Re: [Psidev-qc-dev] Upcoming teleconference 7/10

[Wout B. <wbi...@he...>]

Dear colleagues,

You can find the notes of today's meeting here: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20201007_telco.md


I did some additional work on the specification document, and I have a 
few questions about the CV (to be made clear in section 5.2):

- Can someone please refresh my mind what the difference between 
"corresponding list" and "table" is? Conceptually they both seem to 
represent the same kind of data, although one is the transpose of the 
other. Currently "table" seems to not be used in the CV, while 
"corresponding list" is marked as "obsolete" in PR 102 (and is missing 
from the table in section 7). Should everything be "table" instead?

- We also don't have a CV term of the "matrix" type yet. Can we include 
an example?

- For the current CV on `master` the value types are specified in XML 
style using "xref: value-type:xsd\:int" format. I presume this is to be 
replaced by the "has_units" relationship instead?


Given this incompleteness and inconsistencies, can we prioritize work on 
the CV to have at least the final format, even if not all metrics are 
ready for inclusion yet? Is anything currently still blocking merging 
the relevant PRs?

Thank you everyone for your continued efforts.

Best,
Wout

On 06/10/2020 19:21, Wout Bittremieux via Psidev-qc-dev wrote:
> Dear colleagues,
> 
> We have our next teleconference tomorrow, Wednesday October 7, at 14h00 
> GMT (15h00 London, 16h00 Western Europe, 16h00 Cape Town, 17h00 Turkey, 
> 7h00 San Diego).
> 
> You can connect to our teleconference on Zoom through the
> following link: 
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuchealth.zoom.us%2Fj%2F92419363577%3Fpwd%3DWVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09&data=02%7C01%7Cwout.bittremieux%40uantwerpen.be%7C20557f6c1dea49080f8808d86a6a9529%7C792e08fb2d544a8eaf72202548136ef6%7C0%7C0%7C637376353739944571&sdata=qGt2t9UO5xzhR%2F9Ze4IOOJiqdC4iSFoAaYidHrhsw%2Fg%3D&reserved=0 
> 
> (Password: 012575)
> 
> I propose the following agenda items:
> 
> # Specification document
> 
> I've gone through (part of) the specification document again and tried 
> to make some things clearer and improve legibility. It would be useful 
> if people could have a look at the specification document before the 
> call and especially check the comments.
> 
> Here are some of the major topics to discuss:
> 
> - Is the switch from XML to JSON (section 2.1) sufficiently motivated 
> and is the introduction to JSON sufficient/too detailed/not detailed 
> enough?
> - Difference between mzQC and qcML (section 5.1): This needs to be very 
> convincing to warrant a new file format.
> - Is the QC CV adequately and correctly described (section 5.3)?
>      - Special note to Julian: there are a few outstanding comments that 
> require your attention.
>      - Should we include an example of a correct CV term request or is 
> this not necessary in this document?
>      - Please check whether the text on CV term creation is more clear 
> now, as it was remarked last time that this was hard to understand. I'm 
> not sure whether the text on values is fully correct and would 
> appreciate a close check thereof.
>      - Do we need to provide detailed information about the value types 
> the CV terms can take? I think yes. For example, in the CV example I've 
> added now, the type is `corresponding lists`, but this is not explained 
> anywhere.
>      - Additionally, more information on the `is_a` and `relationship` 
> links is probably useful.
> - Important! We need to make sure that all information about the CV is 
> up to date, as some changes happened since the initial version of the 
> specification document.
> 
> # Metrics that can't be directly traced back to a raw file (Chris)
> 
> Chris asked a question on Slack about how to store metrics that don't 
> directly refer to a raw file.
> 
> # State of mzqc-pylib (Mathias)
> 
> Chris and Yasset have inquired as to the status of mzqc-pylib.
> 
> # CV requests (Julian)
> 
> Several issues open requesting new CV terms.
> 
> 
> Please communicate other agenda items to the mailing list.
> 
> Best,
> Wout
> 
> 
> 
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