Re: [Psidev-qc-dev] Upcoming teleconference 15/07

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

Hi all,

we'll be a small circle today then. I propose that those who have the 
time and want to join meet here: meet.google.com/cqx-obbq-mfh so that 
Wout does not have to keep an eye on the zoom and can focus. I suggest 
we tailor the agenda to the following two points of the ontology 
sections of the spec doc and the necessities for a metabolomics example.

stay safe and well everyone,

  mths

On 15/07/2020 03:26, Wout Bittremieux via Psidev-qc-dev wrote:
> Unfortunately I won't be able to join the call because I'm co-chairing 
> the CompMS session at ISMB the whole day. (*Maybe* I'll be able to 
> join the first 10 minutes.) Final preparations for this have taken up 
> quite some time in the past two weeks as well, so unfortunately I 
> haven't yet had the time to contribute further to the specification 
> document.
>
> I've been thinking about using PURLs or CV references to link quality 
> metrics to CVs, and I'm starting to favor something that was suggested 
> two weeks ago: to stick to the old format, but reserve CV namespaces 
> for the most commonly used CVs. So that would be "QC" for our CV, "MS" 
> for the MS CV, and "UO" for the unit ontology. These cover the 
> majority of use cases I think, and if we identify other commonly used 
> CVs we can still add those as well.
>
> The advantage of this is that it's possible to efficiently query terms 
> in these CVs, because the CV keys are fixed. So they essentially 
> function the same way as the PURLS, without the need of actually 
> having to use PURLs. For other CVs that aren't reserved a two-query 
> solution will still be needed, but considering that such queries 
> should be rare I don't consider that too much of a problem.
> A further advantage is that we can avoid the somewhat clunky PURL 
> specification, don't depend on an external service, and (very 
> importantly imo!) don't require web lookups to the PURL service (i.e. 
> essential for doing stuff in firewalled compute environments).
>
> A small disadvantage would be that to validate these reserved CV keys 
> we'd need to add explicit functionality in the mzQC Python library to 
> do so. But this is hardly a showstopper.
>
> This solution seems to somewhat give us the best of both worlds I 
> think. It's also nice that we don't need to change the JSON schema. 
> (Although we should probably still change the CV references in the 
> JSON schema from a dictionary to a list.)
> The only thing would be to clearly document this behavior and the 
> reserved CV keys in the specification document.
>
> I think we should also adapt and explicitly document some best 
> practices that were discussed in function of adapting PURLs: that CV 
> terms are final and can only ever be deprecated (i.e. an accession 
> will always point to the same CV term) and that we should document an 
> official CV versioning scheme.
>
> Let me know if I've overlooked something here.
>
> Best,
> Wout
>
> On 14/07/2020 19:05, Wout Bittremieux wrote:
>> Dear colleagues,
>>
>> This is a reminder that our next teleconference is scheduled for
>> Wednesday, July 15, 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://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
>> (Password: 012575)
>>
>> I'd like propose the following agenda items:
>>
>> - Update on finalization of specification document 
>> (https://docs.google.com/document/d/132F3MBgDJgtFlXxDZhpJ1oHGbKL8pT6dk9fvL55L5_M/edit). 
>>
>> - New CV requests for PTXQC via mailing list 
>> (https://sourceforge.net/p/psidev/mailman/message/37059772/). @Chris: 
>> Is this not covered yet?
>> - Continue discussion on CV references / PURLs in mzQC schema 
>> (https://github.com/HUPO-PSI/mzQC/pull/103).
>>
>> Thanks,
>> Wout
>
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

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