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<p>Hi Nils,</p>
<p>Thank you for sharing!</p>
<p>How is phoenix about? Does it connects to the ESGF network? It's
the first time I read about this. Looks very very interesting!<br>
</p>
<p><br>
</p>
<p>Thanks everybody for these valuable feedback.<br>
</p>
<p>Best wishes</p>
<p><br>
</p>
<p>Juan<br>
</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 01/06/16 10:09, Nils Hempelmann
wrote:<br>
</div>
<blockquote cite="mid:574EA662.20200@nilshempelmann.de" type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Hi Juan et al <br>
<br>
Thanks a lot for triggering this discussion. <br>
I am currently working on a Web processing service (<a
moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://birdhouse.readthedocs.io/en/latest/"><a class="moz-txt-link-freetext" href="http://birdhouse.readthedocs.io/en/latest/">http://birdhouse.readthedocs.io/en/latest/</a></a>)
including a species distribution model based on the GBIF data (and
climate model data). A good connection to GBIF database is still
missing and all hints were quite useful!!<br>
<br>
If you want to share code:<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://github.com/bird-house/flyingpigeon/blob/master/flyingpigeon/processes/wps_sdm.py">https://github.com/bird-house/flyingpigeon/blob/master/flyingpigeon/processes/wps_sdm.py</a>
<br>
<br>
Merci<br>
Nils <br>
<br>
<div class="moz-cite-prefix">On 31/05/2016 22:08, Juan M.
Escamilla Molgora wrote:<br>
</div>
<blockquote
cite="mid:c2bbd2c0-71dd-9089-e030-644ddac4d7bb@lancaster.ac.uk"
type="cite">
<p>Hi Tim,</p>
<p>Thank you! specially for the DwC-A hint.</p>
<p>The cells are by default in decimal degrees, (wgs84 ) but the
functions for generating them are general enough to use any
projection supported by gdal using postgis. It could be done
"on the fly" or stored on the server side,</p>
<p>I was thinking (day dreaming) in a standard way for coding
unique but universal grids (similar to geohash or open
location code), but didn't find something fast and ready.
Maybe later :) <br>
</p>
<p>I only use Open Source Software, Python, Django, GDAL, Numpy,
Postgis, Conda, Py2Neo, ete2 among others.</p>
<p>Currently I don't have an official release and the project is
quite inmature, unstable as well as the installation could be
non trivial. I'm fixing all these issues but will take some
time,sorry for this.<br>
</p>
<p>The github repository is:<br>
</p>
<p><a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://github.com/molgor/biospytial.git">https://github.com/molgor/biospytial.git</a></p>
<p>An there's a very old documentation here: <br>
</p>
<p><a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://test.holobio.me/modules/gbif_taxonomy_class.html">http://test.holobio.me/modules/gbif_taxonomy_class.html</a><br>
</p>
<p>Please feel free to follow!<br>
</p>
<p><br>
</p>
<p>Best wishes</p>
<p><br>
</p>
<p>Juan<br>
</p>
<p>P.s. The functions for generating the grid are in:
biospytial/SQL_functions</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 31/05/16 19:47, Tim Robertson
wrote:<br>
</div>
<blockquote
cite="mid:6444FDB2-87DB-4835-9AAD-6FDABA1B4890@gbif.org"
type="cite">
<div>Thanks Juan</div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">You're quite right - you need the
DwC-A download format to get those IDs. </div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">Are the cells decimal degrees,
and then partitioned into smaller units, or equal area cells
or maybe UTM grids or something else perhaps? I am just
curious.</div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">Are you developing this as OSS?
I'd like to follow progress if possible?</div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">Thanks,<br>
<div>Tim,</div>
</div>
<div><br>
On 31 May 2016, at 20:31, 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>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<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">
<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"
class="moz-txt-link-abbreviated"
href="mailto:j.escamillamolgora@lancaster.ac.uk">j.escamillamolgora@lancaster.ac.uk</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>
</div>
</div>
<div style="word-wrap:break-word">
<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">maurobio@gmail.com</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"
class="moz-txt-link-abbreviated"
href="mailto:api-users@lists.gbif.org">api-users@lists.gbif.org</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"
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>>:</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="">
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--<span
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<div class="" style="margin:0cm
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font-family:'Times New
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Cavalcanti<br class="">
E-mail:<span
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