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Camille Laibe wrote:
> Dear SBML users,
>
> As you are perhaps aware, some annotations in SBML are not valid RDF[1].
> If you look at the latest specifications (Level 2 Version 3 Release 2), specially at the page 95: the piece of RDF given as an example for the model creator(s) contains several mistakes.
> Let's take the model BIOMD0000000007 (from BioModels Database, cf. http://www.ebi.ac.uk/compneur-srv/biomodels/models-main/publ/BIOMD0000000007.xml) as our example (it follows the syntax given on the page 95 of the specs).
>
> Here is the part of the annotation about the creator(s) (we only focus on the creators' part: the only one which is invalid):
>
> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" >
> <rdf:Description rdf:about="#_000001">
> <dc:creator rdf:parseType="Resource">
> <rdf:Bag>
> <rdf:li rdf:parseType="Resource">
> <vCard:N rdf:parseType="Resource">
> <vCard:Family>Shapiro</vCard:Family>
> <vCard:Given>Bruce</vCard:Given>
> </vCard:N>
> <vCard:EMAIL>bshapiro@jpl.nasa.gov</vCard:EMAIL>
> <vCard:ORG>
> <vCard:Orgname>NASA Jet Propulsion Laboratory</vCard:Orgname>
> </vCard:ORG>
> </rdf:li>
> <rdf:li rdf:parseType="Resource">
> <vCard:N rdf:parseType="Resource">
> <vCard:Family>Le Novere</vCard:Family>
> <vCard:Given>Nicolas</vCard:Given>
> </vCard:N>
> <vCard:EMAIL>lenov@ebi.ac.uk</vCard:EMAIL>
> <vCard:ORG>
> <vCard:Orgname>EMBL-EBI</vCard:Orgname>
> </vCard:ORG>
> </rdf:li>
> </rdf:Bag>
> </dc:creator>
> [...]
> </rdf:Description>
> </rdf:RDF>
>
> If you check the validation of these lines (without the [...]), you will notice that several elements generate errors messages by the validator.
>
> Here are one valid syntax for this case:
>
> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" >
> <rdf:Description rdf:about="#_000001">
> <dc:creator>
> <rdf:Bag>
> <rdf:li rdf:parseType="Resource">
> <vCard:N rdf:parseType="Resource">
> <vCard:Family>Shapiro</vCard:Family>
> <vCard:Given>Bruce</vCard:Given>
> </vCard:N>
> <vCard:EMAIL>bshapiro@jpl.nasa.gov</vCard:EMAIL>
> <vCard:ORG rdf:parseType="Resource">
> <vCard:Orgname>NASA Jet Propulsion Laboratory</vCard:Orgname>
> </vCard:ORG>
> </rdf:li>
> <rdf:li rdf:parseType="Resource">
> <vCard:N rdf:parseType="Resource">
> <vCard:Family>Le Novere</vCard:Family>
> <vCard:Given>Nicolas</vCard:Given>
> </vCard:N>
> <vCard:EMAIL>lenov@ebi.ac.uk</vCard:EMAIL>
> <vCard:ORG rdf:parseType="Resource">
> <vCard:Orgname>EMBL-EBI</vCard:Orgname>
> </vCard:ORG>
> </rdf:li>
> </rdf:Bag>
> </dc:creator>
> </rdf:Description>
> </rdf:RDF>
>
> Two things have been done:
> - remove rdf:parseType="Resource" from <dc:creator>, cf. http://www.w3.org/TR/REC-rdf-syntax/#containers
> - add rdf:parseType="Resource" to all the <vCard:N> (like it is done for the <vCard:N>), cf. http://www.w3.org/TR/rdf-syntax-grammar/#section-Syntax-parsetype-resource

- add rdf:parseType="Resource" to all the <vCard:ORG>

--
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Tel:+441223494521, Mob:+447833147074
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere@hotmail.com
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
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