Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

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Hi all,

I am now including also Emanuele Alpi in the loop. He is representing the UniProt team in the EBI and will join the calls. They are very interested in supporting PEFF in the future, since there is increasing demand from UniProt users for them to provide a better support for variation information and they were already thinking about ways to do this. 

He will also coordinate efforts with the UniProt development team here to produce additional example files (in addition to the human ones provided by neXtProt).

Cheers,

Juan

> On 18 Jun 2015, at 15:29, Eric Deutsch <ede...@sy...> wrote:
> 
> Hi everyone, I know we had planned to call again today to discuss PEFF, but I am behind on the preparations I wanted to get done before the call. And I didn’t send a reminder or anything. So let’s plan on meeting next Thursday at the regular time. In the next week I will send out the revised documents and repository where all the materials are, so that everyone has a chance to review the documents before the call.
>  
> Thanks,
> Eric
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Thursday, May 28, 2015 3:32 PM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, here are my notes from the second PEFF call today. Please let me know if I captured anything incorrectly.
>  
> Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Harald, Karl, Juan Antonio, Simon, Julian, Gerhard, 
> Did I miss anyone?
>  
> Agenda:
>  
> - Review conclusions from last time
> + Explicitly do not support the (CTRL+A) multi-header delimiter
> + For variants, deprecate existing term and create two new terms, one for simple single amino acid substitutions, and another for more complex indels and extended replacements, etc.
> + nonsense mutation supported via * character
> + No regular expressions for the simple SAAV term, but do allow regexp for the more complex
>  
> - Discuss degree of PTM complexity to support
> + Proposed format for PTMs is (startPosition|endPosition|accession|name)
> + Two reasons for start and end: 1) there can be modifications that span multiple residues, 2) only one way to encode for all
> + Would we encode not just the position, but also the residue that can be modified?
> + PSI-MOD has implicit reference of which amino acid is being modified
> + tricky issue
> + Consensus: do not encode the amino acid being modified. Let it be implicit from the CV or inferred by the reading software
> + Describe explicitly how different start and stop positions would be used with examples in the spec doc
>  
> - Support for UniMod vs. PSI-MOD
> + Existing two terms ModRes and ModResPSI
> + ModResPSI requires PSI-MOD identifier
> + Proposal to just support UniMod instead 
> + Karl suggests that we should have explicit names in addition to a modification so that it is human readable
> + Pierre-Alain says that the reason for the two terms is that some resources already use PSI-MOD and some use UniMod. Conversion between the two is difficult.
> + Do neXtProt/UniProt already support PSI-MOD and RESID? So conversion to UniMod might be difficult?
> + It is not possible to have a one-to-one mapping between PSI-MOD and UniMod. Many-to-may mapping is possible.
> + One problem with readability is that PSI-MOD names are very long
> + Is it true that in the UniMod.obo that all term names are unique? We hope so. Is required by OBO format?
> + Continue to use ModResPSI and use a four-part entry (startposition|endposition|accession|name)
> + Add ModResUnimod term and support that
> + But also keep the original ModRes. Discourage use of this except when UniMod and PSI-MOD not feasible
> + Suggest for a single PEFF file, only one of these terms should be used. Don’t mix terms.
> + Settle on (startPosition|endPosition|accession|name)
> + This allows for significant complexity, and we should explicitly allow readers to determine the level of complexity they will support
>  
> We ran out of time again here.
>  
> Major action items:
> + Capture all these sentiments in the spec doc as well as the example files and circulate in advance of the next telecall in 3 weeks time
>  
> - Review examples of PEFF
> - Review PEFF-supporting software
> - Central location for all supporting documentation
> - Another call in 2-3 weeks to review progress on the action items?
> + Yes, same time in 3 weeks
>  
>  
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Wednesday, May 27, 2015 4:15 PM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, this is a reminder that we planned a call Thursday 8am Seattle, 4pm UK time to continue our discussion on PEFF. I hope we can get through the rest of the agenda this time. I have another hard stop at 55 minutes past the hour, so we’ll try to finish efficiently.
>  
> Dial in numbers:
> + Germany: 08001012079
> + Switzerland: 0800000860
> + UK: 08081095644
> + Generic international: +44 2083222500 (UK number)
> + US: 877-420-0272
>  
> access code: 297427 #
>  
> Agenda:
>  
> - Review conclusions from last time
> - Discuss degree of PTM complexity to support
> - Support for UniMod vs. PSI-MOD
> - Review examples of PEFF
> - Review PEFF-supporting software
> - Central location for all supporting documentation
> - Listing of action items
>  
> Thanks,
> Eric
>  
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Thursday, May 21, 2015 11:26 AM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, here are my notes from the PEFF call today. Please let me know if I captured anything incorrectly.
>  
> Note that we agreed to continue to the second part of the posted agenda, which we did not finish today, next Thursday at the same timeslot.
>  
> Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, Gerben, Yasset, Karl, Juan Antonio
> Did I miss anyone?
>  
> Agenda:
>  
> - Review what remains to be done
> + We need to finish spec doc, the extant single hand-crafted example (~dozen entries), and the OBO file
> + neXtProt has been generating PEFF files regularly (not quite compliant the spec as previously written, but are now actively fixing the neXtProt exporter so this discussion is timely)
> + Writer from Alain Gateau? This is the neXtProt exporter?
> + Reader from Harald
> + Settle the open issues below and then update all these elements
> + Full manuscript?
> + General tool to work with PEFF files? Add/subtract elements, adjust annotations? Would be great but not required.
>  
> - Discuss (CTRL+A) header delimiter
> + Not new perhaps, this already exists in FASTA!
> + Or maybe not in the FASTA specification is there is one, but seen in the wild
> + Original NCBI nr already has these (CTRL+A)
> + This PEFF feature was mainly motivated by the fact that this feature is already existing out there in the field, by NCBI nr at least
> + For software implementations, there are several things that could happen when faced with this, which is not good.
> + Some on the call feel this is a problematic feature that should be avoided
> + General consensus is that this should be an explicitly disallowed feature. Keep it simple. Repeat the sequence.
> + Could add a header keyvalue that could point to other redundant entries?
>  
> - Discuss degree of sequence variant complexity to support
> + Explicit examples of usage should be written into the specification. This is not there yet.
> + Discussion at PSI workshop last month moved strongly toward excluding advanced variations completely
> + Karl proposed having two different tags, one for simple substitutions, and one for indels and other complex things
> + Gerben in favor of including indels in separate tags
> + Pierre-Alain okay to splitting into two tags as Karl suggested
> + Karl stands by his suggestion. And also suggests deprecating existing term to avoid confusion
> + Explicitly require that SAAV changes be in the simple SAAV term, and NOT in the more complex term
> + Xiaojing asks what about nonsense mutation?
> + In the simple SAAV, could allow a change to an asterisk: (223:*) General agreement on this.
> + (223|225|KPA) goes in the more complex term
> + There were rumblings that regular expressions should not be supported anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) in complex. Eric is not sure if there was a consensus on this.
>  
> Ran out of time here. Skipped to last agenda item. Will continue here next week.
>  
> - Discuss degree of PTM complexity to support
> - Support for UniMod vs. PSI-MOD
> - Review examples of PEFF
> - Review PEFF-supporting software
> - Central location for all supporting documentation
>  
> - Time slot for future calls
> + Broad agreement that Thursday at this time is good. We will meet again at this time next week and continue with the agenda.
>  
>  
>  
>  
>  
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Wednesday, May 20, 2015 4:18 PM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, just a reminder about the PEFF call tomorrow, see below for details. Dial-in information:
>  
> Dial in numbers:
> + Germany: 08001012079
> + Switzerland: 0800000860
> + UK: 08081095644
> + Generic international: +44 2083222500 (UK number)
> + US: 877-420-0272
>  
> access code: 297427 #
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Monday, May 18, 2015 2:36 PM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, it appears that we have near consensus for Thursday at the earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.
>  
> Agenda:
> - Review what remains to be done
> - Discuss (CTRL+A) header delimiter
> - Discuss degree of sequence variant complexity to support
> - Discuss degree of PTM complexity to support
> - Support for UniMod vs. PSI-MOD
> - Review examples of PEFF
> - Review PEFF-supporting software
> - Central location for all supporting documentation
> - Time slot for future calls
>  
> We may not get through this all, but let’s tackle as much as we can and continue at the next call. I’m presenting at the top of the next hour, so I’d like to limit this call to 55 mins.
>  
> I will send out dial-in information and reminder as we get closer.
>  
> Thanks,
> Eric
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Friday, May 15, 2015 10:05 AM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; Eric Deutsch; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>
> Subject: PEFF progress and call next week and beyond
>  
> Hi everyone, we would like to set up some regular calls to carry PEFF over the finish line. We had a good discussion at the PSI meeting, so we just need to keep some momentum to get it finished.
>  
> I would like to set up a time next week to have conference call to discuss some of the open issues. If you are interested in working to help complete and resubmit PEFF, please complete the Doodle poll below (even if you cannot attend at the suggested times next week) and I will keep you in the loop for continuing development on this. I have sent this to the list of coauthors on the specification and other vocal participants at the workshop that I recall. Anyone else is welcome to join the effort even if I forgot to add you to the list above.
>  
> http://doodle.com/but4z7ihv75byyp7 <http://doodle.com/but4z7ihv75byyp7>
>  
> Attached are the latest document and the notes I took during the PSI workshop.
>  
> Please respond to the doodle poll and I will email some specific agenda point in advance of the meeting.
>  
> We should probably paste some more information here:
> http://www.psidev.info/peff <http://www.psidev.info/peff>
>  
> Please email me if you have specific agenda items or other questions or comments.
>  
> thanks,
> Eric