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From: Jones, A. <And...@li...> - 2016-05-10 10:37:15
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Hi all, We will have a workshop attempting to finalise mzTab format for metabolomics, in Liverpool, UK on 4th and 5th July (two full days). Please can you forward on to your respective groups/collaborators and see if there are people who might be able to attend. The meeting will be free to attend, I will cover lunches and dinner, although participants will need to cover their own travel costs. If anyone is very keen to attend and work on mzTab longer term, but has no travel money, please contact me to see if we can work something out. Ideally I would like to have around 5-10 people attending (but can have more given sufficient interest), with knowledge of a range of MS metabolomics informatics approaches/pipelines, so we can make sure that mzTab is a viable format for input to statistical analysis and public data deposition, covering most common approaches. If anyone is interested in attending, please email me to confirm attendance. I would also appreciate if you can forward this message to any suitable mailing lists or collaborators. Best wishes Andy |
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From: andrewrobertjones <not...@gi...> - 2016-05-10 10:11:46
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These points were provisionally agreed on last call. @germa would you mind updating the mapping and validator. Please email me if anything is unclear. @fghali please can you update our example file before the call tomorrow if possible. 1. 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 --- 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-218115381 |
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From: Jones, A. <And...@li...> - 2016-05-10 08:58:10
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Hi all, Our next mzid 1.2 call is tomorrow at 4pm UK time/ 5pm EU / 8am California: http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160511T16&p1=301&ah=1, dial in details below. We will discuss all other open issues (non crosslinking) tomorrow, working through the issues list: https://github.com/HUPO-PSI/mzIdentML/issues Please can everyone check over any example files they have generated and make sure they are up to date in the SVN. It would also be really useful if you can run the validator over them, and report back any error messages e.g. via checking this in next to your example file. Can someone from the EBI confirm you are able to start the call 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 # |
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From: mayerg97 <ger...@ru...> - 2016-05-06 13:23:18
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Dear proteomics community, attached there's the release candidate 3.87.0_rc1 of the psi-ms.obo file. New CV terms in version 3.87.0_rc1 of psi-ms.obo: ================================================= [Term] id: MS:1002659 name: UniProtKB text sequence format def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI] xref: SWO:http://edamontology.org/format_2187 is_a: MS:1001347 ! database file formats [Term] id: MS:1002660 name: UniProtKB XML sequence format def: "XML-based format used by UniProtKB for sequence entries." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1002661 name: Morpheus def: "Morpheus search engine." [PMID:23323968] is_a: MS:1001456 ! analysis software [Term] id: MS:1002662 name: Morpheus:Morpheus score def: "Morpheus score for PSMs." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for PSMs is_a: MS:1001153 ! search engine specific score is_a: MS:1001405 ! spectrum identification result details relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1002663 name: Morpheus:summed Morpheus score def: "Summed Morpheus score for protein groups." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups is_a: MS:1001153 ! search engine specific score is_a: MS:1001147 ! protein ambiguity group result details relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1002664 name: protein interaction scores derived from cross-linking def: "Parent term for protein interaction scores derived from cross-linking." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002508 ! cross-linking attribute relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}) [Term] id: MS:1002665 name: regular expression for protein interaction scores derived from cross-linking def: "([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})" [PSI:PI] is_a: MS:1002479 ! regular expression Changed CV terms in version 3.87.0_rc1 of psi-ms.obo: ===================================================== ************ added is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1002600 name: PRIDE XML def: "Internal data and submission format of the PRIDE database." [http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd] is_a: MS:1002130 ! identification file format is_a: MS:1001405 ! spectrum identification result details ************ obsoleted the following term [Term] id: MS:1002639 name: peptide start on chromosome def: "OBSOLETE 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] comment: This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome. xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute is_obsolete: true 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: Salvador M. de B. <not...@gi...> - 2016-05-05 00:00:00
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I agree that is the less risky option. So, if we agree on this, I will update my example file accordingly. --- 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/5#issuecomment-217042724 |
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From: Jones, A. <And...@li...> - 2016-05-04 16:05:55
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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... Cc: eug...@tu...; le...@im...; Andrea Sinz <and...@ph...>; Robert Chalkley <cha...@cg...>; eli...@ug...; ju...@ed...; 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: Gerhard M. <not...@gi...> - 2016-05-04 13:58:47
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Closed #18. --- 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/18#event-650215575 |
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From: Gerhard M. <not...@gi...> - 2016-05-04 13:58:47
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Resolved. --- 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/18#issuecomment-216873538 |
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From: Jones, A. <And...@li...> - 2016-05-04 13:27:26
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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... Cc: eug...@tu...; le...@im...; Andrea Sinz <and...@ph...>; Robert Chalkley <cha...@cg...>; eli...@ug...; ju...@ed...; 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...> - 2016-05-04 13:27:04
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Closed #3. --- 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/3#event-650171331 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 13:26:53
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All ported to new issues - closing --- 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/3#issuecomment-216864476 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 13:04:29
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Just opening a comment here to remind us we need to do this. In Ghent, we discussed making different CV terms for all of PSM, peptide, protein, protein group and mod localisation so that reading software could easily tell, say under SpectrumIdentificationItem, whether the score is for a PSM, peptide or mod localisation. Mod localisation will have to specific terms anyway, since the values have a special structure. Most important work therefore is separating PSM and peptide-level scores, so a reader can figure this out. I have assigned to @edeutsch since Eric offered to take a look in Ghent, but other helpers would be very welcome! --- 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 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 12:57:50
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Here is what is written about protocols in the spec doc about the SIProtocol: `The <SpectrumIdentification> element MUST reference a <SpectrumIdentificationProtocol> holding representative parameters used across all search engines (i.e. search tolerances, enzyme and modifications), since these are MANDATORY elements. If the same search parameters were not employed in all source searches, the parameters should be set with superset or widest values i.e. all modifications that have been searched, widest tolerances and so on. All search engines that have been employed SHOULD be represented within the <AnalysisSoftwareList>. It must also be highlighted that mzIdentML cannot be used to model the order in which the software was used (it does not support workflows).` I realise that there is some information loss here, but as noted above, there is no way in a standard to capture all meta-data of every stage in a way that any reading software could really process and understand it. In terms of a wrapper format. This could be useful but I think it is overkill to consider this a way to capture all intermediate files in a workflow. In my opinion, this would for relating together quant, ident, peak list and raw files - e.g. based on the PX XML. I would like to get agreement on this one soon if possible. Can you give this comments thumbs up or down, and if get enough thumbs up, I will close it. If anyone still feels strongly, vote thumbs down and add another comment below. Thanks! Andy --- 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/5#issuecomment-216854400 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 12:43:23
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This appears to be complete - thanks @germa. I will close it now. --- 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/22#issuecomment-216851371 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 12:43:21
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Closed #22. --- 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/22#event-650119349 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 11:38:10
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Here are some CV terms already in existence: ` [Term] id: MS:1001125 name: manual validation def: "Result of quality estimation: decision of a manual validation." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide identification confidence metric is_a: MS:1001198 ! protein identification confidence metric [Term] id: MS:1001058 name: quality estimation by manual validation def: "The quality estimation was done manually." [PSI:PI] is_a: MS:1001060 ! quality estimation method details ` Please try them out in your files and see if they pass validation. If they do, let's just go with that, and I can add a point in the spec doc recommending to use them - probably MS:1001125 for XL ident validation --- 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/14#issuecomment-216835264 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 11:31:56
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Closed #2. --- 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/2#event-650052735 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 11:31:52
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I have closed down long convoluted thread on various CV items: #2. The have made a proposal for how I think we should represent protein interaction evidence in mzid - see attached pdf. [xl_protein_interaction.pdf](https://github.com/HUPO-PSI/mzIdentML/files/248648/xl_protein_interaction.pdf) --- 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/24 |
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From: andrewrobertjones <not...@gi...> - 2016-05-04 09:01:32
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I would like to keep the cardinality such that one SII references one Peptide chain identified, so for the case of L&H, we require four SII elements. Given the problem identified above with "chargeState" attribute, I think we should require that the calculatedMassToCharge and chargeState attributes for each cross-linked pair store identifical values for the calculatedMassToCharge of the whole cross-linked entity, whereby a pair of light would store different values from the pair of heavy. If it is felt necessary, we could also store the calculated neutral mass of each individual chain as a cvParam on each SII. Neutral mass would be better than calculatedMassToCharge anyway, since you may not have a charge value for each chain --- 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/19#issuecomment-216799348 |
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From: Eugen N. <not...@gi...> - 2016-05-03 15:04:48
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In the case of labelled linkers we do not have a mapping of one peptide chain to one spectrum, both the light and heavy spectrum are used to identify both peptides and contain fragments from both peptides. Using light-alpha, light-beta, heavy-alpha, heavy-beta SIItems would store the information, but is very redundant and each SIItem now means something different for each experimental setup (normal identification / labelled CLs / cleavable CLs). Since that is the case anyway, we could actually reduce redundancy by only writing half of the combinations, e.g. light-alpha and heavy-beta. It would look exactly like a case of cleavable cross-linkers and all the information would be there, a reader would just have to know what class of cross-linker was used to interpret the data correctly. But I guess we can live with the redundancy anyway. Still for both CL cases, cleavable and labelled, the precise mapping of each spectrumID in the list to the corresponding expMassToCharge and charge values of the SIItems is lost. This mapping was obvious before CLs were introduced as far as I can tell (since all SIItems under one SIResult referenced the same one spectrum) and I think it would be good to keep it obvious somehow. Now an unordered list of IDs has to be mapped to an unordered list of expMassToCharge values. I guess this could be solved by specifying a certain order in each case, e.g. by ascending expMassToCharge in the ID list and in the order of SIItems (either in the context of one specific "cross-link identification item", or in the context of the whole SIResult block). --- 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/19#issuecomment-216557630 |
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From: andrewrobertjones <not...@gi...> - 2016-05-03 15:01:00
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Further note - I've spotted there is a problem with this encoding. The chargeState is not specified whether it is experimental or calculated. We need to know the charge value for both calculated and experimental, if we go down this route of using the values in this way. The documentation is not very helpful here: `<xsd:attribute name="chargeState" type="xsd:int" use="required"> <xsd:annotation> <xsd:documentation>The charge state of the identified peptide.</xsd:documentation> </xsd:annotation> </xsd:attribute> <xsd:attribute name="experimentalMassToCharge" type="xsd:double" use="required"> <xsd:annotation> <xsd:documentation>The mass-to-charge value measured in the experiment in Daltons / charge. </xsd:documentation> </xsd:annotation> </xsd:attribute> <xsd:attribute name="calculatedMassToCharge" type="xsd:double"> <xsd:annotation> <xsd:documentation>The theoretical mass-to-charge value calculated for the peptide in Daltons / charge. </xsd:documentation> </xsd:annotation> </xsd:attribute>` --- 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/19#issuecomment-216556301 |
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From: andrewrobertjones <not...@gi...> - 2016-05-03 14:57:31
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Thanks all. I don't mind whether it is branched to a new project or stays here. The front page of the GitHub should make it really clear how everyone gets access to the latest validator though. When a new build is made, is it possible to tag is so it automatically appears somewhere? --- 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/21#issuecomment-216555305 |
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From: Yasset Perez-R. <yp...@eb...> - 2016-05-03 14:04:41
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I will do it!!! On 03/05/2016 14:57, Jones, Andy wrote: > > 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...>; > 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 > > 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 > > > > ------------------------------------------------------------------------------ > 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 -- 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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From: Jones, A. <And...@li...> - 2016-05-03 13:58:05
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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...>; 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 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: Yasset Perez-R. <not...@gi...> - 2016-05-03 13:30:40
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@julianu I vote also for this option however should be clear from the readme of the file format where is the official validator. If you let me know where is the current version I can remove the old version and create the repository. --- 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/21#issuecomment-216527977 |
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