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From: Noemi d. T. A. <not...@gi...> - 2016-05-16 08:54:14
|
Hi, Related with OLS too. Max from PSI-MI is updating the ontology-manager to the new version from OLS because it is needed for IntAct. I think it is a dependency for the validator framework too. Previously was hosted in the sourceforge svn with other tools https://sourceforge.net/p/psidev/svn/HEAD/tree/psi/tools/ontology-manager/ We are thinking that if you agree, it can be moved to GitHub under HUPO-PSI and share there our changes because they are common libraries and tools for PSI, however until this moment only the specification documents have been hosted in the organisation. What do you think? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219379176 |
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From: Yasset Perez-R. <not...@gi...> - 2016-05-13 18:19:33
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@germa we implemented the new ols-client and ols-dialog you can used them. Please they are here: OLS-CLIENT https://github.com/PRIDE-Utilities/ols-client OLS_DIALOG https://github.com/PRIDE-Toolsuite/ols-dialog --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219120848 |
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From: Juan A. V. <not...@gi...> - 2016-05-13 17:37:00
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Thanks @germa, I had not realised about this. In the last 2 weeks we had to update some of the OLS related libraries that are used in our tools because of this. We need to investigate this in detail. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219109797 |
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From: Gerhard M. <not...@gi...> - 2016-05-13 16:16:14
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Message 1: PeptideLevelStatsObjectRule The reason is that the EBI-OLS changed. I think the validation framework from the EBI, from which our validator inherits is not yet adapted to the new Open Lookup Service. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219089796 |
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From: andrewrobertjones <not...@gi...> - 2016-05-13 14:07:12
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@germa Can you investigate Message 1, I can't obviously spot what is wrong with our file https://github.com/HUPO-PSI/mzIdentML/blob/master/examples/1_2examples/ProteoAnnotator/ProteoAnnotator_1_2.mzid.gz In terms of Message 2, we decided to role back on this rule so it is no longer required, and can be safely deleted from mapping file: Rule ID: SpectrumIdentificationList_must_rule @fghali Message 3 is something for you to fix. MS:1002404 needs to be on the ProteinDetectionList, with a value of the number of PAGs with passThreshold=true. This should be inserted by ProteoGrouper. If you need help with this part of (my) code, let me know --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219052974 |
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From: Gerhard M. <not...@gi...> - 2016-05-13 10:04:55
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Hello Chris, thanks for these hints. I updated the imports to use the PURL's for pato and uo. But what I don't understand is that the nightly Jenkins build still picks up the old psi-ms.obo file (version 3.77.0) from 'https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo' instead the actual version 3.88.0 from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/psi-ms-CV/issues/4#issuecomment-219003237 |
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From: mayerg97 <ger...@ru...> - 2016-05-13 09:41:14
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Dear proteomics community, attached there's the new version 3.88.0 of the psi-ms.obo file. New CV terms in version 3.88.0 of psi-ms.obo: ============================================= ************ Two new instrument terms [Term] id: MS:1002666 name: impact II def: "Bruker Daltonics' impact II." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002667 name: impact HD def: "Bruker Daltonics' impact HD." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series Changed CV terms in version 3.88.0 of psi-ms.obo: ================================================= ************ replaced the imports to pato and uo by PURL's import: http://purl.obolibrary.org/obo/pato.owl import: http://purl.obolibrary.org/obo/uo.owl ************ added is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002389 name: PIA workflow parameter def: "A parameter set for a single PIA analysis." [PSI:PI] is_a: MS:1002105 ! software specific input parameter is_a: MS:1001302 ! search engine specific input parameter 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/> 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 |
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From: Chris M. <not...@gi...> - 2016-05-12 16:32:23
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Note this is causing the owl conversion to build: ``` >> Parser: OBOFormatOWLAPIParser >> org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://pato.googlecode.com/svn/trunk/quality.obo >> >> >> org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/Users/cjm/tmp/obobuild/src/ms.obo >> Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation. >> The following parsers were tried: >> 1) RDFXMLParser >> 2) OWLXMLParser >> 3) OWLFunctionalSyntaxOWLParser >> 4) TurtleOntologyParser >> 5) KRSS2OWLParser >> 6) ManchesterOWLSyntaxOntologyParser >> 7) OBOFormatOWLAPIParser ``` You can always manually check this yourself with every release, either by: * opening the ms.obo file in Protege5 (__not__ 4) * running `owltools ms.obo` * running `robot convert -i ms.obo -o ms.owl` - see https://github.com/ontodev/robot/ I recommend going one step further and creating a travis job that will automatically check every commit or pull request made on this repo. You might find this useful https://douroucouli.wordpress.com/2015/12/16/creating-an-ontology-project-an-update/ --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/psi-ms-CV/issues/4#issuecomment-218812183 |
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From: Chris M. <not...@gi...> - 2016-05-12 16:28:08
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Moving from here: https://github.com/MICommunity/psimi/issues/17 See https://github.com/owlcs/owlapi/issues/523 You should always use purls for imports, e.g import: http://purl.obolibrary.org/obo/pato.obo import: http://purl.obolibrary.org/obo/uo.obo In fact we recommend that these are OWL. import: http://purl.obolibrary.org/obo/pato.owl import: http://purl.obolibrary.org/obo/uo.owl You can use an OboEdit catalog to have OE resolve these to a local obo cache. But really you should stop using OE, we do not support it any more. Contact me if you have problems --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/psi-ms-CV/issues/4 |
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From: mayerg97 <ger...@ru...> - 2016-05-12 15:47:46
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Dear proteomics community, attached there's the release candidate 3.88.0_rc1 of the psi-ms.obo file. New CV terms in version 3.88.0_rc1 of psi-ms.obo: ================================================= ************ Two new instrument terms [Term] id: MS:1002666 name: impact II def: "Bruker Daltonics' impact II." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002667 name: impact HD def: "Bruker Daltonics' impact HD." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series Changed CV terms in version 3.87.0_rc1 of psi-ms.obo: ===================================================== ************ added is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002389 name: PIA workflow parameter def: "A parameter set for a single PIA analysis." [PSI:PI] is_a: MS:1002105 ! software specific input parameter is_a: MS:1001302 ! search engine specific input parameter 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/> 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 |
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From: Harald B. <not...@gi...> - 2016-05-12 13:20:52
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Thanks Andy. Now implemented in the updated PeptideShaker mzid 1.2 example file. :) --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/9#issuecomment-218754658 |
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From: F. G. <not...@gi...> - 2016-05-12 12:34:56
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I'm getting these errors when trying to validate the file using: mzIdentMLValidator_GUI_v1.4.16-SNAPSHOT
`
Message 1:
Rule ID: PeptideLevelStatsObjectRule
Level: ERROR
Context(/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem )
--> The SpectrumIdentificationItem (id='SIR_3007_SII_2') element at /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem doesn't contain the triplet of terms MS:1002520 (peptide group ID), MS:1002500 (peptide passes threshold) and a child of MS:1002358 (search engine specific score for distinct peptides) required in case of peptide-level scoring
Tip: Add the triplet of terms MS:1002520 (peptide group ID), MS:1002500 (peptide passes threshold) and a child of MS:1002358 (search engine specific score for distinct peptides) to each SpectrumIdentificationItem
Message 2:
Rule ID: SpectrumIdentificationList_must_rule
Level: ERROR
Context(/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/cvParam/@accession' because no values were found:
- Any children term of MS:1002438 (spectrum identification list result details). A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
Message 3:
Rule ID: ProteinDetectionList_must_rule
Level: ERROR
Context(/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/AnalysisData/ProteinDetectionList/cvParam/@accession' because no values were found:
- The sole term MS:1002404 (count of identified proteins) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
`
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From: Lutz F. <not...@gi...> - 2016-05-12 12:02:02
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@sulezinha Sorry for the confusion. The example was a theoretical one - not currently used for any cross-linekr. DSS is currently defined with (K,S,T,Y,N-term)&(K,S,T,Y,N-term). Meaning from and to K,S,T,Y or N-terminal without restriction as to what amino-acid is at the N-terminal. As to whether the second amino-acid is a valid N-terminal depends on a lot of things - like whether your looking at bacteria or not and what is the second amino-acid. For the exact rules for this you have to ask an expert in that field... As a generalised approach we also consider the N-terminal methionine and the following amino-acid as valid n-terminal. If the sequence start with something else then M only the N-terminal residue is considered. But I don't think that is something we should try encode within the cross-linker specificities. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/13#issuecomment-218736780 |
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From: Lutz F. <not...@gi...> - 2016-05-12 11:57:42
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@timosachsenberg yes that case is currently not really supported. What we could do is to extend the format to something like (K)&(Y)|(S)&(T). Only is there a cross-linker like that? And if it is does it have the same composition in both cases? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/13#issuecomment-218736042 |
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From: Harald B. <not...@gi...> - 2016-05-12 11:12:07
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When running the current validator on the PeptideShaker mzid 1.2 example file I now get the following error:
```
Rule ID: PeptideLevelStatsObjectRule
Level: ERROR
Context(/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem )
--> The SpectrumIdentificationItem (id='SII_2388_1') element at /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem doesn't contain the triplet of terms MS:1002520 (peptide group ID), MS:1002500 (peptide passes threshold) and a child of MS:1002358 (search engine specific score for distinct peptides) required in case of peptide-level scoring
Tip: Add the triplet of terms MS:1002520 (peptide group ID), MS:1002500 (peptide passes threshold) and a child of MS:1002358 (search engine specific score for distinct peptides) to each SpectrumIdentificationItem
```
However, the following CV terms are all there:
```
<cvParam cvRef="PSI-MS" accession="MS:1002468" name="PeptideShaker peptide score" value="17.781512503836435"/>
<cvParam cvRef="PSI-MS" accession="MS:1002500" name="peptide passes threshold" value="true"/>
<cvParam cvRef="PSI-MS" accession="MS:1002520" name="peptide group ID" value="AVVTVPAYFNDAQR"/>
```
And MS:1002468 (PeptideShaker peptide score) is a child of MS:1002358 (search engine specific score for distinct peptides), so all should be ok? Note that this error did not show up in previous version of the validator.
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|
From: Harald B. <not...@gi...> - 2016-05-12 11:03:44
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I still get the same info message when running the current validator on the PeptideShaker mzid 1.2 example file: https://github.com/HUPO-PSI/mzIdentML/blob/master/examples/1_2examples/PeptideShaker_mzid_1_2_example/PeptideShaker_mzid_1_2_example.mzid.gz. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/8#issuecomment-218726052 |
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From: Harald B. <not...@gi...> - 2016-05-12 11:03:32
|
Reopened #8. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/8#event-658430226 |
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From: Julian U. <not...@gi...> - 2016-05-12 09:41:17
|
Wrong files, they do not have the 1.2 tag --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/pull/26#issuecomment-218708760 |
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From: Julian U. <not...@gi...> - 2016-05-12 09:41:15
|
Closed #26. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/pull/26#event-658343564 |
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From: sulezinha <not...@gi...> - 2016-05-11 16:13:47
|
In that case, for example, is XLMOD-specificity for DSS going to be _(K,S,T,Y,Protein N-term M)&(K,S,T,Y,Protein N-term M)_? Because, I received one data set from a group and this group also provided me their FASTA file. I ran pLink and Kojak to identify spectra for DSS linking. Their fasta file has one protein sequence that starts with G. Both algorithm gave identification with considering Protein N-term G as linkable, for the validated list. That fasta file has another protein sequence that starts with M. These two algorithms identified both M and also the second residue after M for this protein as linkable, as well. So, if the specificity checks for DSS considers _Protein N-term M _but _Protein N-term_, such identifications will fail and mzIdentML is not going to consider this identification then, is it? Is it right what I understood? What do you mean exactly by saying "So we could define a cross-linker that links Protein-N-terminal methionine or KSTY anywhere else to anything as"? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/13#issuecomment-218509305 |
|
From: Jones, A. <And...@li...> - 2016-05-11 15:56:54
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Hi all (crosslinking people specifically), We would like to schedule the next crosslinking-mzid call for Wed 18th at 4pm (UK); 5pm EU – please can you let me know if this suits. Best wishes Andy From: Jones, Andy Sent: 04 May 2016 17:06 To: psi...@li... Cc: eug...@tu...; le...@im...; Andrea Sinz <and...@ph...>; Robert Chalkley <cha...@cg...>; eli...@ug...; ju...@ed...; sul...@ug... Subject: RE: Cross-linking discussions at PSI meeting Hi all, Brief summary from the call: 1. Agreed that expMassToCharge, calcMassToCharge and chargeState should be identical for alpha and beta PSMs, reflecting the overall values for the cross-linked molecules; a. Also agreed that for consensus spectrum approach, there should be one SpectrumIdentificationItem per peptide chain identified, we acknowledge potential for some loss of information, but probably impossible to second guess everything that people want to encode 2. General agreement over my proposal for interaction scores as per issue pdf 3. Agreed for Lutz to make a provisional release of a very simple CV e.g. XLMOD.1.0.1.csv; and have a second working copy where ideas can be developed; Detail can be added over time, as people need specific terms 4. Proteogenomics – Agreed to move chromosome name and strand to DBSequence (protein-level), also move Genome reference version to DBSequence; Remove “peptide start position on chromosome” as redundant info, this is not needed for the encoding 5. Decide to leave the issue open for now for people to vote on, not enough people on the call to take a decision Proposed date for next call, same time slot next Wed 11th May – please let me know if you can make it. Plan to discuss mzid items, not including cross-linking next week. Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 04 May 2016 14:27 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, The main items to work through today are as follows: 1. The XL encoding with consensus spectra, and more generally what values should go in expMassToCharge, calcMassToCharge and chargeState: https://github.com/HUPO-PSI/mzIdentML/issues/19, as we identified a flaw in the proposed specs a. For background see Section 5.2.8 of the spec doc: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx 2. How to encode protein-level interaction evidence: https://github.com/HUPO-PSI/mzIdentML/issues/24 3. Any issues around CV of reagents: https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv. Looks like it hasn’t been updated since last week – Lutz, any developments here? Time permitting, I would like sign off one or two non-XL issues: 4. Proteogenomics: https://github.com/HUPO-PSI/mzIdentML/issues/4; Specifically encoding of genome reference version; and whether to keep CV term for “peptide start on chromosome” since info is redundant 5. Multiple search engine encoding: https://github.com/HUPO-PSI/mzIdentML/issues/5 Speak in 1.5 hours, Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 03 May 2016 14:58 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, As a reminder, we will have our next mzid 1.2 call tomorrow at 4pm UK time/5pm EU/8am California for those of you who can join: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160504T16&p1=301&ah=1 The dial in details are as usual (below) – Juan, is there someone at the EBI who can start the call for us? Agenda: 1. XL encoding and CV issues (before the call I will update issues and documentation in GitHub) 2. Work through other mzid 1.2 issues (time permitting): https://github.com/HUPO-PSI/mzIdentML/issues 3. Any other business Best wishes Andy 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 Sent: 28 April 2016 15:37 To: 'Jones, Andy' <And...@li...<mailto:And...@li...>>; psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Summary of items we will discuss on the call (30 mins time): 1. Overview of encoding as written in spec doc: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx (section 5.2.8 and Figure 3 and Figure 4) a. Note Figure 4 is subject to change following our discussions 2. Work through issues flagged here, particularly those mentioned by Lutz: https://github.com/HUPO-PSI/mzIdentML/issues/2; a. For this we will also need to look at the proposed XL CV: https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv 3. Action points towards getting the XL part of mzid 1.2 complete Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 27 April 2016 10:22 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, This is to confirm that we will have a call at 4pm UK, 5pm EU, 8am California: http://www.timeanddate.com/worldclock/fixedtime.html?msg=PSI-PI+call+on+crosslinking&iso=20160428T16&p1=301&ah=1 The main topic for discussion will be encoding cross-linking in mzIdentML 1.2. Current issues with mzIdentML 1.2 are being discussed on GitHub here: https://github.com/HUPO-PSI/mzIdentML/issues, I will update it with open issues around cross-linking by tomorrow. The current version of the specifications are here (rather long I’m afraid) along with a powerpoint explaining the encodings for new features: https://github.com/HUPO-PSI/mzIdentML/tree/master/specification_document/specdoc1_2 If Lutz is able to create a CV file for reagents before the call, we will also post that online for discussions. Best wishes Andy 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 Sent: 19 April 2016 15:56 To: tobias <to...@eb...<mailto:to...@eb...>> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; sul...@ug...<mailto:sul...@ug...>; ju...@ed...<mailto:ju...@ed...>; eli...@ug...<mailto:eli...@ug...>; Lutz Fischer <lfi...@st...<mailto:lfi...@st...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; Juan Antonio Vizcaino <ju...@eb...<mailto:ju...@eb...>>; Yasset Perez-Riverol <yp...@eb...<mailto:yp...@eb...>>; psi...@li...<mailto: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 |
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From: andrewrobertjones <not...@gi...> - 2016-05-11 15:40:40
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Agreed to leave this in as a place holder to allow for extensions in the future --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/27#issuecomment-218499070 |
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From: andrewrobertjones <not...@gi...> - 2016-05-11 15:40:32
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Closed #27. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/27#event-657366347 |
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From: andrewrobertjones <not...@gi...> - 2016-05-11 15:38:21
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ACTION: Gerhard going to make a brief report of the terms we have, and we will create new terms where needed separating PSMs and peptides --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-218498282 |
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From: andrewrobertjones <not...@gi...> - 2016-05-11 15:35:38
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Agreed that we would like to have external spectra i.e. “encouraged” but not checked by validator --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/23#issuecomment-218497425 |
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