Re: [Psidev-pi-dev] PSI XML <-> Ontology Mapping File

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Hi all,
I support some pragmatism to help releasing smoothly.
I mean, it's fine to have a reasonable number of attributes, but let's 
try not to be spending too much time in arguing. I'd propose that if one 
tool has a definition of a term that differ from others, we can say go 
for CV for that term.
Version 1 need to grab feedbacks from real usecases and might suffer 
from some weaknesses (loosely constrained limitations). Experience with 
mzData (released, implemented, but then strongly modified in mzML) has 
shown that a proof of principle version does not hurt so much. Go for 
the update of the excel list and fill it with values example to make 
sure we have same/different interpretation of the terms. Reasonable?
Pierre-Alain

Sean L Seymour wrote:
>
> Hi all,
>
> Which is the safe approach? CV right? You can always more solidly 
> integrate into the schema when experience shows it's useful (version 2).
>
> If there's any question, I would just default to whatever is the 
> conservative/safe thing to do. For example, even on the tolerance 
> point, we don't have tolerance settings and internally don't use them 
> the same way everyone else does so that can't be required by schema.
>
> I'm just trying to make the point that I don't think it hurts in the 
> first version to put an awful lot of stuff in as CV, does it?
>
> Sean
>
>
>
>
> *David Creasy <dc...@ma...>*
> Sent by: psi...@li...
>
> 05/14/2008 07:42 AM
>
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> 	Re: [Psidev-pi-dev] PSI XML <-> Ontology Mapping File
>
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>
>
> Thanks, Luisa that's quite clear.
> (I've now sent this message to the list for general input/thoughts)
>
> From a previous message, Luisa said:
> > In general I think number of those terms should be XML attributes in
> > the schema (like 'sample id', or 'date / time search performed' or
> > 'modification position', whereas CV are fine and should be the
> > reference for descriptif information like 'database filtering' or
> > 'search engines scores'.
>
> For the record, one thing that we agreed about in Lyon was that if 2 or
> more search engines supported a particular parameter, then we'd like
> this as a 'node' in the schema.
>
> So, for example with an MS-MS tolerance should this be CV? This
> tolerance is something that all search engines require (or maybe one day
> they estimate it, but we still want to know what value is used). So it's
> something that is 'required' and is not 'descriptive'.
> But a tolerance is no use without units, so this can't be a simple
> attribute.
> Similarly, in Luisa's example above: date / time search performed
> possibly needs a time zone, which would also be CV?
>
> How should we model this? Suggestions from anyone please - or just tell
> me what's already been decided elsewhere and we'll follow that.
>
> Another example: mass values can be calculated as 'monoisotopic' or
> 'average'. This again is required for all search engines and again seems
> like it could be cv to me. Or should we use and xsd:enumeration for
> something like this where there are only 2 possibilities?
>
>
> David
>
>
> Luisa Montecchi wrote:
> > Hi Phil,
> >
> > through the mapping you can limit the unit one can use in a given
> > *schema location* (Xpath), whereas you will need to create a so called
> > 'object rule' in the validator to verify that for each *CVparam term*,
> > only an appropriate subset of units are associated with it.
> >
> > In other words, the mapping allows the discrimination of the various
> > CVparam element in the schema by their Xpath and permits to restrict 
> the
> > subset CVparam terms and/or unit terms that can be used in each 
> location.
> >
> > Dependencies between CVparam terms and unit terms cannot be encoded in
> > the mapping, but can be checked via the validator tool,
> >
> > I hope this is clear,
> >
> > Best regards,
> >
> >
> > Luisa
> >
> >
> >
> >
> > Phil Jones @ EBI wrote:
> >> Hi Luisa,
> >>
> >> Can you confirm for me please - does the mapping file include the
> >> ability to
> >> mandate the presence of particular units for specific CV term usage 
> in an
> >> XML file? (I am thinking now about mzML files, that include the unit
> >> ontology accession and term in the CvParam entry - we wish to use the
> >> same
> >> XML structure in analysisXML).
> >>
> >> Best regards,
> >>
> >> Phil.
> >>
>
> -- 
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
>
> dc...@ma...
> http://www.matrixscience.com
>
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