Talk:Database Interop Hackathon/Metadata Support

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nexml RDFa representation standard

Arlin and Rutger, June 30, 2009

I'm going to put the transcript of our chat here until I'm done with this (arlin 17:25, 30 June 2009 (EDT))

Arlin Stoltzfus

  • hello

Rutger Vos

  • ok
  • ah, good
  • example
<meta content="Bodner M." datatype="xsd:string" id="meta225913" property="dc:contributor"  xsi:type="nex:LiteralMeta"/>
  • example
<otu about="#otu225924" id="otu225924" label="Zenodorus cf. orbiculatus">
<meta href="taxon/uBio:3546132" id="meta225927" rel="dc:relation" xsi:type="nex:ResourceMeta"/>
</otu>
  • so the triple is <#otu225924> <dc:relation> <taxon/uBio:3546132>
  • example
xml:base="http://8ball.sdsc.edu:6666/treebase-web/phylows/"
  • treebase file you can get
http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/uBio:3546132
  • @content == @href == enclosed elements
  • object can be @content, @href, or raw xml inside meta element
  • example
<meta href="taxon/uBio:3546132" id="meta225927" rel="dc:relation" xsi:type="nex:ResourceMeta"/>
  • example
<link href="taxon/uBio:3546132" id="meta225927" rel="dc:relation" xsi:type="nex:ResourceMeta"/>
  • example
<link href="taxon/uBio:3546132" id="meta225927" rel="dc:relation"/>
  • example
<meta content="Bodner M." datatype="xsd:string" id="meta225913" property="dc:contributor"/>

Arlin

  • This is the nasty example of packing two triples in one element. Not to be emulated
<tree id="foo1" about="foo2" xmlns:bs="http://banana.split.org/ontology/example#">
 <annotation rel="bs:myotherterm" href="http://uri.to.somewhere.org/123"
          property="bs:myterm">My Literal value</annotation>
</tree>
  • but this is about what we want, right?
<otu id="foo1" about="foo2" typeof="tc:TaxonConcept"  xmlns:tc="http://rs.tdwg.org/ontology/voc/TaxonConcept#" xmlns:tn="http://rs.tdwg.org/ontology/voc/TaxonName#">
   <meta rel="tc:hasName">
      <meta typeof="tn:TaxonName" about="urn:lsid:ipni.org:names:333114-1:1.5">
         <meta property="tn:genusPart">Rhododendron</meta>
         <meta property="tn:specificEpithet">ponticum</meta>
         <meta property="tn:authorship">L.</meta>
      </meta>
 </meta>
</otu>
  • or better
<otu id="mylocal_id1234" about="#mylocal_id1234" typeof="tc:TaxonConcept"

<meta rel="tc:hasName" xsi:type="nex:ResourceMeta">

<meta rel="tc:hasName" id="my_local_meta12345" xsi:type="nex:ResourceMeta">

Rutger Vos

<meta rel="tc:hasName" xsi:type="nex:ResourceMeta" id="meta3242">
  • use inria rdfa extractor
  • use xsltproc
  • like this "xsltproc RDFa2RDFXML.xsl <filename>"
  • erdfa
  • this is my script
#!/usr/bin/perl
use strict;
use warnings;
die "Need infile(s) to extract RDFa from" unless @ARGV;
my $xsltproc = $ENV{'XSLTPROC'} || 'xsltproc';
my $xsl = '/Users/rvosa/Documents/workspace/nexml/trunk/nexml/xslt/RDFa2RDFXML.xsl';
exec( $xsltproc, $xsl, @ARGV );

1:54 PM

http://8ball.sdsc.edu:6666/treebase-web/search/downloadAStudy.html?id=1787&format=nexml

2:01 PM

http://8ball.sdsc.edu:6666/treebase-web/search/downloadAStudy.html?id=1787&format=rdf

2:01 PM

http://8ball.sdsc.edu:6666/treebase-web/search/downloadAStudy.html?id=1787&format=rdf

Arlin Stoltzfus

  • this is the output i see
1432Zootaxa23-3333232007A basal phylogenetic placement for the salticid spider Eupoa, with   descriptions of two new species (Araneae: Salticidae)2007-03-29Bodner M.Zhang J.Maddison W.

Rutger Vos

  • sure?

http://linkeddata.uriburner.com/about/html/http://8ball.sdsc.edu:6666/treebase-web/search/downloadAStudy.html?id=1787&format=rdf

Arlin Stoltzfus 2:06 PM lost you Rutger Vos 2:06 PM mmm... again