Re: [Psidev-pi-dev] Minutes of Telecon. 11th December

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

Hi Andreas,

I've just looked through the mapping file and I think we have some errors in how
it's being implemented at the moment. Each mapping has the requirementLevel set
as "MAY", which means that the terms are optional and should not throw an error
if they are not provided. 

I think most of these should be set as "MUST" with a few exceptions e.g.
GenericMaterial (where descriptive terms could come from anywhere), which should
be set as "MAY"?

Also, throughout we have the attribute cvTermsCombinationLogic set as "OR". This
means that only one of the terms listed can be provided. Some of these should
definitely be "AND" e.g. AdditionalSearchParams. I would guess that they should
all be set to "AND" by default. If only one term should be provided, this is
almost certainly checked in the schema anyway e.g. SearchType. I can't think of
any other examples where we want to use an OR for restricting the terms that can
be selected. I think this attribute was added to the mapping file XSD in essence
to encode some ontology logic for mzML that couldn't be done in OBO.

Each term has the attribute isRepeatable set to true at the moment. By default,
I think all of these should be set to false (Documentation: "Value is 'True'
when a term can be repeated in the same instance of the associated XML
element.")


Cheers
Andy














> -----Original Message-----
> From: Andreas Bertsch [mailto:be...@in...]
> Sent: 15 December 2008 10:40
> To: psi...@li...
> Subject: Re: [Psidev-pi-dev] Minutes of Telecon. 11th December
> 
> Hi David, hi all,
> 
> > The Mascot examples have been updated and validate against the schema.
> >
> > Andreas, I'm not sure why, but I get this from the validator:
> >
> > Validation against the schema:
> > Error at file Mascot_MSMS_example.axml, line 691, char 193 Message:
> > attribute 'passThreshold' is not declared for element
> > 'SpectrumIdentificationItem'
> > But it is? I must be missing something subtle!
> Sorry, the schema for validation was not up-to-date.
> 
> > Also, for PMF I get:
> >
> > Error: CV term used in invalid element: 'PI:00362 - number of unmatched
> > peaks' at element
> > '/AnalysisXML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbig
> >uityGroup/ProteinDetectionHypothesis' But I think I have put it in the
> > correct place. Or maybe not...
> You're right. I've updated the cv and added the parent PI:00116 "single
> protein result details".
> 
> All allowed terms for a specific location in the schema can be found at
> "http://www-bs2.informatik.uni-
> tuebingen.de/services/OpenMS/analysisXML/mapping_and_cv.html" everything
> which
> is not listed here, will probably not validate!
> 
> Best,
> A.
> 
> 
> 
> --
> Div. for Simulation of Biological Systems, WSI, University of Tuebingen
> Room C322, Sand 14, 72076 Tuebingen, Germany
> phone: +49-7071-29-70461 fax: +49-7071-29-5152
> http://www-bs.informatik.uni-tuebingen.de
> 
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