Biological Taxonomy Vocabulary 0.2 (Core) #

1. Classes #

2. Properties #

3. Examples #

3.1. Basic Example #

A very basic example:

<rdf:RDF xml:lang="en-GB"
  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  xmlns:foaf="http://xmlns.com/foaf/0.1/"
  xmlns:biol="http://purl.org/NET/biol/ns#">

    <foaf:Person rdf:about="http://tobyinkster.co.uk/#i">
        <foaf:name>Toby Inkster</foaf:name>
        <biol:hasTaxonomy rdf:parseType="Resource">
            <biol:name>Homo sapiens sapiens</biol:name>
            <biol:commonName>human</biol:commonName>
        </biol:hasTaxonomy>
    </foaf:Person>
</rdf:RDF>

3.2. Extended Example #

A more complicated example, using most of the properties:

<rdf:RDF xml:lang="en-GB"
  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  xmlns:dc="http://purl.org/dc/terms/"
  xmlns:foaf="http://xmlns.com/foaf/0.1/"
  xmlns:biol="http://purl.org/NET/biol/ns#">

    <foaf:Person rdf:about="http://tobyinkster.co.uk/#i">
        <foaf:name>Toby Inkster</foaf:name>
        <biol:hasTaxonomy>
            <biol:Taxonomy>
			
                <!-- Scientific (binomial or trinomial) name -->
                <biol:name>Homo sapiens sapiens</biol:name>

                <!-- Common name, in whatever language you like -->
                <biol:commonName>human</biol:commonName>
                <biol:commonName xml:lang="la">homo</biol:commonName>
                <biol:commonName xml:lang="eu">Gizakia</biol:commonName>

                <!-- Detailed classification -->
                <biol:kingdom>Animalia</biol:kingdom>
                <biol:phylum>Chordata</biol:phylum>
                <biol:class>Mammalia</biol:class>
                <biol:order>Primates</biol:order>
                <biol:family>Hominidae</biol:family>
                <biol:genus>Homo</biol:genus>
                <biol:species>Sapiens</biol:species>

                <!-- Further information on this classification -->
                <biol:seeAlso
                  rdf:resource="http://species.wikimedia.org/wiki/Homo_sapiens" />

                <!-- The classifier -->
                <biol:authority>Linnaeus, 1758</biol:authority>

                <!-- A date when this taxonomy was thought to be correct. -->
                <dc:date>2008-05-01</dc:date>

            </biol:Taxonomy>
        </biol:hasTaxonomy>
    </foaf:Person>
</rdf:RDF>

3.3. Document Describing a Taxonomy #

Here is an RDF description for a document that discusses the biological classification of cats. This should be contrasted against the next example, of a description for a document that discusses cats (i.e. the creatures, not the classification of them).

<rdf:RDF xml:lang="en-GB"
  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  xmlns:dc="http://purl.org/dc/terms/"
  xmlns:biol="http://purl.org/NET/biol/ns#">

    <foaf:Document rdf:about="http://example.org/taxonomy/cats">
        <dc:title>The Taxonomy of Domestic Cats</dc:title>
        <dc:subject>
            <biol:Taxonomy>
                <biol:name>Felis silvestris catus</biol:name>
                <biol:commonName>domestic shorthair</biol:commonName>
            </biol:Taxonomy>
        </dc:subject>
        <dc:abstract>Should domestic cats be classified as a subspecies
          of the European wildcat, or as a separate species?</dc:abstract>
    </foaf:Document>
</rdf:RDF>

3.4. Document Describing a Life Form #

Here is an RDF description for a document that discusses cats.

<rdf:RDF xml:lang="en-GB"
  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  xmlns:dc="http://purl.org/dc/terms/"
  xmlns:biol="http://purl.org/NET/biol/ns#">

    <foaf:Document rdf:about="http://example.org/animals/cats">
        <dc:title>The Behaviour of Domestic Cats</dc:title>
        <dc:subject rdf:parseType="Resource">
            <biol:hasTaxonomy>
                <biol:Taxonomy>
                    <biol:name>Felis silvestris catus</biol:name>
                    <biol:commonName>domestic shorthair</biol:commonName>
                </biol:Taxonomy>
            </biol:hasTaxonomy>
        </dc:subject>
        <dc:abstract>The cat is a small carnivorous species of crepuscular
          mammal that is often valued by humans for its companionship and its
          ability to hunt vermin.</dc:abstract>
    </foaf:Document>
</rdf:RDF>

3.5. Simple RDFa Example #

Here is a simple example in RDFa using the vocabulary to describe a relationship with a pet cat.

<p typeof="foaf:Person"
  xmlns:foaf="http://xmlns.com/foaf/0.1/"
  xmlns:biol="http://purl.org/NET/biol/ns#">
    <span property="foaf:name">Toby Inkster</span> has a
    <span rel="foaf:knows">
        <span rel="biol:hasTaxonomy">
            <span property="biol:commonName">cat</span>
        </span>
        called <span property="foaf:name">Mr d'Silva</span>
    </span>.
</p>

3.6. Using URIs as Identifiers for Taxonomies #

Well-known URIs may be used to represent taxonomies. The following Turtle provides similar information to the example above but uses URIs.

_:tobyink foaf:name "Toby Inkster" ;
    biol:hasTaxonomy <http://dbpedia.org/resource/Human> ;
    foaf:knows _:mrdsilva .

_:mrdsilva foaf:name "Mr d'Silva" ;
    biol:hasTaxonomy <http://dbpedia.org/resource/Cat> .

3.7. Taxonomies as Classes #

Taxonomies may be used as RDF classes.

_:tobyink a ex:HumanBeing; 
	foaf:name "Toby Inkster" .

ex:HumanBeing a biol:Taxonomy ;
	biol:name "Homo sapiens" .

Similarly, using an anonymous blank node:

_:tobyink foaf:name "Toby Inkster" ;
	a [ biol:name "Homo sapiens" ] .

3.8. Hierarchies of Taxonomies #

Hierarchies of taxonomies can be easily established using the biol:morePrecise predicate.

<rdf:RDF xml:lang="zxx"
  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  xmlns:biol="http://purl.org/NET/biol/ns#"
  xml:base="http://example.org/apes">
  
    <biol:Taxonomy rdf:about="#Hominidae">
    
        <biol:commonName xml:lang="en">Great Ape</biol:commonName>
    
        <biol:kingdom>Animalia</biol:kingdom>
        <biol:phylum>Chordata</biol:phylum>
        <biol:class>Mammalia</biol:class>
        <biol:order>Primates</biol:order>
        <biol:family>Hominidae</biol:family>
    
        <biol:morePrecise>
            <biol:Taxonomy rdf:about="#Orangutan">
                <biol:commonName xml:lang="en">Orangutan</biol:commonName>
                <biol:genus>Pongo</biol:genus>
                <biol:morePrecise>
                    <biol:Taxonomy rdf:about="#BorneanOrangutan">
                        <biol:commonName xml:lang="en">Bornean orangutan</biol:commonName>
                        <biol:name>Pongo pygmaeus</biol:name>
                    </biol:Taxonomy>
                </biol:morePrecise>
                <biol:morePrecise>
                    <biol:Taxonomy rdf:about="#SumatranOrangutan">
                        <biol:commonName xml:lang="en">Sumatran orangutan</biol:commonName>
                        <biol:name>Pongo abelii</biol:name>
                    </biol:Taxonomy>
                </biol:morePrecise>
            </biol:Taxonomy>
        </biol:morePrecise>
    
        <biol:morePrecise>
            <biol:Taxonomy rdf:about="#Gorilla">
                <biol:commonName xml:lang="en">Gorilla</biol:commonName>
                <biol:genus>Gorilla</biol:genus>
                <biol:morePrecise>
                    <biol:Taxonomy rdf:about="#GorillaGorilla">
                        <biol:commonName xml:lang="en">Western gorilla</biol:commonName>
                        <biol:name>Gorilla gorilla</biol:name>
                    </biol:Taxonomy>
                </biol:morePrecise>
                <biol:morePrecise>
                    <biol:Taxonomy rdf:about="#GorillaGraueri">
                        <biol:commonName xml:lang="en">Eastern gorilla</biol:commonName>
                        <biol:name>Gorilla graueri</biol:name>
                    </biol:Taxonomy>
                </biol:morePrecise>
            </biol:Taxonomy>
        </biol:morePrecise>
    
        <biol:morePrecise>
            <biol:Taxonomy rdf:about="#Chimpanzee">
                <biol:commonName xml:lang="en">Chimpanzee</biol:commonName>
                <biol:genus>Pan</biol:genus>
                <biol:morePrecise>
                    <biol:Taxonomy rdf:about="#Chimp">
                        <biol:commonName xml:lang="en">Common chimpanzee</biol:commonName>
                        <biol:name>Pan troglodytes</biol:name>
                    </biol:Taxonomy>
                </biol:morePrecise>
                <biol:morePrecise>
                    <biol:Taxonomy rdf:about="#Bonobo">
                        <biol:commonName xml:lang="en">Bonobo</biol:commonName>
                        <biol:name>Pan paniscus</biol:name>
                    </biol:Taxonomy>
                </biol:morePrecise>
            </biol:Taxonomy>
        </biol:morePrecise>
        
        <biol:morePrecise>
            <biol:Taxonomy rdf:about="#Human">
                <biol:commonName xml:lang="en">Human</biol:commonName>
                <biol:name>Homo sapiens</biol:name>
            </biol:Taxonomy>
        </biol:morePrecise>
    
    </biol:Taxonomy>

</rdf:RDF>

These might then be used as:

<rdf:RDF xml:lang="en"
  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  xmlns:biol="http://purl.org/NET/biol/ns#"
  xmlns:foaf="http://xmlns.com/foaf/0.1/"
  xmlns:ape="http://example.org/apes#">

    <ape:Human>
        <foaf:name>Alice Jones</foaf:name>
    </ape:Human>

    <foaf:Person>
        <foaf:name>Bob Smith</foaf:name>
        <biol:hasTaxonomy rdf:resource="http://example.org/apes#Human" />
    </foaf:Person>

    <ape:Bonobo>
        <foaf:name>Bobo</foaf:name>
    </ape:Bonobo>

</rdf:RDF>

A. References #

A.1. Informative References #

• Taxonomic rank, Wikipedia
• species, microformats.org

B. Changes #

• 2008-10-06: version 0.2; make biol:hasTaxonomy a sub-property of rdf:type and biol:Taxonomy a sub-class of rdfs:Class; made biol:rank a sub-property of ubio:taxonomicGroup (I think this is correct); added biol:morePrecise; add examples that show the use of taxonomies as RDF classes, and show the biol:morePrecise predicate.
• 2008-05-13: range of biol:authority changed to rdfs:Literal to match examples.
• 2008-05-09: changed namespace URI; friendlier labels; added examples.
• 2008-05-08: version 0.1; initial version.

C. Acknowledgments #

Thanks to the members of W3C Semantic Web Interest Group and RDF in XHTML Taskforce for their feedback and suggestions, especially to Richard Cyganiak.