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

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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<http://oboedit.org/> 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<https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/qcML_0_0_10.xsd>.

- 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<https://github.com/HUPO-PSI/qcML-development/pull/37>.

- 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...<mailto: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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psidev-qc-dev Mailing List for Proteomics Standards Initiative (Page 15)

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