examples.tex

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\section{Illustrative examples of the syntax}
\label{examples}

This section contains a worked example showing the encoding of a model 
and associated data in a COMBINE archive. First the \OmexManifest, that 
includes five entries. One of these entries represent the archive itself, 
it has a fixed location \token{location="."}. Additionally 
the archive includes an SBML model and a SED-ML description. It also 
includes a PDF file which format is specified through its Media type. Finally 
associated meta information for clerical data is included in 
\token{location="metadata.rdf"}. 


\begin{example}
<?xml version="1.0" encoding="utf-8"?>
<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
    <content location="." 
		         format="http://identifiers.org/combine.specifications/omex"/>
    <content location="model/model.xml" 
		         format="http://identifiers.org/combine.specifications/sbml"/>
    <content location="simulation.xml" master="true"
		         format="http://identifiers.org/combine.specifications/sed-ml"/>
    <content location="doc/article.pdf" 
		         format="http://purl.org/NET/mediatypes/application/pdf"/>
    <content location="metadata.rdf" 
		         format="http://identifiers.org/combine.specifications/omex-metadata"/>
</omexManifest>
\end{example}

Here a complete example, on how the clerical data could be encoded in the metadata file: 

\begin{example}
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:dcterms="http://purl.org/dc/terms/"
         xmlns:vCard="http://www.w3.org/2006/vcard/ns#"
         xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
    <rdf:Description rdf:about=".">
        <dcterms:description>
            Expanded version of the human metabolic reconstruction Recon 2.1
        </dcterms:description>
        <dcterms:creator rdf:parseType="Resource">
            <vCard:hasName rdf:parseType="Resource">
                <vCard:family-name>Le Novere</vCard:family-name>
                <vCard:given-name>Nicolas</vCard:given-name>
            </vCard:hasName>
            <vCard:hasEmail rdf:resource="lenov@babraham.ac.uk" />
            <vCard:organization-name>
                Babraham Institute
            </vCard:organization-name>
            <vCard:hasURL rdf:resource="http://orcid.org/0000-0002-6309-7327"/>
        </dcterms:creator>
        <dcterms:created rdf:parseType="Resource">
            <dcterms:W3CDTF>2014-06-26T10:29:00Z</dcterms:W3CDTF>
        </dcterms:created>
        <bqmodel:is      
             rdf:resource="http://identifiers.org/biomodels.db/MODEL1311110001" />
        <bqmodel:isDescribedBy       
             rdf:resource="http://identifiers.org/arxiv/1311.5696" />
    </rdf:Description>
</rdf:RDF>
\end{example}