psidev-qc-dev

[Psidev-qc-dev] QC-CV -> MS-CV

[Mathias W. <wa...@eb...>]

Dear PSI-MS CV community,

I am writing on behalf of the PSI-QC working group, as we want to get our 
QC-CV 'into the fold'. Before that however, we thought it'd be best to start a 
conversation on how.
We have been developing a separate CV initially to have some freedoms on 
what/how things work out best for the mzQC format, which relies heavily on 
CV control.
Our CV holds the metric definitions, relations and few additional 
'organisational' terms, so far <300 entries, for which we chose the QC 
prefix (naturally). We ditched the `xref: value-type` declarations in 
favour of defining term values with full CV terms and relations, which 
works nicely with the format. 
The mzQC format is, unlike most PSI formats, JSON based. One of the goals 
in the design was to bring the format closer to the last miles of analysis 
(R/pandas/web) but also as something that works between any steps of a MS 
based study workflow (lightweight with high automation potential). If you 
want to know more, check out our specification document draft (https://hupo-psi.github.io/mzQC/). For mzQC, we 
have to cover a vast range of QC/MS related topics in the CV. For that, 
we've devised a set of templates and rules for adding new term/metrics via 
GitHub issues. To keep better track of the entries, Nils created a GitHub 
workflow for obo-to-markup conversion to enhance browsability. QC-CV is not 
standalone, we base as much as possible on existing definitions, so we 
imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course. 
So, overall I think QC-CV would fit in nicely, either as big PR or 
piece-wise. As for the merge, maybe we can follow the same playbook as the 
PEFF integration did?
What do you think?

TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a 
gargantuan PR, we should talk.

Best,
-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

Re: [Psidev-qc-dev] [Psidev-ms-vocab] QC-CV -> MS-CV

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

Hi everyone, this conversation is now here:

https://github.com/HUPO-PSI/psi-ms-CV/issues/80



Please participate there if you are interested in this.



Thanks,

Eric





*From:* Mathias Walzer <wa...@eb...>
*Sent:* Tuesday, August 17, 2021 9:49 AM
*To:* psi...@li...
*Cc:* psi...@li...
*Subject:* [Psidev-ms-vocab] QC-CV -> MS-CV



Dear PSI-MS CV community,

I am writing on behalf of the PSI-QC working group, as we want to get our
QC-CV 'into the fold'. Before that however, we thought it'd be best to
start a
conversation on how.
We have been developing a separate CV initially to have some freedoms on
what/how things work out best for the mzQC format, which relies heavily on
CV control.
Our CV holds the metric definitions, relations and few additional
'organisational' terms, so far <300 entries, for which we chose the QC
prefix (naturally). We ditched the `xref: value-type` declarations in
favour of defining term values with full CV terms and relations, which
works nicely with the format.
The mzQC format is, unlike most PSI formats, JSON based. One of the goals
in the design was to bring the format closer to the last miles of analysis
(R/pandas/web) but also as something that works between any steps of a MS
based study workflow (lightweight with high automation potential). If you
want to know more, check out our specification document draft (
https://hupo-psi.github.io/mzQC/). For mzQC, we
have to cover a vast range of QC/MS related topics in the CV. For that,
we've devised a set of templates and rules for adding new term/metrics via
GitHub issues. To keep better track of the entries, Nils created a GitHub
workflow for obo-to-markup conversion to enhance browsability. QC-CV is not
standalone, we base as much as possible on existing definitions, so we
imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course.
So, overall I think QC-CV would fit in nicely, either as big PR or
piece-wise. As for the merge, maybe we can follow the same playbook as the
PEFF integration did?
What do you think?

TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a
gargantuan PR, we should talk.

Best,

-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

Re: [Psidev-qc-dev] QC-CV -> MS-CV

[walzer <wa...@eb...>]

Hello Everyone,
thanks for the swift completion of the doodle, this Friday seems like 
the most viable option. On that date, there will be another call for 
some of you, that has graciously been postponed for half an hour, to 
make some time for us.
So we're going to make it short and snappy, slotting 30min. on

Sep 17,Fri, 8 am PST/ 11am EDT / 4pm BST / 5pm CEST

to discuss the QC-CV and how to merge with MS-CV. Zoom/google link will 
follow shortly.

later,
   mths

On 2021-09-13 12:55, walzer wrote:
> Hello Everyone,
> 
> I just started a doodle to find a date (and a channel on HUPO-PSI
> slack for the topic, but since not everyone is there, I'll also post
> here).
> B'cs of timezone spread Wout suggested we'd start with the USI
> timeslot Fridays 8 am PST/ 11am EDT / 4pm BST / 5pm CEST
> https://doodle.com/poll/c76bbv6in2h8ywv3 (admin link in slack if you
> think we need to add new dates/times)
> 
> best,
>   mths
> 
> On 2021-08-17 17:49, Mathias Walzer wrote:
>> Dear PSI-MS CV community,
>> 
>> I am writing on behalf of the PSI-QC working group, as we want to get
>> our
>> QC-CV 'into the fold'. Before that however, we thought it'd be best to
>> start a
>> conversation on how.
>> We have been developing a separate CV initially to have some freedoms
>> on
>> what/how things work out best for the mzQC format, which relies
>> heavily on
>> CV control.
>> Our CV holds the metric definitions, relations and few additional
>> 'organisational' terms, so far <300 entries, for which we chose the QC
>> 
>> prefix (naturally). We ditched the `xref: value-type` declarations in
>> favour of defining term values with full CV terms and relations, which
>> 
>> works nicely with the format.
>> The mzQC format is, unlike most PSI formats, JSON based. One of the
>> goals
>> in the design was to bring the format closer to the last miles of
>> analysis
>> (R/pandas/web) but also as something that works between any steps of a
>> MS
>> based study workflow (lightweight with high automation potential). If
>> you
>> want to know more, check out our specification document draft
>> (https://hupo-psi.github.io/mzQC/). For mzQC, we
>> have to cover a vast range of QC/MS related topics in the CV. For
>> that,
>> we've devised a set of templates and rules for adding new term/metrics
>> via
>> GitHub issues. To keep better track of the entries, Nils created a
>> GitHub
>> workflow for obo-to-markup conversion to enhance browsability. QC-CV
>> is not
>> standalone, we base as much as possible on existing definitions, so we
>> 
>> imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course.
>> So, overall I think QC-CV would fit in nicely, either as big PR or
>> piece-wise. As for the merge, maybe we can follow the same playbook as
>> the
>> PEFF integration did?
>> What do you think?
>> 
>> TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a
>> gargantuan PR, we should talk.
>> 
>> Best,
>> 
>> --
>> Mathias Walzer
>> European Bioinformatics Institute (EMBL-EBI)
>> Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
>> Office: +44 (0)1223 494 2610
>> E-mail: wa...@eb...

Re: [Psidev-qc-dev] [Psidev-ms-vocab] QC-CV -> MS-CV

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

Hi everyone, I sent out the Zoom link to a private list of recipients so
as not to post the Zoom link here on these lists. If you did not get a
Zoom link from me and want to attend, please email me and I'll send you
the Zoom link.

Thanks,
Eric


-----Original Message-----
From: walzer <wa...@eb...>
Sent: Thursday, September 16, 2021 3:39 AM
To: psi...@li...;
psi...@li...
Subject: Re: [Psidev-ms-vocab] QC-CV -> MS-CV

Hello Everyone,
thanks for the swift completion of the doodle, this Friday seems like the
most viable option. On that date, there will be another call for some of
you, that has graciously been postponed for half an hour, to make some
time for us.
So we're going to make it short and snappy, slotting 30min. on

Sep 17,Fri, 8 am PST/ 11am EDT / 4pm BST / 5pm CEST

to discuss the QC-CV and how to merge with MS-CV. Zoom/google link will
follow shortly.

later,
   mths

On 2021-09-13 12:55, walzer wrote:
> Hello Everyone,
>
> I just started a doodle to find a date (and a channel on HUPO-PSI
> slack for the topic, but since not everyone is there, I'll also post
> here).
> B'cs of timezone spread Wout suggested we'd start with the USI
> timeslot Fridays 8 am PST/ 11am EDT / 4pm BST / 5pm CEST
> https://doodle.com/poll/c76bbv6in2h8ywv3 (admin link in slack if you
> think we need to add new dates/times)
>
> best,
>   mths
>
> On 2021-08-17 17:49, Mathias Walzer wrote:
>> Dear PSI-MS CV community,
>>
>> I am writing on behalf of the PSI-QC working group, as we want to get
>> our QC-CV 'into the fold'. Before that however, we thought it'd be
>> best to start a conversation on how.
>> We have been developing a separate CV initially to have some freedoms
>> on what/how things work out best for the mzQC format, which relies
>> heavily on CV control.
>> Our CV holds the metric definitions, relations and few additional
>> 'organisational' terms, so far <300 entries, for which we chose the
>> QC
>>
>> prefix (naturally). We ditched the `xref: value-type` declarations in
>> favour of defining term values with full CV terms and relations,
>> which
>>
>> works nicely with the format.
>> The mzQC format is, unlike most PSI formats, JSON based. One of the
>> goals in the design was to bring the format closer to the last miles
>> of analysis
>> (R/pandas/web) but also as something that works between any steps of
>> a MS based study workflow (lightweight with high automation
>> potential). If you want to know more, check out our specification
>> document draft (https://hupo-psi.github.io/mzQC/). For mzQC, we have
>> to cover a vast range of QC/MS related topics in the CV. For that,
>> we've devised a set of templates and rules for adding new
>> term/metrics via GitHub issues. To keep better track of the entries,
>> Nils created a GitHub workflow for obo-to-markup conversion to
>> enhance browsability. QC-CV is not standalone, we base as much as
>> possible on existing definitions, so we
>>
>> imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course.
>> So, overall I think QC-CV would fit in nicely, either as big PR or
>> piece-wise. As for the merge, maybe we can follow the same playbook
>> as the PEFF integration did?
>> What do you think?
>>
>> TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a
>> gargantuan PR, we should talk.
>>
>> Best,
>>
>> --
>> Mathias Walzer
>> European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome
>> Campus, Hinxton, Cambridge, UK
>> Office: +44 (0)1223 494 2610
>> E-mail: wa...@eb...


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