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 for the [[Taxonomic Intelligence Subgroup]].
  
===Style As Suggested by NeXML Examples===
+
==Style As Suggested by NeXML Examples==
 
This uses the CDAO predicate "has_Taxonomy_Reference" and the objects are OBO OWLs for TTO and NCBI:
 
This uses the CDAO predicate "has_Taxonomy_Reference" and the objects are OBO OWLs for TTO and NCBI:
  
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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>
  
===Alternative With Arbitrary Syntax===
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==Alternative With Arbitrary Syntax==
 
The problem with this one is that it is an arbitrary implementation that is not part of any standard.
 
The problem with this one is that it is an arbitrary implementation that is not part of any standard.
  
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</xml>
 
</xml>
  
===Another Alternative===
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==Another Alternative==
  
 
<xml>
 
<xml>
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</perl>
 
</perl>
  
[[Category:Taxonomic Intellegence]]
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[[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>