Re: [Psidev-qc-dev] Automatic generation of SWATH metrics in mzQC format

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

Great work! 👏

I briefly went through the file and I have a few small comments:

- You forgot the outer curly brackets around the mzQC element, which 
should also be a string.
- Make sure you use the correct capitalization of the JSON keys. For 
example, "URI" in analysisSoftware and the CVs -> "uri".
- runQuality/inputFiles/analysisSoftware should be lists.
- The "location" of input files should be a URI; i.e. prefixed by 
"file://" for local files. Also, the location and name should match.
- It is mandatory to specify the type of the input file (i.e. raw, mzML, 
...).
- Make sure the name of the quality parameters exactly matches the terms 
in the CV, otherwise the semantic validation will fail.
- You should request that the missing terms are added to the CV in an 
issue on the repository.
- Are the units for metrics swDensity50/PeakCapacity/PeakSymmetry 
correct? It's specified as a count, but the values are floats. Similarly 
for metric swDensityIQR/MS2TICTotal/MS1TICTotal, although there at least 
all the floats are xxx.0.
- CV term MS:1000040 can be used to specify an m/z unit.
- Make sure the CV keys in the CV list are the same as used for the 
quality parameters, i.e. capitalization is different here. If these are 
not the same the correct CV can't be found (and the validator will throw 
an error).
- The CV URIs should be the raw obo files rather than the Github web 
pages containing the obo files, otherwise the ontology parser won't be 
able to load it correctly. This is wrong in the current examples files 
that are online as well. Probably ideally we should also use URIs that 
include a specific commit rather than master, as the content of the 
files can change in that case.

It's great to see some tools automatically exporting to mzQC.

On 2019-07-18 06:44, Tabb, David, Prof [dt...@su...] wrote:
> Hi, all.
> 
> I am really proud of Marina Pauw’s progress with her “SwaMe” quality 
> control metric generator for SWATH data sets (with some very helpful 
> input from Paul Brack).  Her prototype now exports its quality metrics 
> in JSON!  I am attaching an example of the output at this early stage.  
> We are still finalizing the list of metrics that will be included in the 
> manuscript introducing the software, but this is what we believe 
> represents the current thinking for our data structures.
> 
> Talk to you shortly,
> Dave
> 
> <http://www.sun.ac.za/english/about-us/strategic-documents>
> 
> The integrity and confidentiality of this email are governed by these 
> terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer >
> Die integriteit en vertroulikheid van hierdie e-pos word deur die 
> volgende bepalings bereël. Vrywaringsklousule 
> <http://www.sun.ac.za/emaildisclaimer >
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>