[Psidev-qc-dev] FW: [Psi-sc] INFO: mzQC SC review

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Hi, all.

I've received this email reflecting three PSI-SC reviews of our mzQC specification.  They've asked that we make some alterations to the document *prior to* its public evaluation period.

I thought the review had been encrypted in the P7S attachment, but the comments appear to be in the email thread itself.

Thanks,
Dave

From: Psi-sc <psi...@eb...> On Behalf Of Martin Eisenacher
Sent: Thursday, February 4, 2021 12:01 PM
To: 'PSI steering committee' <ps...@eb...>
Subject: [Psi-sc] INFO: mzQC SC review

Dear PSI steering group,

just for information:

>From my experience it was a rather vivid SC review of mzQC, I think this

reflects the high impact of such a standard later and what is therefore

expected also in the next review phase.

Some of the SC review comments should be answered BEFORE further

public and invited review and some would profit from potentially

more / other opinions DURING the next review phase. The separation

between both is sometimes not so clear.

I tried (in separate mail to the authors) to mark the comments the

authors should address from my point of view BEFORE the next

phase with "!!!" and decided to have a "mix" between

minor and major restart of the DocProc (as described in the DocProc

definition).

That means that the authors should send their changes / comments for the !!!

to the three specific reviewers (Steffen, Juanan and me) and we should give

our OK before I go on to the next phase (that is quicker than a full restart).

The other comments could be answered later together with the comments

of invited and public review.

  Best regards

     Martin

--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum
Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496
E-mail mar...@ru...<mailto:mar...@ru...>
www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/>

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Von: Psi-sc <psi...@eb...<mailto:psi...@eb...>> Im Auftrag von Martin Eisenacher
Gesendet: Dienstag, 2. Februar 2021 17:41
An: 'PSI steering committee' <ps...@eb...<mailto:ps...@eb...>>
Betreff: [Psi-sc] REMINDER: new DocProc submission mzQC - 30 days steering group review

Dear PSI steering group,

this is a last-minute reminder that the deadline for the PSI SC review of mzQC
is near (tomorrow).

Having a quick look I saw comments from Juan-Antonio and Steffen,
which could be sufficent already as discussed before.

   Bye from Bochum
      Martin

--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum
Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496
E-mail mar...@ru...<mailto:mar...@ru...>
www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/>

[cid:image001.jpg@01D6FAED.772EB070]

Von: Psi-sc <psi...@eb...<mailto:psi...@eb...>> Im Auftrag von Martin Eisenacher
Gesendet: Montag, 4. Januar 2021 17:36
An: PSI steering committee <ps...@eb...<mailto:ps...@eb...>>
Betreff: [Psi-sc] new DocProc submission mzQC - 30 days steering group review

Dear PSI steering group,

there has been a DocProc submission by the Quality Control
working group with a new recommendation, the mzQC format.

Purpose of the format (excerpt from the spec. doc.):
"This document defines the mzQC file format to report and exchange quality-related information
for a mass spectrometry experiment, associated analysis results, or collections thereof.
The mzQC specification defines a simple yet versatile file format with a hierarchical structure
to store quality metrics, thereby providing support for general quality control, (automated)
decision making, visualisation efforts, and easy persistence and exchange of all of the above.
The format and its specification are realized in the widespread JavaScript Object
Notation (JSON) that can be easily implemented in software to produce or consume
mzQC files. The mzQC format is complemented by the Quality Control Controlled
Vocabulary (QC CV), which includes formal definitions of relevant quality metrics.
The combination of the clear, human-readable syntax of the mzQC format and the
rich semantic information associated with quality metrics stored in the QC CV
provides powerful mechanisms to interpret, store, and enable reuse of quality control
data."

It is a file format, but not XML, which is explained / motivated in an own section.
Some examples and - more descriptive - companion documents are linked from
the spec. doc.
There are three "reference implementations" mentioned (two python, one R).

Specification document: attached and https://github.com/HUPO-PSI/mzQC/tree/master/doc
Examples: https://github.com/HUPO-PSI/mzQC/tree/master/doc/examples

Aims of the 30 days steering group review phase are repeated after the end of the mail.

I checked the submission and have some comments to the
submitters already (see also track changes / comments in the attached spec. doc.):
- table of content with only 2 levels would be better readable
- "Implementations" may be own section (e.g. after pending issues) such as in PSI-MI or mzTab-M
- 1.1: address rule-based validation in JSON? (see comment in .docx)
- explicitly mention specific QC samples and blanks also for Proteomics experiments (section 3.1)?
- I could imagine that somewhere it is explicitly stated (and explained), that the format itself
  a) does not make any quality metrics mandatory, even not for specific use cases; and
  b) the format itself does - of course - not judge whether the experiment was of "sufficient", "good", or "bad" quality.
  And that at least a) can than be concretized by users/ journals / repositories (e.g. "PRIDE basic QC metrics").

These comments should at least be considered before the following 60-days public
and expert review phase.
Please send further feedback (and suggestions for expert reviewers)
until Wednesday, February 3rd, 2021.

Best regards
    Martin Eisenacher (PSI Editor)

Aims of the SG review phase:
"[Check:]
1. That it is well formed - that is, it is presented in accordance with the templates and is clearly written.
2. That it is of an appropriate technical standard - that is, it is sufficiently detailed and clearly described to enable its suitability as a PSI MIAPE or Recommendation document to be assessed, and that it is correct in the sense that it doesn't contain obvious errors.
3. That it doesn't present additional problems for the PSI that should be addressed before the specification enters a public review phase. For example, any overlap with an existing PSI specification or a specification in another standards body might be considered to be such an issue.
At the end of this 30-days review period the PSI Editor will determine, based on feedback from the Steering Group, whether the document should proceed to a 60-day public comment period or be returned to the submitter
"

--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum
Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496
E-mail mar...@ru...<mailto:mar...@ru...>
www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/>

[http://www.ruhr-uni-bochum.de/cd/extern/logo/Logo_RUB_BLAU_srgb.jpg]