Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2

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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
>
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