Re: [Psidev-qc-dev] Doing my homework for qcML

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Hi, all.

At long last, I have completed my "homework" for Heidelberg!  I have
created a draft XML to represent the qcML output for computing QuaMeter
IDFree metrics for a single input mzML file (see text inline below).  I
would greatly appreciate answers to the following questions to complete
this project:

1) If I am reporting only a single value for a metric (such as
"XIC-WideFrac"), how do I report the unit for the metric?

2) Do we have an easy way to validate a draft file like this, at least
to determine that I have matching end tags for each one I open?  I've
been using Emacs, which tries to help, but a dedicated XML editor might
be preferable.

3) Who officially designates what each metric will be numbered in the CV?

Thanks,
Dave
--------------------------------------------------------
<?xml version="1.0" encoding="UTF-8"?>
<qcML xmlns="http://www.prime-xs.eu/ms/qcml"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:schemaLocation="http://www.prime-xs.eu/ms/qcml
file:/home/walzer/psi/qcML-development/schema/v0_0_10/qcML_0_0_10.xsd"
version="0.0.10">
     <runQuality ID="ID001">
         <metaDataParameters ID="fileprovenance001" cvRef="?"
accession="?" name="?" description="do we need cv for toplevel"
value="all cv attributes are optional anyway">
             <InputFiles>
                 <RawFile
location="C:\Research\20171124-Lizex-Chia\1091_Pool_start.mzML"
id="ID001" name="1091_Pool_start.mzML">
                     <FileFormat>
                         <cvParam cvRef="PSI-MS" accession="MS:1000584"
name="mzML format"/>
                     </FileFormat>
             <!-- In the following line, I computed the md5sum for the
peak-picked mzML, not the RAW! -->
             <cvParam cvRef="PSI-MS" accession="MS:1000568" name="MD5"
value="b583f6d2a91b4749d5a75885330f6e5d" />
             <cvParam cvRef="PSI-MS" accession="MS:1000747"
name="completion time" value="2017-12-08-T15:38:57Z" />
                 </RawFile>
         </InputFiles>
     </metaDataParameters>
     <!-- Question to consider: how should I link a metric below to the
concept of "liquid chromatography" or "electrospray ionization?"  Is
this appropriate-->
     <!-- Units I employ below: -->
     <!-- UO:0000191 "fraction" -->
     <!-- UO:0000010 "second" -->
     <!-- UO:0010006 "ratio" -->
     <!-- UO:0000189 "count" -->
     <!-- UO:0000106 "hertz" -->
     <!-- When a line gives a single metric, where do I indicate the
unit type?  UO:0000191 "fraction" -->
         <qualityParameter ID="XIC-WideFrac" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Fraction of precursor ions
accounting for the top half of all peak width" value="0.206807"/>
     <qualityParameter ID="XIC-FWHM" cvRef="PSI-QC-CV" accession="QC:"
name="QuaMeter IDFree Metric- Distribution of peak widths for the wide
XICs">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="3">{'UO:0000010':[12.5377,14.2244,16.9234]}</content></qualityParameter>
     <!-- UO:0010006 is "ratio" rather than "log ratio"-->
     <qualityParameter ID="XIC-Height" cvRef="PSI-QC-CV" accession="QC:"
name="QuaMeter IDFree Metric- Distribution of peak log ratio heights for
the wide XICs">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="3">{'UO:0010006':[0.776393,0.93114,6.6283]}</content></qualityParameter>
     <!-- In the following, where do I indicate the unit type?
UO:0000010 "second" -->
         <qualityParameter ID="RT-Duration" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Highest scan time observed
minus the lowest scan time observed" value="4920.17"/>
     <qualityParameter ID="RT-TIC" cvRef="PSI-QC-CV" accession="QC:"
name="QuaMeter IDFree Metric- Distribution of TIC accumulation as
fraction of RT-Duration">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="4">{'UO:0000191':[0.301236,0.13286,0.174576,0.391328]}</content></qualityParameter>
     <qualityParameter ID="RT-MS" cvRef="PSI-QC-CV" accession="QC:"
name="QuaMeter IDFree Metric- Distribution of MS1 acquisition as
fraction of RT-Duration">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="4">{'UO:0000191':[0.217794,0.272976,0.275845,0.233385]}</content></qualityParameter>
     <qualityParameter ID="RT-MSMS" cvRef="PSI-QC-CV" accession="QC:"
name="QuaMeter IDFree Metric- Distribution of MS2 acquisition as
fraction of RT-Duration">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="4">{'UO:0000191':[0.268157,0.233516,0.236373,0.261954]}</content></qualityParameter>
     <qualityParameter ID="MS1-TIC-Change" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Distribution of log ratios
of MS1 scan-to-scan TIC changes">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="3">{'UO:0010006':[0.870774,0.900585,4.66521]}</content></qualityParameter>
     <qualityParameter ID="MS1-TIC" cvRef="PSI-QC-CV" accession="QC:"
name="QuaMeter IDFree Metric- Log ratios of MS1 scan TICs">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="3">{'UO:0010006':[0.568866,0.815636,1.18124]}</content></qualityParameter>
     <!-- In the following, where do I indicate the unit type?
UO:0000189 "count" -->
         <qualityParameter ID="MS1-Count" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Number of MS1 scans
acquired" value="7832"/>
     <!-- In the following, where do I indicate the unit type?
UO:0000106 "hertz" -->
         <qualityParameter ID="MS1-Freq-Max" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Maximum frequency for MS1
scan acquisition" value="2.41814"/>
     <qualityParameter ID="MS1-Density" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Distribution of peak
counts for MS1 scans">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="3">{'UO:0000189:[693,1205,1424]}</content></qualityParameter>
     <!-- In the following, where do I indicate the unit type?
UO:0000189 "count" -->
         <qualityParameter ID="MS2-Count" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Number of MS2 scans
acquired" value="33495"/>
     <!-- In the following, where do I indicate the unit type?
UO:0000106 "hertz" -->
         <qualityParameter ID="MS2-Freq-Max" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Maximum frequency for MS2
scan acquisition" value="7.33107"/>
     <qualityParameter ID="MS2-Density" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Distribution of peak
counts for MS2 scans">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="3">{'UO:0000189:[27,44,70]}</content></qualityParameter>
     <!-- How do we specify that the values of a vector sum to 1?  How
about this case, where two vectors together sume to 1?-->
     <qualityParameter ID="MS2-PrecZ-Known" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Fraction of known
precursor charges for +1, +2, ..., n, more than n">
     <content cvRef="PSI-QC-CV" accession="QC:3000008"
value="4">{'UO:0000191':[0,0.15047,0.0687565,0.00877743,0.000507538,0.000268697]}</content></qualityParameter>
     <!-- For the final metric, I used a reporting type where the number
of elements in vector is fixed: QC:3000007-->
     <qualityParameter ID="MS2-PrecZ-Unknown" cvRef="PSI-QC-CV"
accession="QC:" name="QuaMeter IDFree Metric- Fraction of unknown
precursor charges for +1, more than +1">
     <content cvRef="PSI-QC-CV" accession="QC:3000007"
value="2">{'UO:0000191':[0.54235,0.22887]}</content></qualityParameter>
     </runQuality>
     <cvList>
         <cv fullName="The HUPO-PSI QC WG metrics ontology in obo
format" uri="http://www.github.com/HUPO-PSI/.../" ID="PSI-QC-CV"/>
     </cvList>
</qcML>
--------------------------------------------------------

On 4/5/2018 9:47 AM, David Tabb wrote:
> Hi, all.
>
> In creating my hand-crafted example of qcML from QuaMeter IDFree, I've
> installed Protege, an ontology viewer.  It's useful for perusing the
> HUPO-PSI MS ontology (http://purl.obolibrary.org/obo/ms/4.1.2/ms.owl).
>
> I'm a bit confused, though, in how to review the qcML ontology. At
> present, I can find an OBO to download
> (https://github.com/HUPO-PSI/qcML-development/raw/master/cv/v0_0_10/qc-cv.obo),
>
> but I do not see an OWL equivalent.  Helpfully, I can simply review the
> OBO in a text editor.
>
> In particular, I am trying to determine which QC accessions each of my
> IDFree metrics will represent.  Does each metric generator get a
> particular series of numbers that relate to that software's outputs?
> Can I reuse a metric accession from other software if my tool generates
> the same values (such as the number of MS/MS scans)?
>
> Jinmeng Jia, will you be able to share your paragraph that meets the
> draft MIAPE QC standard with Weimin Zhu for him to present at
> Heidelberg?  I was sorry to hear you won't be able to attend yourself.
>
> Thanks,
> Dave
>
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