[Psidev-ms-dev] mzml schema location outdated

[Andreas S. <as...@eb...>]

Dear all,

I want to report that the schema at 
http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd is out of date. Since 
the example files use exactly this schema location, XML validation fails.

Let's have a look at tiny.pwiz.1.1.mzML:

Within the chromatogram element the precursor and product elements are 
not allowed by the referenced schema.
This does not happen with the latest schema version in the CVS 
repository 
(http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/schema/mzML1.1.0.xsd). 
This version is also linked from the psidev homepage.

Best regards,
Andreas Schoenegger

PS:
Oxygen validation output of tiny...:

Invalid content was found starting with element 'precursor'. One of 
'{"http://psi.hupo.org/ms/mzml":cvParam, 
"http://psi.hupo.org/ms/mzml":userParam, 
"http://psi.hupo.org/ms/mzml":binaryDataArrayList}' is expected.

Comparison of the two schema versions:

Schema (http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd)
<xs:complexType name="ChromatogramType">
     [...]
<xs:complexContent mixed="false">
<xs:extension base="dx:ParamGroupType">
<xs:sequence>
<xs:element minOccurs="1" maxOccurs="1" name="binaryDataArrayList" 
type="dx:BinaryDataArrayListType" />
</xs:sequence>
         [...]
</xs:extension>
</xs:complexContent>
</xs:complexType>

  Schema 
(http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/schema/mzML1.1.0.xsd)
<xs:complexType name="ChromatogramType">
     [...]
<xs:complexContent mixed="false">
<xs:extension base="dx:ParamGroupType">
<xs:sequence>
<xs:element minOccurs="0" name="precursor" type="dx:PrecursorType" />
<xs:element minOccurs="0" name="product" type="dx:ProductType" />
<xs:element minOccurs="1" maxOccurs="1" name="binaryDataArrayList" 
type="dx:BinaryDataArrayListType" />
</xs:sequence>
         [...]
</xs:extension>
</xs:complexContent>
</xs:complexType>

Notice the presence of the precursor and product elements in the latest 
schema version.

-- 
Andreas Schoenegger
Trainee - PRIDE Project Team
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom