Updating the text guidelines layout. Tables still need to be done

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Markus Döring 2015-01-13 18:43:09 +01:00 committed by Peter Desmet
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@ -1,269 +1,81 @@
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<h1>Darwin Core Text Guide</h1>
</div>
<td>
<center><h1>Darwin Core Text Guide</h1></center>
<p></p>
<table cellspacing="0" class="docinfo">
<tbody>
<tr>
<th>Title:</th>
<td>Darwin Core Text 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 implementing Darwin Core in Text files.</td>
</tr>
<tr>
<th>Contributors:</th>
<td>Tim Robertson (GBIF), Markus D&#246;ring (GBIF), John
Wieczorek (MVZ), Renato De Giovanni (CRIA), 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/text/</td>
</tr>
<tr>
<th>Latest Version:</th>
<td>
<a href=
"http://rs.tdwg.org/dwc/terms/guides/text/index.htm">http://rs.tdwg.org/dwc/terms/guides/text/</a>
</td>
</tr>
<tr>
<th>Replaces:</th>
<td>
<a href=
"http://rs.tdwg.org/dwc/2009-12-07/terms/guides/text/index.htm">
http://rs.tdwg.org/dwc/2009-12-07/terms/guides/text/</a>
</td>
</tr>
<tr>
<th>Document Status:</th>
<td>Current Standard</td>
</tr>
</tbody>
</table>
</td>
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</tbody>
</table><a id="introduction" name="introduction"></a>
<h2>1. Introduction</h2><b>Audience</b>: This document is targeted toward
<h2 id="introduction">1. Introduction</h2>
<p><b>Audience</b>: This document is targeted toward
those who wish to use or share information based on the Darwin Core terms
using text files. It provides technical details on how to construct these
files and complementary metadata files that describe their content.
files and complementary metadata files that describe their content.</p>
<p>This document provides guidelines for formatting and sharing Darwin Core
terms [<a href="../../index.htm">TERMS</a>] in <em>fielded text</em> formats,
@ -272,9 +84,11 @@
format and having the first row include Darwin Core standard term names) can
be shared in a single file, while a non-standard text file can be understood
using an [<a href="http://www.w3.org/XML/">XML</a>] metafile to describe its
contents and formatting.<br>
<img src="images/usage.png"><br>
More complex structure can be shared in multiple related files. The
contents and formatting.</p>
<img src="images/usage.png">
<p>More complex structure can be shared in multiple related files. The
description of content and relationships between files can be achieved using
the metafile. This guideline makes recommendations for the simple case of a
<em>core</em> file, upon which Darwin Core <em>records</em> are based, and
@ -285,15 +99,21 @@
contains one or more identifications for those specimens, with one
identification per row in the extension file, and with an identifier to the
specimen for each identification row. This example would allow many
identifications to be associated with each specimen.</p>
identifications to be associated with each specimen.</p>
<h3 id="simple">1.1 Simple Example Metafile Content</h3>
<p>A simple comma separated values
(CSV) data file with the following content:</p>
<h3>1.1 Simple Example Metafile Content</h3>A simple comma separated values
(CSV) data file with the following content:
<pre class="example">
ID,Species,Count
123,"Cryptantha gypsophila Reveal & C.R. Broome",12
124,"Buxbaumia piperi",2
</pre>can be described with the following Darwin Core metafile:
</pre>
<p>can be described with the following Darwin Core metafile:</p>
<pre class="example">
&lt;?xml version="1.0" encoding="UTF-8"?&gt;
&lt;archive xmlns="http://rs.tdwg.org/dwc/text/"
@ -312,8 +132,10 @@ ID,Species,Count
&lt;/core&gt;
&lt;/archive&gt;
</pre>
<p>These same data could be understood without the metafile if the first row
of the CSV file contained the term names:
of the CSV file contained the term names:</p>
<pre class="example">
type,institutionCode,collectionCode,catalogNumber,scientificName,individualCount,datasetID
PhysicalObject,ANSP,PH,123,"Cryptantha gypsophila Reveal & C.R. Broome",12,urn:lsid:tim.lsid.tdwg.org:collections:1
@ -341,9 +163,9 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
another system. It could be that this system would then serve the data in
another format such as XML.</li>
</ul>
<p><a id="metafile" name="metafile"></a>
<h2>2. Metafile Content</h2>
<h2 id="metafile">2. Metafile Content</h2>
<p>The text metafile schema [<a href=
"../../../text/tdwg_dwc_text.xsd">TEXTSCHEMA</a>] provides technical details
@ -352,12 +174,14 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
elements and attributes, with descriptions and specifications for their use
in a metafile, are described in the following table.</p>
<h3>2.1 The &lt;archive&gt; element</h3>The &lt;archive&gt; element is the
<h3>2.1 The &lt;archive&gt; element</h3>
<p>The &lt;archive&gt; element is the
container for the list of related files (one core and zero or more
extensions). The &lt;archive&gt; element has just one attribute,
<em>metadata</em>.
<em>metadata</em>.</p>
<p></p>Attributes
<h4>Attributes</h4>
<table class="border">
<thead>
@ -433,12 +257,11 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
</tr>
</tbody>
</table>
<p>
<h3><a id="coreTag" name="coreTag">2.2 The &lt;core&gt; or &lt;extension&gt;
element</a></h3>
<p></p>Attributes
<h3 id="coreTag">2.2 The &lt;core&gt; or &lt;extension&gt; element</h3>
<h4>Attributes</h4>
<table class="border">
<thead>
@ -689,9 +512,9 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
</tr>
</tbody>
</table>
<p>
<h3><a id="files" name="files">2.3 The &lt;files&gt; element</a></h3>
<h3 id="files">2.3 The &lt;files&gt; element</h3>
<p>The files element must contain one or more &lt;location&gt; elements, each
defining where a file resides. Each core or extension entity can be composed
@ -699,7 +522,7 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
&lt;location&gt; element multiple times, once for each file that makes up the
entity.</p>
<p></p>Elements
<h4>Elements</h4>
<table class="border">
<thead>
@ -730,15 +553,15 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
</tr>
</tbody>
</table>
<p>
<h3><a id="fieldTag" name="fieldTag">2.4 The &lt;field&gt;
element</a></h3>The field element is used to specify the location and content
<h3 id="fieldTag">2.4 The &lt;field&gt; element</h3>
<p>The field element is used to specify the location and content
of data within a file. There must be one field element for every term being
shared for the entity, whether explicitly or through the use of a default
value for all rows in the file.
value for all rows in the file.</p>
<p></p>Attributes
<h4>Attributes</h4>
<table class="border">
<thead>
@ -806,11 +629,13 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
</tr>
</tbody>
</table>
<p><a id="implement" name="implement"></a>
<h2>3. Implementation Guide</h2>
<h3>3.1 Extension example</h3>The following example illustrates the use of
<h2 id="implement">3. Implementation Guide</h2>
<h3>3.1 Extension example</h3>
<p>The following example illustrates the use of
extensions. In this example there are three files in the archive, all of
which are located in the same directory as the metafile. The whales.txt file
acts as a core file of Taxon records. The whales.txt file is extended by two
@ -823,8 +648,10 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
files are related to the core file by the taxonNameID fields. Presumably,
this archive contains information about whale species, type specimen records
for those species, and lists of countries and the threat status for those
species.<br>
<img src="images/extension.png"><br>
species.</p>
<img src="images/extension.png">
<pre class="example">
&lt;?xml version="1.0" encoding="UTF-8"?&gt;
&lt;archive xmlns="http://rs.tdwg.org/dwc/text/"
@ -870,16 +697,20 @@ PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:colle
&lt;field index=&quot;3&quot; term=&quot;http://rs.tdwg.org/dwc/terms/occurrenceStatus&quot;/&gt;
&lt;/extension&gt;
&lt;/archive&gt;
</pre><a id="database" name="database"></a>
</pre>
<h2>4. Database Example</h2>
<h3>4.1 MySQL</h3>It is very easy to produce <em>fielded text</em> using the
<h2 id="database">4. Database Example</h2>
<h3>4.1 MySQL</h3>
<p>It is very easy to produce <em>fielded text</em> using the
<code>SELECT INTO outfile</code> command from MySQL. The encoding of the
resulting file will depend on the server variables and collations used, and
might need to be modified before the operation is done. Note that MySQL will
export NULL values as \N by default. Use the IFNULL() function as shown in
the following example to avoid this.
the following example to avoid this.</p>
<pre class="example">
SELECT
IFNULL(id, ''), IFNULL(scientific_name, ''), IFNULL(count,'')
@ -891,30 +722,43 @@ FROM
dwc;
</pre><a id="tools" name="tools"></a>
<h2>5. Tools</h2>
<h2 id="tools">5. Tools</h2>
<p>For tools and applications, including a Java-based application to read
Darwin Core text archives, see the <i>Darwin Core Tools and Applications</i>
page [<a href=
"https://github.com/tdwg/dwc-documentation/blob/master/doc/resources.md">TOOLS</a>].</p>
<hr>
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