Re: [Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[Jones, A. <And...@li...>]

Hi all,

The issues list is getting a bit messy with essentially a mailing list
discussion so I'll shift the discussion back here :-)

There are two points up for discussion.

1) Use of identifiers for input spectra
2) CV terms shared between psi-ms and psi-pi

> Comment 54  by matthew....@vanderbilt.edu, Nov 28 (2 days ago)

> Both a & b to emphasize the fact that the nativeID is defined no matter what
the
>format of the source file is. Also, just like mzML, you would define that
format at
>the top of the file, although it doesn't appear there is an analysisXML
equivalent to
>"fileContent/fileDescription" in mzML. The nativeID formats are defined in the
mzML
>CV and the terms map to that top header to define the nativeID format for every
>spectrum in the file: see CV terms starting at MS:1000767
>in
>http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledV
ocabulary/psi-ms.obo

In terms of 1) I've worked through Matt's argument and I'm in general agreement
that we would like to use the same system for identifying the input spectrum -
these CV terms have only been added relatively recently. I did not realise that
the nativeID attribute had been specified to this level, since there is no
documentation about this is in the XSD or mzML specification document.

I don't think we should change the name of the attribute though, since nativeID
makes sense for an element called <Spectrum> in mzML but not for an element
<SpectrumIdentificationResult> in analysisXML. For referencing mzML spectra, I'm
still not sure which attribute we should choose to reference since the "true"
(and guaranteed unique) spectrum identifier in mzML is actually the ID
attribute. I can envisage a case where instruments output mzML directly and the
nativeID is not implemented sensibly. The xs:ID datatype on "ID" guarantees that
these will always be unique whatever changes happen to documentation in the
future or whatever tools are used to create the file.

So I agree with Matt but I don't want to change the schema :-) I'm happy to add
something to the documentation specifying how different identifiers should be
implemented, following the rules in the psi-ms CV.

In terms of 2), we had made a decision in the past that we would simply create
terms as we need them in PSI-PI, rather than worrying if they should be common
between psi-ms and psi-pi and trying to coordinate updates across groups. If a
term is present in psi-ms with the exact meaning that we want (taking into
account its position in the hierarchy), I think we should just use it and update
the mapping file to reference it. Are there many terms from psi-ms that we want
to use?

I am working on the spec document today and would like to get all issues tidied
up ASAP... 
Cheers
Andy






> -----Original Message-----
> From: cod...@go... [mailto:cod...@go...]
> Sent: 30 November 2008 19:36
> To: psi...@li...
> Subject: [Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV
> 
> 
> Comment #56 on issue 42 by matthew....@vanderbilt.edu: Issues with the CV
> http://code.google.com/p/psi-pi/issues/detail?id=42
> 
> Yes, I was at that meeting too. :) The one (important, IMO) use case we did
> not
> consider at that time is output of analysisXML without a corresponding mzML
> document.
> In such a case, the mzML arbitrary id does not exist, but the nativeID
> does. This
> fact convinces me that nativeID is a better reference than the arbitrary id.
> 
> The change of attribute name to nativeID is not so critical, but I think
> the risk of
> confusing the spectrumID with the id attribute when it actually points to
> the
> nativeID attribute is worse than the risk of confusing the nativeID
> attribute with
> some property of the search engine. I think the documentation for the
> nativeID
> attribute can easily make it clear what it's supposed to reference,
> especially since
> it's on a spectrum-centric element; you can copy it from the mzML schema
> (although I
> think this documentation could be improved upon):
> <xs:documentation>The native identifier for the spectrum, used by the
> acquisition
> software.</xs:documentation>
> 
> It's good to know about the header information. The nativeID (or whatever
> it's called
> in analysisXML) format term would go in the spectra input definition as a
> CV Param
> required by the mapping file.
> 
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