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

[Eric D. <ede...@sy...>]

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...]
*Sent:* Wednesday, May 20, 2015 4:18 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
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...]
*Sent:* Monday, May 18, 2015 2:36 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
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...]
*Sent:* Friday, May 15, 2015 10:05 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; Eric Deutsch; ju...@eb...; Ger...@gm...
*Cc:* Mass spectrometry standard development;
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