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Re: Biological Taxonomy Vocabulary 0.1

From: Toby Inkster <tai@g5n.co.uk>
Date: Fri, 9 May 2008 11:42:58 +0100 (BST)
Message-ID: <62835.81.2.120.180.1210329778.squirrel@goddamn.co.uk>
To: "Renato Golin" <renato@ebi.ac.uk>
Cc: "Toby A Inkster" <tai@g5n.co.uk>, public-rdf-in-xhtml-tf@w3.org, "Semantic Web" <semantic-web@w3.org>

> Have you checked OBO?
> http://www.berkeleybop.org/ontologies/
>
> Your proposition has taxonomy and stuff like it, all of that already
> covered by most biological vocabularies.

My aim has been somewhat different to most existing biological namespaces.
Modelled on FOAF, it aims to be small, simple and useful. Anyone with even
a moderate (high school level) level of knowledge about biology, and who
is reasonably comfortable with RDF can learn a useful subset (hasTaxonomy,
Taxonomy, name, commonName, seeAlso) in about five minutes and start using
it.

Existing taxonomy vocabs tend to follow a theme of every species requiring
a unique identifying URI. That approach is not very scalable and certainly
not memorable. If you take a look at the FlyBase vocab, the RDF schema
weighs in at over 3 MB - and that vocab only covers fruit flies! The vocab
I've written does not require species to have a unique URI - as a result
the entire spec (which includes a schema in RDFa) is 28 kB (or 50 kB if
you include the 22 kB RDF/XML alternative schema as well).

But my approach is not fundamentally incompatible with most of the
existing vocabs. They can be used in conjunction:

<rdf:RDF
    xmlns:owl ="http://www.w3.org/2002/07/owl#"
    xmlns:rdf ="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:fb  ="&fb;"
    xmlns:biol="&biol;">

 <!-- Here is a flybase class for a particular type of fly. -->
 <owl:Class rdf:about="&fb;FBsp_00000074">
  <!-- Specify that all such flies have a certain taxonomy. -->
  <rdfs:subClassOf>
   <owl:Restriction>
    <owl:onProperty rdf:resource="&biol;hasTaxonomy" />
    <owl:hasValue>
     <biol:Taxonomy>
      <biol:name>Drosophila busckii</biol:name>
     </biol:Taxonomy>
    </owl:hasValue>
   </owl:Restriction>
  </rdfs:subClassOf>
 </owl:Class>

 <!-- Kevin is a fly. -->
 <fb:FBsp_00000074 rdf:ID="kev">
  <foaf:name>Kevin the Fly</foaf:name>
 </fb:FBsp_00000074>

</rdf:RDF>


-- 
Toby Inkster
<mailto:mail@tobyinkster.co.uk>
<http://tobyinkster.co.uk>
Received on Friday, 9 May 2008 10:43:43 GMT

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