[Psidev-ms-dev] MANIFESTO TIME! (was RE: more is_a vs. part_of errors?)

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Eh, it's even more broken than I thought.  I've amended my amendments inline
below, new changes in double parenthesis.  

After a day so of messing with this, it is now:

MANIFESTO TIME!

RESOLVED:

The mzML specification process should be schema-centric, and the CV should
be generated from the schema (should be a fairly simple matter of XSLT,
since XSD is itself XML).  

REASON 1: THE CV-CENTRIC APPROACH IS ERROR PRONE.

The kinds of inheritance errors shown below are, if not actually impossible,
much harder to make in the context of a W3C schema when using readily
available software tools to create and maintain the schema.

REASON 2: OBO/CV IS AN INSUFFICIENT TOOL FOR THE JOB OF PRODUCING A READILY
AND THOROUGHLY VALIDATABLE DATA FORMAT.

CV apparently provides no means for specifying range or formatting of
instance values.  An "isolation width" (MS:1000023) could happily have a
value of "-2", "2", "two", or "extra sprinkles, please".  You could (and
should) certainly put some text in the description along the lines of "this
is a non-negative floating point value" but that's no help to a validating
parser.  XSD on the other hand has standardized syntax for enforcing
precisely these kinds of restrictions, meaning that validating parsers and
code generators (for both read and write) don't need any special-purpose
logic added.  

There are a handful of places where value range restrictions have been
attempted in the MS CV, but these are awkward because of the tools. The
reflectron_state, for example, has two children "on" and "off", but this
only confuses things, since these are not *values* of reflectron state but
rather *are* reflectron states, a distinction which may be meaningless in
English but significant when attempting to create a data structure.
Picture how this looks in an instance doc:

<cvParam cvLabel="MS" accession="MS:1000105" name="off" value="" />

I can't think of anything nice to say about that.  Better it should read:

            <reflectronState accession="MS:1000021" off/>

CONCLUSION: THE CV WORK TO DATE IS IMPORTANT AND USEFUL, BUT SHOULD BE
RECAST AS SCHEMA WORK

The CV should not attempt to be a replacement for the schema - it just
hasn't got the requisite mechanisms to do the job. The information CV can
convey is only a subset of the information that is needed to fully specify a
data format.  The information in the CV as it stands should be folded into
the mzML schema, and maintained therein moving forward.  An actual OBO/CV
file can be generated as needed. 

- Brian

  _____  

From: Brian Pratt [mailto:bri...@in...] 
Sent: Friday, October 05, 2007 11:52 PM
To: 'Mass spectrometry standard development'
Subject: more is_a vs. part_of errors?

There are a handful of other cases where it appears that the authors have
gotten "is a" and "part_of" confused.   My proposed corrections (IN CAPS)
inline:

MS:1000025 "magnetic field strength"

        part of ((IS_A)) MS:1000480 "analyzer attribute"

                is a (PART_OF) MS:1000451 "analyzer description"

                        part of MS:1000463 "instrument description"

                                part of MS:0000000 "MZ controlled
vocabularies"

MS:1000024 "final MS exponent"

        part of ((IS_A)) MS:1000480 "analyzer attribute"

                is a (PART_OF) MS:1000451 "analyzer description" 

                        part of MS:1000463 "instrument description"

                                part of MS:0000000 "MZ controlled
vocabularies"

MS:1000022 "TOF Total Path Length"

        part of ((IS_A)) MS:1000480 "analyzer attribute"

                is a (PART_OF) MS:1000451 "analyzer description"

                        part of MS:1000463 "instrument description"

                                part of MS:0000000 "MZ controlled
vocabularies"

MS:1000014 "accuracy"

        part of ((IS_A)) MS:1000480 "analyzer attribute"

                is a (PART_OF) MS:1000451 "analyzer description"

                        part of MS:1000463 "instrument description"

                                part of MS:0000000 "MZ controlled
vocabularies"

((note, these next two are just ugly, see notes at top of message))

MS:1000106 "on"

        is a MS:1000021 "reflectron state"

                part of ((IS_A)) MS:1000480 "analyzer attribute"

                        is a (PART_OF) MS:1000451 "analyzer description"

                                part of MS:1000463 "instrument description"

                                        part of MS:0000000 "MZ controlled
vocabularies"

MS:1000105 "off"

        is a MS:1000021 "reflectron state"

                part of ((IS_A)) MS:1000480 "analyzer attribute"

                        is a (PART_OF) MS:1000451 "analyzer description"

                                part of MS:1000463 "instrument description"

                                        part of MS:0000000 "MZ controlled
vocabularies"

The following changes would  make the Thermo and ABI stuff look like all the
other vendors:

MS:1000495 "Applied Biosystems"

        part of (IS_A) MS:1000121 "ABI / SCIEX"

                is a MS:1000031 "model  by vendor"

                        part of MS:1000463 "instrument description"

                                part of MS:0000000 "MZ controlled
vocabularies"

MS:1000176 "MAT95XP Trap"

        is a (IS_A) MS:1000493 "Finnigan MAT"

                part of MS:1000483 "Thermo Fisher Scientific"

                        is a MS:1000031 "model  by vendor"

                                part of MS:1000463 "instrument description"

                                        part of MS:0000000 "MZ controlled
vocabularies"

MS:1000175 "MAT95XP"

        is a MS:1000493 "Finnigan MAT"

                part of (IS_A) MS:1000483 "Thermo Fisher Scientific"

                        is a MS:1000031 "model  by vendor"

                                part of MS:1000463 "instrument description"

                                        part of MS:0000000 "MZ controlled
vocabularies"

MS:1000174 "MAT900XP Trap"

        is a MS:1000493 "Finnigan MAT"

                part of (IS_A) MS:1000483 "Thermo Fisher Scientific"

                        is a MS:1000031 "model  by vendor"

                                part of MS:1000463 "instrument description"

                                        part of MS:0000000 "MZ controlled
vocabularies"

MS:1000173 "MAT900XP"

        is a MS:1000493 "Finnigan MAT"

                part of (IS_A) MS:1000483 "Thermo Fisher Scientific"

                        is a MS:1000031 "model  by vendor"

                                part of MS:1000463 "instrument description"

                                        part of MS:0000000 "MZ controlled
vocabularies"

MS:1000172 "MAT253"

        is a MS:1000493 "Finnigan MAT"

                part of (IS_A) MS:1000483 "Thermo Fisher Scientific"

                        is a MS:1000031 "model  by vendor"

                                part of MS:1000463 "instrument description"

                                        part of MS:0000000 "MZ controlled
vocabularies"

I still think there's a schema in there, albeit jammed in slightly sideways
at the moment.

(( I don't think that anymore.  I think there's a subset of a schema in
there. ))

- Brian