Re: [Psidev-pi-dev] mzid 1.2 updates

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

Hi Eric,

can you please rerun the script for generating the spec docs using the 
latest examples?
Wasn't there before also a link generated for content, which can be 
directly pasted into Word?

Thanks, and best regards,
Gerhard

Am 12.04.2016 um 22:54 schrieb Eric Deutsch:
>
> 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... 
> <mailto:And...@li...>]
> *Sent:* Tuesday, April 05, 2016 4:21 AM
> *To:* psi...@li... 
> <mailto: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...]
> *Sent:* 05 April 2016 10:44
> *To:* Jones, Andy <jo...@li... 
> <mailto:jo...@li...>>; psi...@li... 
> <mailto: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
>
>
>
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>
>
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>
> -- 
> Yasset Perez-Riverol PhD.
> Bioinformatician
> Proteomics Services Team, PRIDE Group European Bioinformatics 
> Institute (EMBL-EBI)
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Twitter: @ypriverol
>
>
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