Difference between revisions of "NeXML OTU Decoration"

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(Encoding Taxonomic Metadata in NeXML)
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Working through how to encode taxonomic metadata in Nexml files.
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Working through how to encode taxonomic metadata in [[NeXML]] files for the [[Taxonomic Intelligence Subgroup]].
  
 
==Style As Suggested by NeXML Examples==
 
==Style As Suggested by NeXML Examples==
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<dict id="mydict" xmlns:cdao="http://evolutionaryontology.org/cdao/1.0/cdao.owl">
 
<dict id="mydict" xmlns:cdao="http://evolutionaryontology.org/cdao/1.0/cdao.owl">
 
<any id="any1">
 
<any id="any1">
<cdao:TU rdf:id="t1">
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<cdao:TU rdf:id="t1" label="Ictalurus punctatus"/>
<!-- here is where we identify the relation and assign a value -->
 
<!-- which is here a concept from another ontology: -->
 
<!-- Ictalurus punctatus, the Channel catfish -->
 
 
<cdao:has_Taxonomy_Reference rdf:resource="http://purl.org/obo/owl/TTO#TTO_1054206"/>
 
<cdao:has_Taxonomy_Reference rdf:resource="http://purl.org/obo/owl/TTO#TTO_1054206"/>
 
<cdao:has_Taxonomy_Reference rdf:resource="http://purl.org/obo/owl/NCBITaxon#NCBITaxon_7998"/>
 
<cdao:has_Taxonomy_Reference rdf:resource="http://purl.org/obo/owl/NCBITaxon#NCBITaxon_7998"/>
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</dict>
 
</dict>
 
</otu>
 
</otu>
<otu id="t2"/>
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<otu id="t2"  label="Homo sapiens"/>
 
</otus>
 
</otus>
 
</xml>
 
</xml>
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[[Category:Taxonomic Intelligence]]
 
[[Category:Taxonomic Intelligence]]
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[[Category:NeXML]]
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[[Category:DB Interop Hackathon]]

Latest revision as of 16:06, 12 March 2009

Working through how to encode taxonomic metadata in NeXML files for the Taxonomic Intelligence Subgroup.

Style As Suggested by NeXML Examples

This uses the CDAO predicate "has_Taxonomy_Reference" and the objects are OBO OWLs for TTO and NCBI:

<xml> <otus id="tax1"> <otu id="t1"> <dict id="mydict" xmlns:cdao="http://evolutionaryontology.org/cdao/1.0/cdao.owl"> <any id="any1"> <cdao:TU rdf:id="t1" label="Ictalurus punctatus"/> <cdao:has_Taxonomy_Reference rdf:resource="http://purl.org/obo/owl/TTO#TTO_1054206"/> <cdao:has_Taxonomy_Reference rdf:resource="http://purl.org/obo/owl/NCBITaxon#NCBITaxon_7998"/> </cdao:TU> </any> <integer id="count">2</integer> </dict> </otu> <otu id="t2" label="Homo sapiens"/> </otus> </xml>

Alternative With Arbitrary Syntax

The problem with this one is that it is an arbitrary implementation that is not part of any standard.

<xml> <otus id="tax1">

    <otu id="t1">
         <dict id="mydict">
               <any id="taxonomic_refrerences">
                     <Object namespace="NCBI" ID="8782"/>
                     <Object resolver="http://bob.org/">
               </any>
          </dict>
    </otu>
    <otu id="t2"/>

</otus> </xml>

Another Alternative

<xml> <otus id="tax1">

    <otu id="t1">
         <dict id="taxonRefDict">
               <uri id="resolver">http://bob.org/</uri>
               <string id="namespace">NCBI</string>
               <string id="id">8782</string>
          </dict>
     </otu>
     <otu id="t2"/>

</otus> </xml>

<perl> my $taxonRefDict = {

  "resolver" => "http://bob.org/",
  "namespace" => "NCBI",
  "id" => "8782"

}; </perl>