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<p>I convert the backbone to an elasticsearch index for taxon name
matching at iDigBio. The code is public, but not particularly
built for re-use. I also pre-process the backbone files to enforce
sorting on id/coreid, which makes the extension matching code
easier to write.<br>
</p>
<p><a class="moz-txt-link-freetext" href="https://github.com/iDigBio/idb-backend/blob/master/idb/data_tables/build_taxon_index.py">https://github.com/iDigBio/idb-backend/blob/master/idb/data_tables/build_taxon_index.py</a></p>
<p>It could probably be fairly easily adapted to another search
engine or NoSQL database that can handle nested JSON structures if
SQL is not a hard and fast requirement.</p>
<p>- Alex<br>
</p>
<div class="moz-cite-prefix">On 11/14/2016 11:40 AM, Scott
Chamberlain wrote:<br>
</div>
<blockquote
cite="mid:CAD-oS=9Tc3_90T=4oB2S_kzWsjmnhGPQ1E+fc6HtHZ5rrrvJHw@mail.gmail.com"
type="cite">
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<div dir="ltr">Hi Chris, I started something a while back to
automate building a SQLite version of the backbone taxonomy (<a
moz-do-not-send="true"
href="https://github.com/ropensci/gbif-backbone-sql">https://github.com/ropensci/gbif-backbone-sql</a>)
but it's not quite done yet. Idea is to run on Heroku (e.g.,
once a day), resulting in a fresh SQLite version of the backbone
taxonomy on Amazon S3.
<div><br>
</div>
<div>Scott</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Mon, Nov 14, 2016 at 7:50 AM Markus Döring
<<a moz-do-not-send="true" href="mailto:mdoering@gbif.org">mdoering@gbif.org</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="gmail_msg">
Hi Chris,
<div class="gmail_msg">the latest GBIF backbone is always
available as a Darwin Core archive. This is mostly a
collection of tab delimited text files with the accepted
and synonym names at its core.</div>
<div class="gmail_msg">You can find the latest and previous,
archived versions here:</div>
<div class="gmail_msg"><a moz-do-not-send="true"
href="http://rs.gbif.org/datasets/backbone/"
class="gmail_msg" target="_blank">http://rs.gbif.org/datasets/backbone/</a></div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">Best,</div>
<div class="gmail_msg">Markus</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg"><br class="gmail_msg">
<div class="gmail_msg">
<div
style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"
class="gmail_msg">
--<br class="gmail_msg">
Markus Döring</div>
<div
style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"
class="gmail_msg">
Software Developer<br class="gmail_msg">
Global Biodiversity Information Facility (GBIF)<br
class="gmail_msg">
<div class="gmail_msg"><a moz-do-not-send="true"
href="mailto:mdoering@gbif.org" class="gmail_msg"
target="_blank">mdoering@gbif.org</a></div>
<div class="gmail_msg"><a moz-do-not-send="true"
href="http://www.gbif.org" class="gmail_msg"
target="_blank">http://www.gbif.org</a></div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
</div>
<br
class="m_6703429565373641011Apple-interchange-newline
gmail_msg">
</div>
</div>
</div>
<div style="word-wrap:break-word" class="gmail_msg">
<div class="gmail_msg">
<br class="gmail_msg">
<div class="gmail_msg">
<blockquote type="cite" class="gmail_msg">
<div class="gmail_msg">On 14 Nov 2016, at 16:42,
Köhler Christian <<a moz-do-not-send="true"
href="mailto:C.Koehler@zfmk.de" class="gmail_msg"
target="_blank">C.Koehler@zfmk.de</a>> wrote:</div>
<br
class="m_6703429565373641011Apple-interchange-newline
gmail_msg">
<div class="gmail_msg">
<div class="gmail_msg">Hi,<br class="gmail_msg">
<br class="gmail_msg">
we are developing an application to curate
taxonomic and morphological<br class="gmail_msg">
data for scientists. At the moment we are
evaluating different taxonomic<br
class="gmail_msg">
backbones to be used within our application. The
GIBF taxonomic backbone<br class="gmail_msg">
seems to be an good choice in regards to quality,
number of entries and<br class="gmail_msg">
acceptance.<br class="gmail_msg">
<br class="gmail_msg">
Due to the nature of our application, a web
service to browse the<br class="gmail_msg">
taxonomy will not fulfil our requirements. A local
copy of the GIBF data<br class="gmail_msg">
as SQL would be an ideal solution. I looked for
this data publicly<br class="gmail_msg">
available to no avail. "Harvesting" the GBIF rest
api seems not a good<br class="gmail_msg">
option. Are there plans to provide current
taxonomic backbone data in<br class="gmail_msg">
the future? Maybe the data is already available,
but I failed to find it<br class="gmail_msg">
yet.<br class="gmail_msg">
<br class="gmail_msg">
Regards<br class="gmail_msg">
Chris<br class="gmail_msg">
<br class="gmail_msg">
--<br class="gmail_msg">
Christian Köhler<br class="gmail_msg">
Tel.: 0228 9122-434<br class="gmail_msg">
<br class="gmail_msg">
Zoologisches Forschungsmuseum Alexander Koenig<br
class="gmail_msg">
Leibniz-Institut für Biodiversität der Tiere<br
class="gmail_msg">
Adenauerallee 160, 53113 Bonn, Germany<br
class="gmail_msg">
<a moz-do-not-send="true"
href="http://www.zfmk.de" class="gmail_msg"
target="_blank">www.zfmk.de</a><br
class="gmail_msg">
<br class="gmail_msg">
Stiftung des öffentlichen Rechts<br
class="gmail_msg">
Direktor: Prof. J. Wolfgang Wägele<br
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Sitz: Bonn<br class="gmail_msg">
--<br class="gmail_msg">
Zoologisches Forschungsmuseum Alexander Koenig<br
class="gmail_msg">
- Leibniz-Institut für Biodiversität der Tiere -<br
class="gmail_msg">
Adenauerallee 160, 53113 Bonn, Germany<br
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target="_blank">www.zfmk.de</a><br
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<br class="gmail_msg">
Stiftung des öffentlichen Rechts; Direktor: Prof.
J. Wolfgang Wägele<br class="gmail_msg">
Sitz: Bonn<br class="gmail_msg">
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