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<p>Hi Annie,</p>
<p><br>
</p>
<p>With additional RAM allocated, the IPT can publish proportionally
larger datasets. However, this can be inefficient (or expensive
in terms of RAM), especially if the dataset has extensions.<br>
</p>
<p><br>
</p>
<p>To construct the DWCA outside an IPT you will need:</p>
<p>- data files. It's a good idea to check them for common errors
-- incorrect number of columns, duplicate occurrenceIds and so on
(the IPT does several checks like this).<br>
</p>
<p>- a meta.xml data description file, linking columns to Darwin
Core terms. This can be written by hand, using various programming
languages, or (often easiest if the process isn't to be repeated)
by using an IPT to make a suitable mapping and extracting the
resulting file.<br>
- an eml.xml metadata file, describing the dataset. The same
applies here -- the IPT is useful for providing a UI to write this
metadata, especially if all 8 are similar.<br>
</p>
<p><br>
</p>
<p>Once the DWCA exists, it should be copied to a webserver.<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>Note that using the registry API is not strictly necessary, and a
publisher with a small, unchanging number of datasets outside the
IPT need not use it. They can simply give the helpdesk a URL for
each dataset's DWCA file, and update the DWCA files at those URLs
as necessary.<br>
</p>
<p><br>
</p>
<p>Using the API is useful for adding additional datasets, making
changes (e.g. changing the URL) of the existing 8, or prompting
GBIF to reprocess a dataset. To use the API the technical team
should create a suitable username (e.g. "usgs" or "bison") on both
gbif.org and gbif-uat.org. The latter is our test system. They
should then contact <a class="moz-txt-link-abbreviated" href="mailto:helpdesk@gbif.org">helpdesk@gbif.org</a> to ask for permission for
that account to make changes under the <a moz-do-not-send="true" href="https://www.gbif.org/publisher/c3ad790a-d426-4ac1-8e32-da61f81f0117">USGS</a>
publisher, or whichever publisher is/are appropriate. This will
only be on the test system at first.</p>
<p><br>
</p>
<p>It's then possible to register a new dataset under that
publisher, following the example here:
<a class="moz-txt-link-freetext" href="https://github.com/gbif/registry/tree/master/registry-examples/src/test/scripts">https://github.com/gbif/registry/tree/master/registry-examples/src/test/scripts</a>
and see the result.</p>
<p><br>
</p>
<p>For general questions on this, the GBIF API mailing list is
probably most appropriate:
<a class="moz-txt-link-freetext" href="https://lists.gbif.org/mailman/listinfo/api-users">https://lists.gbif.org/mailman/listinfo/api-users</a></p>
<p><br>
</p>
<p>If you have problems or errors with a specific dataset,
<a class="moz-txt-link-abbreviated" href="mailto:helpdesk@gbif.org">helpdesk@gbif.org</a> will be the best contact. (They also read both
mailing lists.)</p>
<p><br>
</p>
<p>Cheers</p>
<p><br>
</p>
<p>Matt</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 07/07/2020 17:48, Simpson, Annie
wrote:<br>
</div>
<blockquote type="cite" cite="mid:MN2PR09MB575467261B0862E0FCA372CFAC660@MN2PR09MB5754.namprd09.prod.outlook.com">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
<div style="font-family: Times, "Times New Roman",
serif; font-size: 11pt; color: rgb(0, 0, 0);">
Thank you, Laura, for your replies.</div>
<div style="font-family: Times, "Times New Roman",
serif; font-size: 11pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Times, "Times New Roman",
serif; font-size: 11pt; color: rgb(0, 0, 0);">
The datasets have been exported from databases and cleaned. They
are generally UTF-8 tab delimited files. So i<span style="color:
rgb(0, 0, 0); font-family: Times, "Times New Roman",
serif; font-size: 11pt;">t seems that the GBIF Registry API
would be the correct solution. </span></div>
<div style="font-family: Times, "Times New Roman",
serif; font-size: 11pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: Times,
"Times New Roman", serif; font-size: 11pt;"><br>
</span></div>
<div style="font-family: Times, "Times New Roman",
serif; font-size: 11pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: Times,
"Times New Roman", serif; font-size: 11pt;">We
currently have 8 of these large datasets, only 2 of which
would not be updated in the future. Do you have names of GBIF
Product Team Members whom my technical team should contact to
begin this process? Is there "how to" documentation you can
point me to that they should read first?</span></div>
<div style="font-family: Times, "Times New Roman",
serif; font-size: 11pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Times, "Times New Roman",
serif; font-size: 11pt; color: rgb(0, 0, 0);">
Annie</div>
<div>
<div style="font-family:Times,"Times New Roman",serif;
font-size:11pt; color:rgb(0,0,0)">
<br>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b>
Laura Anne Russell <a class="moz-txt-link-rfc2396E" href="mailto:larussell@gbif.org"><larussell@gbif.org></a><br>
<b>Sent:</b> Tuesday, July 7, 2020 11:17 AM<br>
<b>To:</b> Simpson, Annie <a class="moz-txt-link-rfc2396E" href="mailto:asimpson@usgs.gov"><asimpson@usgs.gov></a>;
<a class="moz-txt-link-abbreviated" href="mailto:ipt@lists.gbif.org">ipt@lists.gbif.org</a> <a class="moz-txt-link-rfc2396E" href="mailto:ipt@lists.gbif.org"><ipt@lists.gbif.org></a><br>
<b>Subject:</b> [EXTERNAL] Re: [IPT] How does one upload
large datasets to GBIF?</font>
<div> </div>
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<br>
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<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span lang="EN-GB">I could also mention that it is
possible to script the creation of the Darwin Core
Archives and then use the GBIF Registry API for the
connections with GBIF. Symbiota, PlutoF and some
others are successfully doing this. It does require
some initial coordination with our Product Team on how
to set up and coordinate the registration process and
potentially with our Informatics Team.</span></p>
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<span style="font-family:"Verdana",sans-serif" lang="EN-GB">Best,</span></p>
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<span style="font-family:"Verdana",sans-serif" lang="EN-GB">Laura</span></p>
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<span style="font-size:10.0pt;
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<span style="font-size:10.0pt;
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font-size: 11pt; font-family: Calibri, sans-serif;">
<b><span style="font-size:12.0pt; color:black">From: </span></b><span style="font-size:12.0pt; color:black">IPT
<a class="moz-txt-link-rfc2396E" href="mailto:ipt-bounces@lists.gbif.org"><ipt-bounces@lists.gbif.org></a> on behalf of
"Simpson, Annie" <a class="moz-txt-link-rfc2396E" href="mailto:asimpson@usgs.gov"><asimpson@usgs.gov></a><br>
<b>Date: </b>Tuesday, 7 July 2020 at 16.48<br>
<b>To: </b><a class="moz-txt-link-rfc2396E" href="mailto:ipt@lists.gbif.org">"ipt@lists.gbif.org"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:ipt@lists.gbif.org"><ipt@lists.gbif.org></a><br>
<b>Subject: </b>[IPT] How does one upload large
datasets to GBIF?</span></p>
</div>
<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
</p>
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<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span style="font-family:Times; color:black">Colleagues:</span></p>
</div>
<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span style="font-family:Times; color:black"> </span></p>
</div>
<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span style="font-family:Times; color:black">What is
the easiest or most popular way to send large
datasets to GBIF, ones that are too large for the
IPT software (I think that is more than 100MB
zipped, 10+million records)? Does one modify their
IPT instance? How? Or is there another process that
is preferred?</span></p>
</div>
<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span style="font-family:Times; color:black"> </span></p>
</div>
<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span style="font-family:Times; color:black">We
currently have IPT Version 2.3.6-r3985b6a installed
and plan to upgrade to 2.4.0 soon.</span></p>
</div>
<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span style="font-family:Times; color:black"> </span></p>
</div>
<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span style="font-family:Times; color:black">A
technical answer is what I seek (on behalf of our
technical team).</span></p>
</div>
<div>
<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
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<p class="x_MsoNormal" style="margin: 0cm 0cm 0.0001pt;
font-size: 11pt; font-family: Calibri, sans-serif;">
<span style="font-family:Times; color:black">Again my
apologies if the answer to my question is easily
found and I'm just not finding it.</span></p>
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font-family:"Tahoma",sans-serif"><a href="https://bison.usgs.gov/" target="_blank" moz-do-not-send="true"><span style="text-decoration:none">Biodiversity
Information Serving Our Nation
(BISON)</span></a></span></p>
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<span style="font-size:10.5pt;
font-family:"Tahoma",sans-serif;
color:#666666">USGS Biodiversity
Information Serving Our Nation
(BISON) is a unique, web-based
Federal mapping resource for species
occurrence data in the United States
and its Territories and Canada,
including marine Exclusive Economic
Zones (EEZs).</span></p>
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font-family: Calibri, sans-serif;">
<span style="font-size:10.5pt;
font-family:"Tahoma",sans-serif;
color:#A6A6A6">bison.usgs.gov</span></p>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
IPT mailing list
<a class="moz-txt-link-abbreviated" href="mailto:IPT@lists.gbif.org">IPT@lists.gbif.org</a>
<a class="moz-txt-link-freetext" href="https://lists.gbif.org/mailman/listinfo/ipt">https://lists.gbif.org/mailman/listinfo/ipt</a>
</pre>
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