CellML Metadata Framework Citation Specification 2.0

Authors:Michael T. Cooling (m.cooling@auckland.ac.nz)

Dependencies

This specification is dependent on the CellML Metadata Framework Core Specification 2.0.

Introduction

This document describes how to make annotation linking the CellML model document, or an element of that document, to one or more citable works such as journal articles or conference presentations.

Realisation Strategy

Citable works are linked to a CellML model document or an element of that document by making the cmeta:id of the element an RDF Subject, and the reference to the citable work the RDF Object, of an RDF statement. The Predicate for this relationship should be the Biomodels Qualifier (http://biomodels.net/qualifiers/) ‘description’.

Where multiple citable works are required, multiple RDF statements could be made. Alternatively, multiple citable works could be specified using the RDF ‘Bag’ container. See http://www.w3.org/TR/rdf-primer/#containers for more information on RDF containers.

Citable works (the RDF Objects) should be specified as URIs wherever possible. If the work has a record in a persistent database such as Pubmed (http://www.ncbi.nlm.nih.gov/pubmed/), then the recommended method is to use an Identifiers.org URI (see http://identifiers.org/ for more on Identifiers.org). Where this is not applicable (if, for example, the work does not have a record, or perhaps is not published at all) another URI may be used (in some examples below, ISSN URNs are used). Care should be taken that the URI be as discoverable and long-lived as possible in order for someone to gain meaningful information from it.

If an appropriate URI is not available, an alternative method is to provide a BIBO (http://bibliontology.com/specification) Object in the RDF to represent the bibliographic resource. This object can then be linked to the model element of interest with ‘description’. Any BIBO object may be encoded, and it is recommended that as many BIBO properties should be added as necessary so that someone can clearly identify the cited work. At the time of writing, the recommended BIBO version is that labelled as ‘Revision 1.3’. A browsable list of BIBO classes and properties can be found at http://bibotools.googlecode.com/svn/bibo-ontology/trunk/doc/index.html.

The recommended BIBO and Biomodels qualifer namespaces are as follows:

Suggested prefix Namespace URI
bibo "http://purl.org/ontology/bibo/"
bqmodel "http://biomodels.net/model-qualifiers"

Several of the BIBO properties are ‘borrowed’ from other collections of properties such as the Dublin Core, and FOAF which are also used elsewhere in the CellML Metadata Framework 2.0 (see the CellML Metadata Framework Basic Information Specification 2.0 for details), hence using those properties in a BIBO object may also require the specification of additional namespaces, if they are not already defined.

Examples

1. A model is described in a published journal article that is identified in Pubmed

<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
         xmlns:bibo="http://purl.org/ontology/bibo/">

    <rdf:Description rdf:about="./model.cellml#ip3_model">
        <bqmodel:description rdf:resource="http://identifiers.org/pubmed/17693463"/>
    </rdf:Description>

</rdf:RDF>

2. A model is described in a published journal article which lacks an identifier in Pubmed

<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
         xmlns:bibo="http://purl.org/ontology/bibo/"
         xmlns:dcterms="http://purl.org/dc/terms/">

    <rdf:Description rdf:about="./model.cellml#ip3_model">
        <bqmodel:description rdf:resource="#example_article"/>
    </rdf:Description>

    <bibo:Article rdf:ID="example_article">
        <dcterms:creator>Fred Bagg</dcterms:creator>
        <dcterms:issued>1981</dcterms:issued>
        <dcterms:title>Pertubations in calcium signaling activate immune system function</dcterms:title>
        <bibo:volume>66</bibo:volume>
        <bibo:issue>10</bibo:issue>
        <bibo:pageStart>1102</bibo:pageStart>
        <bibo:pageEnd>1111</bibo:pageEnd>
        <dcterms:isPartOf rdf:resource="urn:issn:0027-8128"/>
    </bibo:Article>

</rdf:RDF>

3. Extending the previous example: the Article declaration contains an ordered list of authors

<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
         xmlns:bibo="http://purl.org/ontology/bibo/"
         xmlns:dcterms="http://purl.org/dc/terms/"
         xmlns:foaf="http://xmlns.com/foaf/0.1/">

    <rdf:Description rdf:about="./model.cellml#ip3_model">
        <bqmodel:description rdf:resource="#example_article"/>
    </rdf:Description>

    <bibo:Article rdf:ID="example_article">

        <bibo:authorList>
            <rdf:Seq>
                <rdf:li rdf:resource="#fred_bagg"/>
                <rdf:li rdf:resource="#joe_fligs"/>
            </rdf:Seq>
        </bibo:authorList>

        <dcterms:issued>1981</dcterms:issued>
        <dcterms:title>Perturbations in calcium signaling activate immune system function</dcterms:title>
        <bibo:volume>66</bibo:volume>
        <bibo:issue>10</bibo:issue>
        <bibo:pageStart>1102</bibo:pageStart>
        <bibo:pageEnd>1111</bibo:pageEnd>
        <dcterms:isPartOf rdf:resource="urn:issn:0027-8128"/>

    </bibo:Article>

    <foaf:Person rdf:ID="fred_bagg" foaf:name="Fred Bagg"/>
    <foaf:Person rdf:ID="joe_fligs" foaf:name="Joe Fligs"/>

</rdf:RDF>

4. The model that a component represents is described in a book chapter which is not in Pubmed

<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
         xmlns:bibo="http://purl.org/ontology/bibo/"
         xmlns:dcterms="http://purl.org/dc/terms/"
         xmlns:foaf="http://xmlns.com/foaf/0.1/">

    <rdf:Description rdf:about="./model.cellml#example_component">
        <bqmodel:description rdf:resource="#the_chapter"/>
    </rdf:Description>

    <bibo:chapter rdf:ID="the_chapter">
        <dcterms:isPartOf rdf:resource="#the_book"/>
        <dcterms:creator rdf:resource="#sam_smith"/>
        <bibo:chapter>14</bibo:chapter>
        <dcterms:title>Marsh-warbler feeding calls</dcterms:title>
        <bibo:pageStart>160</bibo:pageStart>
        <bibo:pageEnd>164</bibo:pageEnd>
    </bibo:chapter>

    <bibo:EditedBook rdf:ID="the_book">
       <dcterms:publisher rdf:resource="#the_publisher"/>
       <bibo:editorList>
          <rdf:Seq>
              <rdf:li rdf:resource="#hamish_wang"/>
              <rdf:li rdf:resource="#fred_ming"/>
              <rdf:li rdf:resource="#gertrude_brown" />
          </rdf:Seq>
       </bibo:editorList>
       <dcterms:issued>September, 2010</dcterms:issued>
       <bibo:isbn>3273876876K</bibo:isbn>
    </bibo:EditedBook>

    <foaf:Organisation rdf:ID="the_publisher" foaf:name="Marsh Animals Press" />

    <foaf:Person rdf:ID="hamish_wang" foaf:name="Hamish Wang"/>
    <foaf:Person rdf:ID="fred_ming" foaf:name="Fred Ming"/>
    <foaf:Person rdf:ID="gertrude_brown" foaf:name="Gertrude Brown"/>
    <foaf:Person rdf:ID="sam_smith" foaf:name="Sam Smith"/>

</rdf:RDF>

5. The model that a component represents is described in a presentation at a conference

<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
         xmlns:bibo="http://purl.org/ontology/bibo/"
         xmlns:dcterms="http://purl.org/dc/terms/"
         xmlns:foaf="http://xmlns.com/foaf/0.1/"
         xmlns:event="http://purl.org/NET/c4dm/event.owl#"
         xmlns:timeline="http://purl.org/NET/c4dm/timeline.owl#">

    <rdf:Description rdf:about="./model.cellml#example_component">
        <bqmodel:description rdf:resource="#the_presentation"/>
    </rdf:Description>

    <bibo:Slideshow rdf:ID="the_presentation">
        <dcterms:creator rdf:resource="#sam_smith"/>
        <dcterms:date>16-April-2010</dcterms:date>
        <dcterms:title>Marsh Warblers I have known</dcterms:title>
        <bibo:presentedAt rdf:resource="#the_conference" />
    </bibo:Slideshow>

    <foaf:Person rdf:ID="sam_smith" foaf:name="Sam Smith"/>

    <bibo:Conference rdf:ID="the_conference" >
        <event:place rdf:resource="http://sws.geonames.org/2193733/" />
        <timeline:at rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2010-10-25T12:00:00</timeline:at>
        <timeline:duration rdf:datatype="http://www.w3.org/2001/XMLSchema#duration">PT5D</timeline:duration>
        <dcterms:title>Marsh Warbler Symposium 2010</dcterms:title>
    </bibo:Conference>

</rdf:RDF>