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Re: [Psidev-ms-dev] mzML validator experiences
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From: Matt C. <mat...@va...> - 2007-10-16 01:49:49
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<div class="Section1">
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">Hi Brian,
thank you for your continued
input and effort. I’m sorry I’ve been slow to respond on many of
your posts, I have a bunch of other pots boiling over here. However, I
think I can answer your questions here and promote further testing.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">1) Regarding
2min.mzML, we’ll fix
it, thanks.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">2) Regarding
how does the validator know
that MS:1000528 is invalid, please download:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><a
href="http://tools.proteomecenter.org/software/mzMLKit/mzML_0.99.0_large.zip">http://tools.proteomecenter.org/software/mzMLKit/mzML_0.99.0_large.zip</a><o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">(this is
hyperlinked from the main
development page <a href="http://www.psidev.info/index.php?q=node/257">http://www.psidev.info/index.php?q=node/257</a>)<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">In it, you
will find the semantic
validator software. One of the files in the distro is ms-mapping.xml.
It
is this file that encodes these rules and is what is used by the
semantic
validator. This file should be more prominently posted and will be.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">3) The
semantic validator is FOSS, please
see the PSI SVN repository and contribute!<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><a
href="https://psidev.svn.sourceforge.net/svnroot/psidev/psi/mzml/">https://psidev.svn.sourceforge.net/svnroot/psidev/psi/mzml/</a><o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">(this is
hyperlinked from the main
development page <a href="http://www.psidev.info/index.php?q=node/257">http://www.psidev.info/index.php?q=node/257</a>)<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">4) So, it
turns out that the semantic
validator is using an XML file to enforce the semantic rules, it is NOT
reading
the doc. It should be noted that this software and the mapping
mechanism was
developed originally for the PSI molecular interactions schema. That
format
uses the same built-in flexibility with semantic validation. We are
borrowing
that mechanism and software for mzML.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">5) Further,
in the doc, the cvParams
section for each element is meant to represent “Some examples of
allowed
cvParams (not necessarily complete)”. I will clarify that in the
doc. Further, one of the things I realized that we need to do, is
include
in the doc the rules set forth in the ms-mapping.xml file. These rules
are NOT currently in the doc, but they should be and will be. The doc
is
actually autogenerated from the other files, so I just need to include
some
code that parses this ms-mapping file and includes that information in
the doc.
This will be done for 0.99.1. Thanks!<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">6) Regarding
your Observation Two: It is
true that the standard relies on the maintenance of three artifacts:
xsd, cv,
mapping-ms.xml (not the doc as you had inferred; the doc is essentially
autogenerated from the former) (and behind the scenes, the example
instance
documents also need to be maintained). This translates to the
desired-stable
schema, the evolving controlled vocabulary, and the evolving ruleset on
how you
may use the CV within the xsd. This is where we are led by the
requirement that the schema be stable with provisions for flexibility
in
annotating many kinds of mass spec data.</span></font></p>
</div>
</blockquote>
>From my perspective, it should be possible to hand-maintain only the CV
and a templated schema which gets fleshed out by an autogenerator when
the CV changes. The mapping file seems like a hack to compensate for
two missing features in the CV: 1) the ability to distinguish between
values and categories, and 2) to specify the types and ranges of the
uncontrolled values. I think it's less contrived to extend the
capabilities of the CV format that we use so that it has those
features, or alternately, set conventions in the CV (like how to
interpret IS_A and PART_OF relationships) which provide the illusion of
those features in a well-defined way.<br>
<br>
I just looked up the OBO format in more detail and it seems to me that
we can very legitimately use convention to solve our CV problems:<br>
1) Distinguish between value/category terms:<br>
We can use [Typedef] stanzas to define a new relationship type,
"value_of", like:<br>
[Typedef]<br>
id: value_of<br>
name: value_of<br>
range: OBO:TERM_OR_TYPE ! there should be some way to say "not a term
which has a value_of relationship" but I don't know how and it's not
really necessary<br>
domain: OBO:TERM_OR_TYPE<br>
def: Indicates that the subject term is a controlled value of the
object term (which implies the object is a category)<br>
<br>
2) Add types, min and max properties:<br>
There are several ways to specify data type and min and max ranges, and
OBO is even aware of XSD types in some contexts. But because I'm not
exactly sure what those contexts are, it would be just as easy to add
type, min, and max properties to our category terms (which don't have
any value_of relationships pointing to them) as "trailing modifiers",
like:<br>
<pre>[Term]
id: MS:1000016
name: scan time {type="decimal", min="0"} ! a missing min or max implies no limit (or limit defined by the type; "xsd:" prefix is implied for the type
def: "The time taken for an acquisition by scanning analyzers." [PSI:MS]
is_a: MS:1000503 ! scan attribute</pre>
<br>
Such a CV, combined with a stable, templated schema, we can
auto-generate a full-fledged semantic validating schema and we can
avoid using any non-standard approaches.<br>
<br>
-Matt<font color="navy"><font size="2"><font face="Arial"><br>
<br>
</font></font></font>
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<p class="MsoNormal"><b><font face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font
face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma;">
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a>
[<a class="moz-txt-link-freetext" href="mailto:psi...@li...">mailto:psi...@li...</a>] <b><span
style="font-weight: bold;">On Behalf Of </span></b>Brian Pratt<br>
<b><span style="font-weight: bold;">Sent:</span></b> Monday, October
15, 2007
3:19 PM<br>
<b><span style="font-weight: bold;">To:</span></b> 'Mass spectrometry
standard
development'<br>
<b><span style="font-weight: bold;">Subject:</span></b>
[Psidev-ms-dev] mzML
validator experiences</span></font><o:p></o:p></p>
</div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span
style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Hello All,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">I decided to fool around
with the validator at <a
href="http://eddie.thep.lu.se/prodac_validator/validator.pl">http://eddie.thep.lu.se/prodac_validator/validator.pl</a>
to see how well that can be done in the presence of an inadequately
specified
file format. My plan was to take a valid file, mess with it, and
see if the validator would notice.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">A little hiccup at first
- I gave it the automatically
generated file <a
href="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/instanceFile/2min.mzML">http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/instanceFile/2min.mzML</a><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">- it doesn’t actually
validate, claiming a missing
index element. Somebody might want to check that out.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Then I gave it the
handrolled <a
href="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/instanceFile/tiny4_LTQ-FT.mzML0.99.0.mzML">http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/instanceFile/tiny4_LTQ-FT.mzML0.99.0.mzML</a>
- this validates fine. So, let the mayhem begin. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">I tried removing the
selectionWindow element surrounding the
cvParams declaring the upper and lower bounds of the selection window,
but the
validator is XSD aware so it caught that easily. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Then I tried changing
the accession numbers in the
selection window for others that might be honestly conceptually
mistaken by an
incautious output module author:<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-indent: 0.5in;"><font face="Arial"
size="2"><span style="font-size: 10pt; font-family: Arial;">accession="MS:1000501"
name="scan m/z lower limit"<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">changed to<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-indent: 0.5in;"><font face="Arial"
size="2"><span style="font-size: 10pt; font-family: Arial;">accession="MS:1000528"
name="lowest m/z value"<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">the validator caught this
as well, flagging the use of
accession numbers that were incorrect for that context. But the
knowledge
behind this doesn’t seem to come from the XSD or the CV file. So,
how does the validator know? <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><b><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; font-weight: bold;">Observation
one</span></font></b><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">: the
validator doesn’t appear to be open source (or if it is, a prominent
link
to the source should be provided). The use of a closed source tool
like
this in a standards effort isn’t a good idea, since it’s hard to
answer questions like the one above.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Apparently the author of
the validator made excellent use of
the documentation at<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><a
href="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/document/mzML0.99.0_specificationDocument.doc">http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/document/mzML0.99.0_specificationDocument.doc</a><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">which stipulates in
English that the only valid cvParams in
that context are:<o:p></o:p></span></font></p>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"><cvParam cvLabel="MS" accession="MS:1000501" name="scan m/z lower limit" value="400.000000"/><o:p></o:p></span></font></pre>
<pre><font face="Courier New" size="2"><span style="font-size: 10pt;"><cvParam cvLabel="MS" accession="MS:1000500" name="scan m/z upper limit" value="1800.000000"/><o:p></o:p></span></font></pre>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Ignore for the moment
that this appears to be an example
rather than a spec. Do note though that there’s nothing to say that
one of each has to be present. Of course a reasonable human would
probably infer this, but words like “reasonable human” and
“infer” are not really what you want to hear when discussing a
machine readable data format standard.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><b><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; font-weight: bold;">Observation
two</span></font></b><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">: I’m
not at all keen on the idea of a data format that relies on the
understanding
and simultaneous maintenance of three different artifacts (xsd, cv,
doc), one
of which (.doc) is not really machine readable.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">I think (but I can’t be
100% sure without seeing the
code) that the author has done a very good job under the circumstances,
but
probably had a harder time then was necessary given the bizarre
construction of
the spec. He or she probably would have appreciated more xsd content
to
do the heavy lifting, and certainly had to make a few fairly safe
guesses along
the way like the “must have one of each of </span></font>MS:1000501 <font
face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">and </span></font>MS:1000500<font
face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"> “
thing.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">- Brian<o:p></o:p></span></font></p>
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