the list any parts you
> feel need adapting or comments for discussion.
> 
> It might be useful to have one or two conference calls on mzid 1.2
> before Ghent. How would following dates suit:
> 
> -          This Thurs (24th March) at 4pm GMT
> 
> -          Next Thurs (31st March) at 4pm GMT
> 
> Best wishes
> 
> Andy
> 
> 
> 
> Links:
> ------
> [1]
> http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo
> [2]
> http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo
> [3] 
> http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html
> [4]
> http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
> [5]
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&amp;iso=20160331T16&amp;p1=301
> [6]
> http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&amp;p1=1440
> 
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
> 
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Thanks Gerhard!

Sent from Samsung Mobile

-------- Original message --------
From: mayerg97
Date:01/04/2016 14:35 (GMT+00:00)
To: psi...@li...,psi...@li...,psi...@li...
Subject: [Psidev-ms-vocab] Release candidate 3.84.0_rc2 of psi-ms.obo

Dear proteomics community,

here's the release candidate 3.84.0_rc2 of the psi-ms.obo file.
It contains mainly new terms for proteogenomics searches.

New CV terms in version 3.84.0_rc2 of psi-ms.obo:
=================================================
************
[Term]
id: MS:1002631
name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def: "A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1002632
name: jPOST dataset identifier
def: "Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002633
name: jPOST dataset URI
def: "URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002634
name: Q Exactive Plus
def: "Thermo Scientific Q Exactive Plus." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002635
name: proteogenomics search
def: "Proteogenomics search performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002636
name: proteogenomics attribute
def: "Proteogenomics attribute." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002637
name: chromosome name
def: "The name or number of the chromosome to which a given peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002638
name: chromosome strand
def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002639
name: peptide start on chromosome
def: "The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002640
name: peptide end on chromosome
def: "The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002641
name: peptide exon count
def: "The number of exons to which the peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002642
name: peptide exon nucleotide sizes
def: "A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002644
name: genome reference version
def: "The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

Changed CV terms in version 3.84.0_rc2 of psi-ms.obo:
=====================================================
************ added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001031
name: spectral library search
def: "A search using a library of spectra." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

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 <mailto:ger...@ru...> ger...@ru...<mailto:ger...@ru...>
<http://www.medizinisches-proteom-center.de/>www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de>
[cid:par...@ru...]

Dear proteomics community,

here's the release candidate 3.84.0_rc2 of the psi-ms.obo file.
It contains mainly new terms for proteogenomics searches.

New CV terms in version 3.84.0_rc2 of psi-ms.obo:
=================================================
************
[Term]
id: MS:1002631
name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def: "A dissociation process combining electron-transfer and 
higher-energy collision dissociation (EThcD). It combines ETD (reaction 
time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1000044 ! dissociation method