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<p>Hi Tim, <br>
</p>
<p>The grid is made by selecting a square area and divide it in nxn
subsquares which form a partition on the bigger square.</p>
<p>Each grid is a table in postgis and there's a mapping between
this table to a django model (class).</p>
<p>The class constructor have attributes: id, cell and neighbours
(next release).</p>
<p>The cell is a polygon (square) and with geodjango inherits the
properties of the osgeo module for polygons. <br>
</p>
<p>I've tried to use the CSV data (downloaded as a CSV request ) but
I couldn't find a way to obtain the global id's for each taxonomic
level (idspecies, idgenus, idfamily, etc).</p>
<p>Do you know a way for obtaining these fields?</p>
<p><br>
</p>
<p>Thank you for your email and best wishes,</p>
<p><br>
</p>
<p>Juan<br>
</p>
<br>
<div class="moz-cite-prefix">On 31/05/16 19:03, Tim Robertson wrote:<br>
</div>
<blockquote cite="mid:E15AFFAF-7262-4096-A6EC-CBAB9F00E27E@gbif.org"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<div>Hi Juan</div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">That sounds like a fun project!</div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">Can you please describe your grid /
cells? </div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">Most likely your best bet will be to
use the download API (as CSV data) and ingest that. The other
APIs will likely hit limits (e.g. You can't page through
indefinitely).<br>
<br>
Thanks,<br>
<div>Tim</div>
</div>
<div><br>
On 31 May 2016, at 18:55, Juan M. Escamilla Molgora <<a
moz-do-not-send="true"
href="mailto:j.escamillamolgora@lancaster.ac.uk"><a class="moz-txt-link-abbreviated" href="mailto:j.escamillamolgora@lancaster.ac.uk">j.escamillamolgora@lancaster.ac.uk</a></a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<p>Dear all,</p>
<p><br>
</p>
<p>Thank you very much for your valuable feedback!</p>
<p><br>
</p>
<p>I'll explain a bit what I'm doing just to clarify, sorry if
this spam to some.</p>
<p><br>
</p>
<p>I want to build a model for species assemblages based on
co-occurrence of taxa within an arbitrary area. I'm building
a 2D lattice in which for each cell I'm collapsing the data
into a taxonomic tree (the occurrences). For doing this I
need first to obtain the data from the gbif api and later,
based on the ids (or names) of each taxonomic level (from
kingdom to occurrence) build a tree coupled to each cell.
<br>
</p>
<p><br>
</p>
<p>The implementation is done with postgresql (postgis) for
storing the raw gbif data and neo4j for storing the relation
<br>
</p>
<p>"Being a member of the [ specie, genus, family,,,]
[name/id]" The idea is to include data from different
sources similar to the project Matthew and Jennifer had
mentioned (which I'm very interested and like to hear more)
and traverse the network looking for significant merged
information. <br>
</p>
<p><br>
</p>
<p>One of the immediate problems I've found is to import big
chunks of the gbif data into my specification. Thanks to
this thread I've found the tools that are the most used by
the community (pygbif,rgbif, and python-dwca-reader). I was
using urlib2 and things like that. <br>
</p>
<p>I'll be happy to share any code or ideas with the people
interested.</p>
<p><br>
</p>
<p>Btw, I've checked the tinkerpop project which uses the
Gremlin traversal language as independent from the DBMS.
<br>
</p>
<p>Perhaps it's possible to use it with spark and Guoda as
well?</p>
<p><br>
</p>
<p><br>
</p>
<p>Does GOuda is working now?</p>
<p><br>
</p>
<p>Best wishes</p>
<p><br>
</p>
<p>Juan.<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 31/05/16 17:02, Collins,
Matthew wrote:<br>
</div>
<blockquote cite="mid:1464710544965.30033@acis.ufl.edu"
type="cite">
<p>Jorrit pointed out this thread to us at iDigBio.
Downloading and importing data into a relational database
will work great, especially if as Jan said you can cut the
data size down to a reasonable amount.<br>
</p>
<p><span style="font-size: 12pt;"><br>
</span></p>
<p><span style="font-size: 12pt;">Another approach we've
been working on in a collaboration called GUODA [1] is
to build an Apache Spark environment with pre-formatted
data frames with common data sets in them for
researchers to use. This approach would offer a remote
service where you could write arbitrary Spark code,
probably in Jupyter notebooks, to iterate over data.
Spark does a lot of cool stuff including GraphX which
might be of interest. This is </span>definitely
pre-alpha at this point and if anyone is interested, I'd
like to hear your thoughts.<span style="font-size: 12pt;"> I'll
also be at SPNHC talking about this.</span></p>
<p><span style="font-size: 12pt;"><br>
</span></p>
<p>One thing we've found in working on this is that
importing data into a structured data format isn't always
easy. If you only want a few columns, it'll be fine. But
getting the data typing, format standardization, and
column name syntax of the whole width of an iDigBio record
right requires some code. <span style="font-family:
Calibri, Arial, Helvetica, sans-serif; font-size: 16px;
background-color: rgb(255, 255, 255);">
I looked to see if </span><span style="font-family:
Calibri, Arial, Helvetica, sans-serif; font-size: 16px;
background-color: rgb(255, 255, 255);">EcoData R</span><span
style="font-family: Calibri, Arial, Helvetica,
sans-serif; font-size: 16px; background-color: rgb(255,
255, 255);">etriever [2] had a GBIF data source and they
have an eBird o</span><span style="font-family: Calibri,
Arial, Helvetica, sans-serif; font-size: 16px;
background-color: rgb(255, 255, 255);">ne that perhaps
you might find useful as a</span> starting point if you
wanted to try to use someone else's code to download and
import data.<br>
</p>
<p><br>
</p>
<p>For other data structures like BHL, we're kind of making
stuff up since we're packaging a relational structure and
not something nearly as flat as GBIF and DWC stuff.
<br>
</p>
<p><br>
</p>
<p>[1] <a moz-do-not-send="true" href="http://guoda.bio/">http://guoda.bio/</a><br>
</p>
<p>[2] <a moz-do-not-send="true"
href="http://www.ecodataretriever.org/">http://www.ecodataretriever.org/</a><br>
</p>
<p><br>
</p>
<div id="Signature">
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<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">Matthew
Collins<br>
Technical Operations Manager<br>
Advanced Computing and Information Systems Lab, ECE<br>
University of Florida<br>
<span class="Object"
id="OBJ_PREFIX_DWT1049_com_zimbra_phone"><a
moz-do-not-send="true"
href="callto:352-392-5414" tabindex="0"
id="NoLP">352-392-5414</a></span></div>
</div>
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<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" color="#000000" face="Calibri,
sans-serif"><b>From:</b> jorrit poelen
<a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:jhpoelen@xs4all.nl"><jhpoelen@xs4all.nl></a><br>
<b>Sent:</b> Monday, May 30, 2016 11:16 AM<br>
<b>To:</b> Collins, Matthew; Thompson, Alexander M;
Hammock, Jennifer<br>
<b>Subject:</b> Fwd: [API-users] Is there any NEO4J or
graph-based driver for this API ?</font>
<div> </div>
</div>
<div>Hey y’all:
<div class=""><br class="">
</div>
<div class="">Interesting request below on the GBIF
mailing list - sounds like a perfect fit for the GUODA
use cases. </div>
<div class=""><br class="">
</div>
<div class="">Would it be too early to jump onto this
thread and share our efforts/vision?</div>
<div class=""><br class="">
</div>
<div class="">thx,<br>
</div>
<div class="">-jorrit<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">Begin forwarded message:</div>
<br class="Apple-interchange-newline">
<div class="" style="margin-top:0px;
margin-right:0px; margin-bottom:0px;
margin-left:0px">
<span class="" style=""><b class="">From: </b></span><span
class="" style="">Jan Legind <<a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:jlegind@gbif.org"><a class="moz-txt-link-abbreviated" href="mailto:jlegind@gbif.org">jlegind@gbif.org</a></a>><br
class="">
</span></div>
<div class="" style="margin-top:0px;
margin-right:0px; margin-bottom:0px;
margin-left:0px">
<span class="" style=""><b class="">Subject: </b></span><span
class="" style=""><b class="">Re: [API-users]
Is there any NEO4J or graph-based driver for
this API ?</b><br class="">
</span></div>
<div class="" style="margin-top:0px;
margin-right:0px; margin-bottom:0px;
margin-left:0px">
<span class="" style=""><b class="">Date: </b></span><span
class="" style="">May 30, 2016 at 5:48:51 AM
PDT<br class="">
</span></div>
<div class="" style="margin-top:0px;
margin-right:0px; margin-bottom:0px;
margin-left:0px">
<span class="" style=""><b class="">To: </b></span><span
class="" style="">Mauro Cavalcanti <<a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:maurobio@gmail.com"><a class="moz-txt-link-abbreviated" href="mailto:maurobio@gmail.com">maurobio@gmail.com</a></a>>,
"Juan M. Escamilla Molgora" <<a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:j.escamillamolgora@lancaster.ac.uk"><a class="moz-txt-link-abbreviated" href="mailto:j.escamillamolgora@lancaster.ac.uk">j.escamillamolgora@lancaster.ac.uk</a></a>><br
class="">
</span></div>
<div class="" style="margin-top:0px;
margin-right:0px; margin-bottom:0px;
margin-left:0px">
<span class="" style=""><b class="">Cc: </b></span><span
class="">"<a moz-do-not-send="true"
href="mailto:api-users@lists.gbif.org"
class="">api-users@lists.gbif.org</a>" <<a
moz-do-not-send="true"
href="mailto:api-users@lists.gbif.org"
class=""><a class="moz-txt-link-abbreviated" href="mailto:api-users@lists.gbif.org">api-users@lists.gbif.org</a></a>><br
class="">
</span></div>
<br class="">
<div class="">
<div class="WordSection1"
style="font-family:Helvetica; font-size:12px;
font-style:normal; font-weight:normal;
letter-spacing:normal; orphans:auto;
text-align:start; text-indent:0px;
text-transform:none; white-space:normal;
widows:auto; word-spacing:0px">
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">Dear Juan,</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">Unfortunately we
have no tool for creating these kind of
SQL like queries to the portal. I am sure
you are aware that the filters in the
occurrence search pages can be applied in
combination in numerous ways. The API can
go even further in this regard[1], but it
not well suited for retrieving occurrence
records since there is a 200.000 records
ceiling making it unfit for species
exceeding this number.</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">There is going be
updates to the pygbif package[2] in the
near future that will enable you to launch
user downloads programmatically where a
whole list of different species can be
used as a query parameter as well as
adding polygons.[3]</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">In the meantime,
Mauro’s suggestion is excellent. If you
can narrow your search down until it
returns a manageable download (say less
than 100 million records), importing this
into a database should be doable. From
there, you can refine using SQL queries.</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">Best,</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">Jan K. Legind, GBIF
Data manager </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">[1]<span
class="Apple-converted-space"> </span><a
moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.gbif.org/developer/occurrence#search"><a class="moz-txt-link-freetext" href="http://www.gbif.org/developer/occurrence#search">http://www.gbif.org/developer/occurrence#search</a></a></span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">[2]<span
class="Apple-converted-space"> </span><a
moz-do-not-send="true"
class="moz-txt-link-freetext"
href="https://github.com/sckott/pygbif"><a class="moz-txt-link-freetext" href="https://github.com/sckott/pygbif">https://github.com/sckott/pygbif</a></a></span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)">[3]<span
class="Apple-converted-space"> </span><a
moz-do-not-send="true"
class="moz-txt-link-freetext"
href="https://github.com/jlegind/GBIF-downloads"><a class="moz-txt-link-freetext" href="https://github.com/jlegind/GBIF-downloads">https://github.com/jlegind/GBIF-downloads</a></a></span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<span class=""
style="font-family:Calibri,sans-serif;
color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
<b class=""><span class=""
style="font-size:10pt;
font-family:Tahoma,sans-serif">From:</span></b><span
class="" style="font-size:10pt;
font-family:Tahoma,sans-serif"><span
class="Apple-converted-space"> </span>API-users
[<a moz-do-not-send="true"
href="mailto:api-users-bounces@lists.gbif.org"
class="" style="color:purple;
text-decoration:underline">mailto:api-users-bounces@lists.gbif.org</a>]<span
class="Apple-converted-space"> </span><b
class="">On Behalf Of<span
class="Apple-converted-space"> </span></b>Mauro
Cavalcanti<br class="">
<b class="">Sent:</b><span
class="Apple-converted-space"> </span>30.
maj 2016 14:06<br class="">
<b class="">To:</b><span
class="Apple-converted-space"> </span>Juan
M. Escamilla Molgora<br class="">
<b class="">Cc:</b><span
class="Apple-converted-space"> </span><a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:api-users@lists.gbif.org"><a class="moz-txt-link-abbreviated" href="mailto:api-users@lists.gbif.org">api-users@lists.gbif.org</a></a><br
class="">
<b class="">Subject:</b><span
class="Apple-converted-space"> </span>Re:
[API-users] Is there any NEO4J or
graph-based driver for this API ?</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt;
font-size:12pt; font-family:'Times New
Roman',serif">
</div>
<div class="">
<div class="">
<div class="">
<p class="MsoNormal" style="margin:0cm
0cm 12pt; font-size:12pt;
font-family:'Times New Roman',serif">
Hi,</p>
</div>
<p class="MsoNormal" style="margin:0cm 0cm
12pt; font-size:12pt; font-family:'Times
New Roman',serif">
One solution I have successfully adopted
for this is to download the records
(either "manually" via browser or, yet
better, using a Python script using the
fine pygbif library), storing them into
a MySQL or SQLite database and then
perform the relational queries. I can
provide examples if you are interested.</p>
</div>
<div class="" style="margin:0cm 0cm
0.0001pt; font-size:12pt;
font-family:'Times New Roman',serif">
Best regards,</div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm
0.0001pt; font-size:12pt;
font-family:'Times New Roman',serif">
</div>
<div class="">
<div class="" style="margin:0cm 0cm
0.0001pt; font-size:12pt;
font-family:'Times New Roman',serif">
2016-05-30 8:59 GMT-03:00 Juan M.
Escamilla Molgora <<a
moz-do-not-send="true"
href="mailto:j.escamillamolgora@lancaster.ac.uk"
target="_blank" class=""
style="color:purple;
text-decoration:underline"><a class="moz-txt-link-abbreviated" href="mailto:j.escamillamolgora@lancaster.ac.uk">j.escamillamolgora@lancaster.ac.uk</a></a>>:</div>
<div class="" style="margin:0cm 0cm
0.0001pt; font-size:12pt;
font-family:'Times New Roman',serif">
Hola,<br class="">
<br class="">
Is there any API for making relational
queries like taxonomy, location or
timestamp?<br class="">
<br class="">
Thank you and best wishes<br class="">
<br class="">
Juan<br class="">
_______________________________________________<br class="">
API-users mailing list<br class="">
<a moz-do-not-send="true"
href="mailto:API-users@lists.gbif.org"
target="_blank" class=""
style="color:purple;
text-decoration:underline">API-users@lists.gbif.org</a><br
class="">
<a moz-do-not-send="true"
href="http://lists.gbif.org/mailman/listinfo/api-users"
target="_blank" class=""
style="color:purple;
text-decoration:underline">http://lists.gbif.org/mailman/listinfo/api-users</a></div>
</div>
<div class="" style="margin:0cm 0cm
0.0001pt; font-size:12pt;
font-family:'Times New Roman',serif">
<br class="">
<br class="" clear="all">
<br class="">
--<span class="Apple-converted-space"> </span></div>
<div class="">
<div class="" style="margin:0cm 0cm
0.0001pt; font-size:12pt;
font-family:'Times New Roman',serif">
Dr. Mauro J. Cavalcanti<br class="">
E-mail:<span
class="Apple-converted-space"> </span><a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:maurobio@gmail.com"><a class="moz-txt-link-abbreviated" href="mailto:maurobio@gmail.com">maurobio@gmail.com</a></a><br
class="">
Web:<span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://sites.google.com/site/maurobio"><a class="moz-txt-link-freetext" href="http://sites.google.com/site/maurobio">http://sites.google.com/site/maurobio</a></a></div>
</div>
</div>
</div>
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widows:auto; word-spacing:0px">http://lists.gbif.org/mailman/listinfo/api-users</a></div>
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<pre wrap="">_______________________________________________
API-users mailing list
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:API-users@lists.gbif.org">API-users@lists.gbif.org</a>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://lists.gbif.org/mailman/listinfo/api-users">http://lists.gbif.org/mailman/listinfo/api-users</a>
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<div><span>_______________________________________________</span><br>
<span>API-users mailing list</span><br>
<span><a moz-do-not-send="true"
href="mailto:API-users@lists.gbif.org">API-users@lists.gbif.org</a></span><br>
<span><a moz-do-not-send="true"
href="http://lists.gbif.org/mailman/listinfo/api-users">http://lists.gbif.org/mailman/listinfo/api-users</a></span><br>
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