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Write script readme and migrate xml guide to new design

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Markus Döring 2015-01-14 18:24:08 +01:00 committed by Peter Desmet
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build/README.md
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add DOI explanations The build folder contains a python script to rebuild the terms index page and all resources.
It will use the current terms/dwc_normaltive.rdf and some yaml configurations inside this build folder for term definitions and order.
## Run the script
Install the required libraries for this script with PIP once:
$ easy_install pip
$ sudo pip install -r requirements.txt
To run the script just run it from inside the build folder:
$ ./update_terms.py
## Adding new terms
Simple changes for definitions should just be done in the RDF file.
In case a DwC term has been renamed, removed or added this also needs to be reflected in the following files:
### dc.yaml
This file contains the Dublin Core terms to be used in the record level group in the right order and their DwC definitions.
### term_order.yaml
This file contains a nested list of all DwC terms to be shown in the terms index.
The order and grouping of terms is defined here, but the definitions and other metadata is taken from the dwc_normative.rdf
### term_type.yaml
In order to generate the postgres sql table definition the script needs to know all data types different from the default _text_.
This file contains a list of those terms with the exact data type as used in postgres.
## TODO
- add DOI explanations

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build/update_terms.py
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#!/usr/bin/env python #!/usr/bin/env python
''' '''
easy_install pip Install the required libraries for this script with PIP:
pip install -r requirements.txt $ easy_install pip
$ sudo pip install -r requirements.txt
To run the script just run it from inside the build folder:
$ ./update_terms.py
''' '''
import yaml, re, csv, codecs import yaml, re, csv, codecs

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guides/rdf/index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Darwin Core RDF Guide</title>
<link href="http://rs.tdwg.org/dwc/" rel="schema.DwC">
<meta content="Darwin Core RDF Guide" name="DC.title">
<meta content="Guidelines for implementing Darwin Core as RDF." name="DC.description">
<meta name="DC.modified" content="2015-01-13"><!-- Also update in footer -->
<meta name="dcterms.subject" content="biodiversity, standards">
<meta name="dcterms.creator" content="Darwin Core Task Group">
<meta name="dcterms.contributor" content="John Wieczorek (MVZ)">
<meta name="dcterms.contributor" content="Markus Döring (GBIF)">
<meta name="dcterms.contributor" content="Renato De Giovanni (CRIA)">
<meta name="dcterms.contributor" content="Tim Robertson (GBIF)">
<meta name="dcterms.contributor" content="Dave Vieglais (KUNHM)">
<meta name="dcterms.contributor" content="Peter Desmet (INBO)">
<meta name="dcterms.publisher" content="Biodiversity Information Standards (TDWG)">
<meta name="dcterms.license" content="http://creativecommons.org/licenses/by/4.0/legalcode">
<meta name="dcterms.language" content="en">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="../../assets/bootstrap.min.css">
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<div class="content">
<div class="container">
<div class="page-header">
<h1>Darwin Core RDF Guide</h1>
</div>
<h2 id="introduction">1. Introduction</h2>
<p>This guide has to be added still.</p>
</div>
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</div>
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<ul class="list-inline pull-right">
<li>Page last modified on 2015-01-13</li>
<li><a href="https://github.com/tdwg/dwc/blob/gh-pages/resources.html">Edit on GitHub</a></li>
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guides/xml/index.html
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<!DOCTYPE html> <!DOCTYPE html>
<html lang="en"> <html lang="en">
<head> <head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type"> <meta charset="utf-8">
<title>Darwin Core XML Guide</title>
<title>Darwin Core XML Guide</title> <link href="http://rs.tdwg.org/dwc/" rel="schema.DwC">
<link href="http://rs.tdwg.org/dwc/" rel="schema.DwC"> <meta content="Darwin Core XML Guide" name="DC.title">
<meta content="Darwin Core XML Guide" name="DC.title"> <meta content="Guidelines for implementing Darwin Core as XML." name="DC.description">
<meta content="Guide for implementing Darwin Core in XML." name= <meta name="DC.modified" content="2015-01-13"><!-- Also update in footer -->
"DC.description">
<meta content="biodiversity, standards" name="DC.subject"> <meta name="dcterms.subject" content="biodiversity, standards">
<meta content="Darwin Core Task Group" name="DC.creator"> <meta name="dcterms.creator" content="Darwin Core Task Group">
<meta content="John Wieczorek (MVZ)" name="DC.contributor"> <meta name="dcterms.contributor" content="John Wieczorek (MVZ)">
<meta content="Markus Döring (GBIF)" name="DC.contributor"> <meta name="dcterms.contributor" content="Markus Döring (GBIF)">
<meta content="Renato De Giovanni (CRIA)" name="DC.contributor"> <meta name="dcterms.contributor" content="Renato De Giovanni (CRIA)">
<meta content="Tim Robertson (GBIF)" name="DC.contributor"> <meta name="dcterms.contributor" content="Tim Robertson (GBIF)">
<meta content="Dave Vieglais (KUNHM)" name="DC.contributor"> <meta name="dcterms.contributor" content="Dave Vieglais (KUNHM)">
<meta content="2009-02-12" name="DC.dateAccepted"> <meta name="dcterms.contributor" content="Peter Desmet (INBO)">
<meta content="http://rs.tdwg.org/dwc/2010-05-23/terms/guides/xml/" name= <meta name="dcterms.publisher" content="Biodiversity Information Standards (TDWG)">
"DC.replaces"> <meta name="dcterms.license" content="http://creativecommons.org/licenses/by/4.0/legalcode">
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<meta content="text/html" name="DC.format"> <link rel="stylesheet" type="text/css" href="../../assets/main.css">
<meta content="Biodiversity Information Standards TDWG" name="DC.publisher"> <link href="http://www.tdwg.org/" rel="meta">
<meta content="http://creativecommons.org/licenses/by/4.0/legalcode" name=
"DC.license">
<meta content="public" name="DC.accessRights">
<meta content="Darwin Core XML Guide. 2014" name="DC.bibliographicCitation">
<meta content="en" name="DC.language">
<link href="http://www.tdwg.org/" rel="meta">
<link href="../../../DarwinCore_files/default.css" rel="stylesheet" type=
"text/css">
<script src="../../../DarwinCore_files/default.js" type="text/javascript"></script>
</head> </head>
<body> <body>
<table border="0" cellpadding="0" cellspacing="0" style= <nav class="navbar navbar-default navbar-fixed-top">
"background-color: #617394" width="100%"> <div class="container">
<tbody> <div class="navbar-header">
<tr> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target=".navbar-collapse">
<td> <span class="sr-only">Toggle navigation</span>
<a href="http://www.tdwg.org"><img alt= <span class="icon-bar"></span><span class="icon-bar"></span><span class="icon-bar"></span>
"Biodiversity Information Standards (TDWG) logo" height="89" src= </button>
"../../../DarwinCore_files/TDWGlogo_Twiki.gif" width="148"></a> <a class="navbar-brand" href="../index.html">Darwin Core</a>
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<td align="right" height="100" valign="top" width="100%"></td>
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<table border="0" cellpadding="0" cellspacing="0" width="100%">
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<tr>
<td style="background-color: #617394" width="15%">
<div id="menu">
<div class="topMenu" id="nav">
<div class="menuItem level1">
<a href="../../../index.htm" onfocus=
"blurLink(this);">Introduction</a>
</div>
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<div class="menuItem">
<a href="../../../index.htm#references" onfocus=
"blurLink(this);">References</a>
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<a href="../../index.htm" onfocus="blurLink(this);">Quick
Reference Guide</a>
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"blurLink(this);">Simple Darwin Core</a>
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<a href="../../namespace/index.htm" onfocus=
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Model</a>
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Containment</a>
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<div class="content">
<div class="container">
<div class="page-header">
<h1>Darwin Core XML Guide</h1>
</div>
<td> <h2 id="introduction">1. Introduction</h2>
<center><h1>Darwin Core XML Guide</h1><center> <p>
<b>Audience</b>: This document is targeted toward
<p></p>
<table cellspacing="0" class="docinfo">
<tbody>
<tr>
<th>Title:</th>
<td>Darwin Core XML Guide</td>
</tr>
<tr>
<th>Date Issued:</th>
<td>2009-02-12</td>
</tr>
<tr>
<th>Date Modified:</th>
<td>2014-11-08</td>
</tr>
<tr>
<th>Abstract:</th>
<td>Guidelines for the implementation of Darwin Core in
XML.</td>
</tr>
<tr>
<th>Contributors:</th>
<td>John Wieczorek (MVZ), Markus Döring (GBIF), Renato De
Giovanni (CRIA), Tim Robertson (GBIF), Dave Vieglais
(KUNHM)</td>
</tr>
<tr>
<th>Legal:</th>
<td>This document is governed by the standard legal, copyright,
licensing provisions and disclaimers issued by the Taxonomic
Databases Working Group.</td>
</tr>
<tr>
<th>Part of TDWG Standard:</th>
<td>
<a href=
"http://www.tdwg.org/standards/450/">http://www.tdwg.org/standards/450/</a>
</td>
</tr>
<tr>
<th>Creator:</th>
<td>Darwin Core Task Group</td>
</tr>
<tr>
<th>Identifier:</th>
<td>http://rs.tdwg.org/dwc/2014-11-08/terms/guides/xml/</td>
</tr>
<tr>
<th>Latest Version:</th>
<td>
<a href=
"http://rs.tdwg.org/dwc/terms/guides/xml/index.htm">http://rs.tdwg.org/dwc/terms/guides/xml/</a>
</td>
</tr>
<tr>
<th>Replaces:</th>
<td>
<a href=
"http://rs.tdwg.org/dwc/2010-05-23/terms/guides/xml/index.htm">
http://rs.tdwg.org/dwc/2010-05-23/terms/guides/xml/</a>
</td>
</tr>
<tr>
<th>Document Status:</th>
<td>Current Standard</td>
</tr>
</tbody>
</table><br>
<br>
</td>
</tr>
</tbody>
</table><a id="introduction" name="introduction"></a>
<h2>1. Introduction</h2><b>Audience</b>: This document is targeted toward
those who wish to use or construct application schemas using Darwin Core those who wish to use or construct application schemas using Darwin Core
terms in XML. It includes explanations of existing schemas such as the Simple terms in XML. It includes explanations of existing schemas such as the Simple
Darwin Core [<a href="../../simple/index.htm">SIMPLEDWC</a>] and how to build Darwin Core [<a href="../../simple/index.htm">SIMPLEDWC</a>] and how to build
new schemas to meet specific models of information. new schemas to meet specific models of information.</p>
<p>This document provides guidelines for implementing application schemas <p>This document provides guidelines for implementing application schemas
based on Darwin Core terms [<a href="../../index.htm">TERMS</a>] using based on Darwin Core terms [<a href="../../index.htm">TERMS</a>] using
@ -304,31 +88,28 @@
<p>This document does not provide guidelines for encoding Darwin Core in <p>This document does not provide guidelines for encoding Darwin Core in
RDF/XML. Nor does it take a position on the relative merits of encoding RDF/XML. Nor does it take a position on the relative merits of encoding
metadata in &#39;plain&#39; XML rather than RDF/XML. This document provides metadata in &#39;plain&#39; XML rather than RDF/XML. This document provides
guidelines in those cases where RDF/XML is not considered appropriate. <a id= guidelines in those cases where RDF/XML is not considered appropriate.</p>
"implement" name="implement"></a></p>
<h2>2. Implementation Guide</h2> <h2 id="implement">2. Implementation Guide</h2>
<p><a id="xmlschema" name="xmlschema"></a></p> <h3 id="xmlschema">2.1 XML Schema</h3>
<p>Implementors should base their XML applications on
<h3>2.1 XML Schema</h3>Implementors should base their XML applications on
<i>XML Schemas</i> [<a href="http://www.w3.org/XML/Schema">XMLSCHEMA</a>] <i>XML Schemas</i> [<a href="http://www.w3.org/XML/Schema">XMLSCHEMA</a>]
rather than <i>XML DTDs</i>. Approaches based on <i>XML Schemas</i> are more rather than <i>XML DTDs</i>. Approaches based on <i>XML Schemas</i> are more
flexible and are more easily re-used within other XML applications. flexible and are more easily re-used within other XML applications.</p>
<p><a id="xmlnamespaces" name="xmlnamespaces"></a></p>
<h3>2.2 XML Namespaces</h3>Implementors should use <i>XML Namespaces</i> <h3 id="xmlnamespaces">2.2 XML Namespaces</h3>
<p>Implementors should use <i>XML Namespaces</i>
[<a href="http://www.w3.org/TR/1999/REC-xml-names-19990114/">XMLNS</a>] to [<a href="http://www.w3.org/TR/1999/REC-xml-names-19990114/">XMLNS</a>] to
uniquely identify elements. Darwin Core namespaces are defined in the uniquely identify elements. Darwin Core namespaces are defined in the
<i>Darwin Core Namespace Policy</i> [<a href= <i>Darwin Core Namespace Policy</i> [<a href=
"../../namespace/index.htm">NAMESPACEPOLICY</a>], while Dublin Core "../../namespace/index.htm">NAMESPACEPOLICY</a>], while Dublin Core
namespaces are defined in the <i>DCMI Namespace Recommendation</i> [<a href= namespaces are defined in the <i>DCMI Namespace Recommendation</i> [<a href=
"http://dublincore.org/documents/dcmi-namespace/">DCMINS</a>]. "http://dublincore.org/documents/dcmi-namespace/">DCMINS</a>].</p>
<p><a id="abstractmodel" name="abstractmodel"></a></p>
<h3>2.3 Abstract model</h3> <h3 id="abstractmodel">2.3 Abstract model</h3>
<p>The Darwin Core follows the <i>Dublin Core Metadata Initiative Abstract <p>The Darwin Core follows the <i>Dublin Core Metadata Initiative Abstract
Model</i> [<a href= Model</i> [<a href=
@ -353,18 +134,12 @@
record</em> describe that record.</li> record</em> describe that record.</li>
<li>A <em>Darwin Core record</em> must include all required <li>A <em>Darwin Core record</em> must include all required
<em>properties</em>, if any, and their associated <em>values</em>.</li> <em>properties</em>, if any, and their associated <em>values</em>.</li>
<!--
<LI>Each literal string <EM>value</EM> may have an associated language (e.g., en-GB).</LI>
<LI>Each <EM>value</EM> may have an associated <EM>encoding scheme</EM>.</LI>
<LI>Each <EM>encoding scheme</EM> has a <EM>name</EM>.</LI></UL>
-->
</ul> </ul>
<p><a id="propsandvalues" name="propsandvalues"></a></p>
<h3>2.4 Properties and Values</h3>
<h3 id="propsandvalues">2.4 Properties and Values</h3>
<p>The Darwin Core follows the guidelines for expressing Dublin Core metadata <p>The Darwin Core follows the guidelines for expressing Dublin Core metadata
using XML [<a href= using XML [<a href=
"http://dublincore.org/documents/dc-xml/">DCMIXMLGUIDE</a>] except in that "http://dublincore.org/documents/dc-xml/">DCMIXMLGUIDE</a>] except in that
@ -375,6 +150,7 @@
value given in the <em>Term name</em> attribute in the Darwin Core Terms value given in the <em>Term name</em> attribute in the Darwin Core Terms
recommendation [<a href="../../index.htm">TERMS</a>] with the appropriate recommendation [<a href="../../index.htm">TERMS</a>] with the appropriate
namespace name. For example, use</p> namespace name. For example, use</p>
<pre class="example"> <pre class="example">
&lt;xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" &lt;xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://rs.tdwg.org/dwc/terms/" targetNamespace="http://rs.tdwg.org/dwc/terms/"
@ -384,58 +160,29 @@
</pre> </pre>
<p>rather than</p> <p>rather than</p>
<pre class="example"> <pre class="example">
&lt;dwc:basisOfRecord value=&quot;HumanObservation&quot; /&gt; &lt;dwc:basisOfRecord value=&quot;HumanObservation&quot; /&gt;
</pre> </pre>
<p><!--
<H3>2.5 Encoding Schemes</H3>
If an encoding scheme is recommended in the <EM>Description</EM> attribute of the term, use that encoding scheme or
a refinement of it to constrain the values of the term.
<P>
Implementors should encode <EM>encoding schemes</EM> using the &#39;xsi:type&#39; attribute of the XML element for the property.
The name of the encoding scheme should be given as the attribute value, and should be in the form of an XML qualified name
(QName), which associates the scheme name with the appropriate namespace name. For example:
<PRE class="example">
&lt;xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://rs.tdwg.org/dwc/terms/"
xmlns:dc="http://purl.org/dc/terms/"
xmlns:dwc="http://rs.tdwg.org/dwc/terms/"&gt;
&lt;dwc:countryCode xsi:type=&quot;dc:ISO3166&quot;&gt;COL&lt;/dwc:countryCode&gt;
</PRE>
or
<PRE class="example">
&lt;xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://rs.tdwg.org/dwc/terms/"
xmlns:dwc="http://rs.tdwg.org/dwc/terms/"&gt;
&lt;dwc:basisOfRecord xsi:type=&quot;dwc:DwCType&quot;&gt;PreservedSpecimen&lt;/dwc:basisOfRecord&gt;
</PRE>
This allows implementors to take some advantage of the data typing functionality provided by the W3C XML Schema specifications <h3 id="nullvalues">2.5 Null values</h3>
[<A href="http://www.w3.org/XML/Schema">XMLSCHEMA</A>].
-->
<a id="nullvalues" name="nullvalues"></a></p>
<h3>2.5 Null values</h3>
<p>Elements for which the value is null should be omitted from the document <p>Elements for which the value is null should be omitted from the document
or explicitly coded using the attribute <i>xsi:nil="true"</i>.</p> or explicitly coded using the attribute <i>xsi:nil="true"</i>.</p>
<pre class="example"> <pre class="example">
&lt;dwc:locality xsi:nil=&quot;true&quot;/&gt; &lt;dwc:locality xsi:nil=&quot;true&quot;/&gt;
</pre>Do not use an empty string - an element with no content: </pre>
<p>Do not use an empty string - an element with no content:</p>
<pre class="example"> <pre class="example">
&lt;dwc:locality&gt;&lt;/dwc:locality&gt; &lt;dwc:locality&gt;&lt;/dwc:locality&gt;
</pre><!-- </pre>
<H3>2.7 Language</H3>
<P>
It is permissible to indicate the language of the <EM>value</EM> using the &#39;xml:lang&#39; attribute. For example:
<PRE class="example">&lt;dwc:country xml:lang=&quot;es&quot;&gt;España&lt;/dwc:country&gt;
&lt;dwc:sex xml:lang=&quot;en&quot;&gt;female&lt;/dwc:sex&gt;
</PRE>
-->
<a id="simpledarwincore" name="simpledarwincore"></a>
<h3>2.6 Simple Darwin Core</h3>
<h3 id="simpledarwincore">2.6 Simple Darwin Core</h3>
<p>The <i>Simple Darwin Core</i> [<a href= <p>The <i>Simple Darwin Core</i> [<a href=
"../../../xsd/tdwg_dwc_simple.xsd">SIMPLEXMLSCHEMA</a>] most closely models "../../../xsd/tdwg_dwc_simple.xsd">SIMPLEXMLSCHEMA</a>] most closely models
@ -469,6 +216,7 @@ It is permissible to indicate the language of the <EM>value</EM> using the &#39;
link shows a blank page in your browser, use the View Source option to see link shows a blank page in your browser, use the View Source option to see
the XML document) shows detail for a single record having a more complete set the XML document) shows detail for a single record having a more complete set
of elements.</p> of elements.</p>
<pre class="example"> <pre class="example">
&lt;?xml version=&quot;1.0&quot;?&gt; &lt;?xml version=&quot;1.0&quot;?&gt;
&lt;dwr:SimpleDarwinRecordSet &lt;dwr:SimpleDarwinRecordSet
@ -494,9 +242,8 @@ It is permissible to indicate the language of the <EM>value</EM> using the &#39;
&lt;/dwr:SimpleDarwinRecordSet&gt; &lt;/dwr:SimpleDarwinRecordSet&gt;
</pre> </pre>
<p><a id="classes" name="classes"></a></p>
<h3>2.7 Classes and Containment</h3> <h3 id="classes">2.7 Classes and Containment</h3>
<p>Many Darwin Core terms (<i>properties</i>) are defined as being associated <p>Many Darwin Core terms (<i>properties</i>) are defined as being associated
with another term (a <i>class</i>). For example, <a href= with another term (a <i>class</i>). For example, <a href=
@ -542,6 +289,7 @@ It is permissible to indicate the language of the <EM>value</EM> using the &#39;
of which has had a second identification) at one location following this of which has had a second identification) at one location following this
class-based schema. Note that you can reuse the location definition here by class-based schema. Note that you can reuse the location definition here by
referring to it via locationID:</p> referring to it via locationID:</p>
<pre class="example"> <pre class="example">
&lt;?xml version="1.0"?&gt; &lt;?xml version="1.0"?&gt;
&lt;dwr:DarwinRecordSet &lt;dwr:DarwinRecordSet
@ -633,10 +381,13 @@ It is permissible to indicate the language of the <EM>value</EM> using the &#39;
&lt;dwc:relationshipOfResource&gt;mother of&lt;/dwc:relationshipOfResource&gt; &lt;dwc:relationshipOfResource&gt;mother of&lt;/dwc:relationshipOfResource&gt;
&lt;/dwc:ResourceRelationship&gt; &lt;/dwc:ResourceRelationship&gt;
&lt;/dwr:DarwinRecordSet&gt; &lt;/dwr:DarwinRecordSet&gt;
</pre>Here is different example demonstrating area count observations for </pre>
<p>Here is different example demonstrating area count observations for
events on two different days at one location. Note that we omit the events on two different days at one location. Note that we omit the
identification class here as there is not identification related data and link identification class here as there is not identification related data and link
via the taxonID directly: via the taxonID directly:</p>
<pre class="example"> <pre class="example">
&lt;?xml version=&quot;1.0&quot;?&gt; &lt;?xml version=&quot;1.0&quot;?&gt;
&lt;dwr:DarwinRecordSet &lt;dwr:DarwinRecordSet
@ -728,24 +479,37 @@ via the taxonID directly:
&lt;/dwc:Occurrence&gt; &lt;/dwc:Occurrence&gt;
&lt;/dwr:DarwinRecordSet&gt; &lt;/dwr:DarwinRecordSet&gt;
</pre> </pre>
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