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Re: [Psidev-pi-dev] mzid 1.2 updates
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From: Eric D. <ede...@sy...> - 2016-06-21 18:52:58
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Hi Gerhard, certainly. I have generated a set of new HTML documentations with the autogenerator. Note that many of the example files still have incorrect CV terms. I have just now updated the GitHub issues list with problems that I see today. Some of these errors may have made their way into the autogenerated documentation, so it would be desirable to fix these issues and rerun the generator before the documentation is properly used, but that’s up to you. Here are the files: http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_all.html http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_PeptideShaker.html http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_combined.html http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_xiFDR.html The first one is the same as the one with the “all” tag, where “all” really means these: INFO: Reading examples file 'combined_fdr_1.2.mzid' INFO: Reading examples file 'mzidLib_peaklist2a_plus_ecoli_versus_unimod_full_xtandem_fdr_threshold_groups.mzid' INFO: Reading examples file 'mzidLib_Rosetta2a_Ecoli_spectra_msgfplus_fdr_threshold_groups.mzid' INFO: Reading examples file 'mzidLib_rosetta_2a_uniprot_proteogrouped.mzid' INFO: Reading examples file 'OpenxQuest_example_added_annotations.mzid' INFO: Reading examples file 'OpenxQuest_example.mzid' INFO: Reading examples file 'PAnalyzer_rosetta_2a_ecoli_uniprot.mzid' INFO: Reading examples file 'PAnalyzer_rosetta_2a_uniprot.mzid' INFO: Reading examples file 'PAnalyzer_rosetta_2b_ecoli_uniprot.mzid' INFO: Reading examples file 'PAnalyzer_rosetta_2b_uniprot.mzid' INFO: Reading examples file 'PeptideShaker_mzid_1_2_example.mzid' INFO: Reading examples file 'xiFDR-CrossLinkExample.mzid' And then there’s also a version of “all” that is better formatted for pasting into a Word doc (I know it used to work when copying and pasting from a Firefox window, but vaguely recall that maybe it didn’t work in another browser type?) http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_paste.html Regards, Eric *From:* mayerg97 [mailto:ger...@ru...] *Sent:* Tuesday, June 21, 2016 7:41 AM *To:* psi...@li... *Subject:* Re: [Psidev-pi-dev] mzid 1.2 updates 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...] *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 ------------------------------------------------------------------------------ Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- *--* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail *ger...@ru... www.medizinisches-proteom-center.de [image: RUB Logo] ANNOUNCEMENT de.NBI summer school September 2016: *Analysis of Mass-Spectrometric Data - * *Big Data Bioinformatics in Proteomics and Metabolomics* http://www.denbi.de/index.php/11-training-cat/95-lss2016 |
