psidev-qc-dev Mailing List for Proteomics Standards Initiative (Page 15)

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Well done, Wout!

I like that you were able to show instrument readings this way; I 
remember your working on capturing these readings in the iMonDB 
database, so it makes sense that we'd want to represent them in qcML.

As we move to the outlier.qcml, I see that you're using RawFile to point 
to a source qcML document (I had earlier used RawFile to point to an 
mzML rather than a RAW).  We may want to work out just what RawFile is 
supposed to represent or create other terms to represent later products 
in the pipeline.  As Wout notes, though, the RawFile section allows us 
to specify the file type.

The "Meta-analysis settings" set thresholds for variability; as I 
understand it, though, these thresholds would be applied on individual 
metrics rather than a dimensionality-reduced set (e.g. via PCA).  When 
we dip down to the comment below below the metaDataParameters section, 
though, it appears that Wout is giving weights to show how to combine 
scores, perhaps in a linear combination of metrics to optimize the 
amount of variability explained?  A PCA would really only be feasible 
for a defined set of metrics from a bunch of input files.  This same 
transform, however, might then be applied to new qcML files that were 
not part of the set used to conduct PCA.  The transform itself does not 
tell us that a qcML is an outlier or not.  Instead, it accepts the 
quality metrics as an input and outputs the coordinates of this qcML in 
the transformed space; we can then compute distances in PC space between 
pairs of qcML files, and an abnormally large distance in PC space 
implies an outlier.

Wout, thank you for trying the multi-file analysis for us!  Yes, I think 
this highlights some areas where we have been vague to date.

Merci,
Dave

On 4/11/2018 10:48 PM, Bittremieux Wout wrote:
> Dear colleagues,
>
> I have also prepared two handcrafted example files:
> - one from the iMonDB containing instrument parameters as opposed to 
> ID-free/ID-based spectral metrics
> - one from a meta-analysis to detect low-quality experiments
>
> The files include some annotations about things to discuss. As you can 
> see especially for the meta-analysis I'm currently not sure how to 
> correctly store this information in a qcML file.
>
> Best,
> Wout
>
>
> > On 10 Apr 2018, at 10:15, Bittremieux Wout 
> <wou...@ua...> wrote:
> >
> > Hi Dave,
> >
> > Sorry for the delayed answer to your questions. As far as I'm aware 
> (please someone correct me if I'm wrong):
> >
> > - OBO and OWL are two alternative file formats to specify controlled 
> vocabularies and ontologies. We use the OBO format for our CV. This is 
> indeed a simpler format than OWL and can be viewed relatively easily 
> in a simple text editor. Alternatively, Martin has previously 
> recommended OBO-Edit to visualize the relationships between the 
> various terms.
> >
> > - In our previous discussions we have indeed said that in principle 
> every tool gets its own range of CV accessions. This would enable a 
> new tool to easily start producing compliant qcML files without having 
> to check dependencies on other tools. It might make sense to reuse 
> some trivial definitions though for metrics that don't involve any 
> computations, such the number of MS/MS scans. On the other hand, how 
> will downstream tools handle conflicting metrics coming from different 
> tools? Although in that case maybe the tool authors should be the main 
> persons responsible to worry about this rather than us.
> > In any case, it would be useful to explicitly document how tools can 
> get CV accessions.
> >
> > - To report the unit for a single QC metric you can use the 
> unitAccession/unitName/unitCvRef attributes for any XML element that 
> is derived from the CVParamType, which qualityParameter elements are. 
> The CVParamType is specified in our XML schema.
> >
> > - This XML schema can also be used for simple syntactic validation 
> and some semantic validation. Because we have a mix between XML and 
> JSON unfortunately some external semantic validation will have to be 
> explicitly coded as well though.
> > Any decent XML editor should have built-in functionality to validate 
> XML files against a schema, and otherwise there are various 
> command-line tools and linters you can use to do that as well. 
> However, the previously linked v0.0.10 XML schema on GitHub does not 
> seem to be fully up to date anymore at the moment, and I think the 
> most recent XML schema is available in Mathias' ongoing pull request.
> >
> > - As to metrics numbering I don't think we have a process for that 
> yet. I guess now it's just first-come-first-served.
> >
> > Best,
> > Wout
> >
> >> On 09 Apr 2018, at 23:56, David Tabb <dt...@su...> wrote:
> >>
> >> Hi, all.
> >>
> >> I have not yet received an answer to the three questions below.  I 
> have,
> >> however, uploaded it to qcdev, where you can find it at this URL:
> >> 
> https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml.
> >>
> >> Merci!
> >> Dave
> >>
> >> On 4/5/2018 11:29 AM, David Tabb wrote:
> >>> 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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