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

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Hi everyone,

I have to catch a train at 5:40 tonight. I will try to arrive in advance 
at the train station and join the call from there from 5:00 to 5.30.

I got some precisions from my team regarding neXtProt's Peff generator:

- the source code is publicly available but conceived to communicate 
with neXtProt (uses neXtProt's new  API)
- as is, it is not applicable on UniProt entries. Adaptation to UniProt 
content would require rewriting the DAO classes (links between database 
and services).

If you need to generate Peff from (non human) Swiss-Prot entries, I'd 
suggest you to contact the Swiss-Prot development team.

Best,

Lydie

On 28.05.2015 01:15, Eric Deutsch wrote:
>
> 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
>
> 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
>
> Please email me if you have specific agenda items or other questions 
> or comments.
>
> thanks,
>
> Eric
>

-- 
Lydie Lane, Ph. D
CALIPHO group co-director
SIB-Swiss Institute of Bioinformatics
Department of Human Protein Sciences, University of Geneva
CMU, Michel-Servet 1,
1211 Geneva 4,
Switzerland
+ 41 (0) 22 379 58 41