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Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting
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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 |
