<div dir="ltr"><div class="gmail_default" style="font-size:small">Thanks Alex. Food for thought.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Best,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Eduardo</div><img width="0" height="0" class="mailtrack-img" src="https://mailtrack.io/trace/mail/6655d41fb9a15716c27b7dd6bdf4b107477a7bf2.png"></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font face="verdana, sans-serif"><br></font><font face="verdana, sans-serif"><font size="1">--------------------------------</font></font><div><b><span style="line-height:14.720000267028809px"><font face="verdana, sans-serif" size="1"><a href="https://mailtrack.io/trace/link/216b27d1db9fb6d2aa5a6d7b07aaf7a6b6b19ed9?url=http%3A%2F%2Feduardo.dalc.in&signature=fd3c844b73e3c400" target="_blank">Eduardo Dalcin</a></font></span></b></div><div><font face="verdana, sans-serif" size="1"><b><span style="line-height:11.5px"></span></b><span style="line-height:11px">Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ</span></font></div><div><span style="font-size:x-small">e-mail: </span><a href="mailto:edalcin@jbrj.gov.br" style="font-size:x-small" target="_blank">edalcin@jbrj.gov.br</a><br></div><div><font face="verdana, sans-serif" size="1"><span style="line-height:11px"></span><span style="line-height:11px">Trabalho / Work: +55 21 3204 2116</span></font></div><div><span style="font-family:verdana,sans-serif;font-size:x-small">--------------------------------</span><br></div><div><div style="font-family:verdana,sans-serif"><font face="verdana, sans-serif" size="1" color="#ff0000" style="font-size:x-small"><b>e-mail alternativo / </b></font><span style="color:rgb(68,68,68);line-height:16px"> </span><b><span style="line-height:16px"><font size="1" color="#ff0000">alternate email</font></span><span style="font-size:x-small;color:rgb(255,0,0)">:</span></b><b style="font-size:x-small;color:rgb(255,0,0)"> <a href="mailto:edalcin@jbrj.org" target="_blank">edalcin@jbrj.org</a></b></div></div><div style="font-family:verdana,sans-serif"><span style="font-size:x-small">--------------------------------</span></div><div><span style="font-family:verdana,sans-serif;font-size:x-small">Agendar reunião / </span><font face="verdana, sans-serif" size="1">Schedule a meeting: <a href="https://mailtrack.io/trace/link/dc51cf0b6ea2d4897c2ae7a70bab52163650de15?url=http%3A%2F%2Fagendar.dalc.in&signature=c87a5e78e01a7976" target="_blank">http://agendar.dalc.in</a></font></div><div style="font-family:verdana,sans-serif"></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Sep 9, 2015 at 2:28 PM, Alex Thompson <span dir="ltr"><<a href="mailto:godfoder@acis.ufl.edu" target="_blank">godfoder@acis.ufl.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
I'm kind of seconding Rod here.<br>
<br>
It might make more sense, depending on your use case and local
computer resources, to just get a download of Plantae *AND* Brazil
from GBIF periodically, then process that to exclude existing
Brazilian datasets. You could then use something like Apache hadoop
/ spark to efficiently split the file by dataset or by institution
code.<br>
<br>
This would greatly simplify your interactions with GBIF (down to
just periodically generating a download programmatically) and you
would have an easy place to insert any additional data
transformations you want. This is the path i take for my work at
least - the incremental cost of a couple million more records is
worth the reduction in complexity overall.<span class="HOEnZb"><font color="#888888"><br>
<br>
- Alex</font></span><div><div class="h5"><br>
<br>
<div>On 09/09/2015 12:16 PM, Eduardo Dalcin
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default">
<div class="gmail_default">
<div class="gmail_default">Hi Rod,</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">The real purpose is to have a
list of UUID and the "source web page" for the data set.
Thus, one way to do it is to select those resources that
counts <> 0 for PLANTAE *AND* Brazil.</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">I don't want to do any stats
analysis, but feed up one local harverster / agregator.</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">The problem is, considering the
reply from Jan Legind at Sep 3, we have to check one by
one (<a href="https://goo.gl/3wysaA" target="_blank">https://goo.gl/3wysaA</a>)
to check if it is a Herbarium / Preserved Specimen
(Plantae) or not, from the request <a href="http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN" target="_blank">http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN</a>.</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">Does it make sense?<br>
</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">Thanks for your curiosity! :)</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">Cheers,</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">Eduardo</div>
</div>
</div>
<img src="data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7" height="0" width="0"></div>
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<div><font size="1" face="verdana, sans-serif"><b><span style="line-height:11.5px"></span></b><span style="line-height:11px">Instituto de
Pesquisas Jardim Botânico do Rio de Janeiro
- JBRJ</span></font></div>
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<br>
<div class="gmail_quote">On Mon, Sep 7, 2015 at 12:33 PM,
Roderic Page <span dir="ltr"><<a href="mailto:Roderic.Page@glasgow.ac.uk" target="_blank">Roderic.Page@glasgow.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi Eduardo,
<div><br>
</div>
<div>I’m curious, is the purpose to get counts by dataset
by country, or to get all the plant occurrences for
Brazil? The later can be obtained by downloading all
plant occurrences in Brazil <a href="http://www.gbif.org/occurrence/search?TAXON_KEY=6&COUNTRY=BR" target="_blank">http://www.gbif.org/occurrence/search?TAXON_KEY=6&COUNTRY=BR</a> (you
could then compute the per-dataset stats locally). I
realise that this isn’t as convenient as having GBIF
slice the data for you in the API.<br>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Rod</div>
<div><br>
<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">
<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">
<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">
<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">---------------------------------------------------------<br>
Roderic Page<br>
Professor of Taxonomy<br>
Institute of Biodiversity, Animal Health and
Comparative Medicine<br>
College of Medical, Veterinary and Life
Sciences<br>
Graham Kerr Building<br>
University of Glasgow<br>
Glasgow G12 8QQ, UK<br>
<br>
Email: <span style="white-space:pre-wrap"> </span><a href="mailto:Roderic.Page@glasgow.ac.uk" target="_blank">Roderic.Page@glasgow.ac.uk</a><br>
Tel: <span style="white-space:pre-wrap"> </span><a href="tel:%2B44%20141%20330%204778" value="+441413304778" target="_blank">+44
141 330 4778</a><br>
Skype: <span style="white-space:pre-wrap"> </span>rdmpage<br>
Facebook: <span style="white-space:pre-wrap">
</span><a href="http://www.facebook.com/rdmpage" target="_blank">http://www.facebook.com/rdmpage</a><br>
LinkedIn: <span style="white-space:pre-wrap">
</span><a href="http://uk.linkedin.com/in/rdmpage" target="_blank">http://uk.linkedin.com/in/rdmpage</a><br>
Twitter: <span style="white-space:pre-wrap">
</span><a href="http://twitter.com/rdmpage" target="_blank">http://twitter.com/rdmpage</a><br>
Blog: <span style="white-space:pre-wrap"> </span><a href="http://iphylo.blogspot.com" target="_blank">http://iphylo.blogspot.com</a><br>
ORCID: <span style="white-space:pre-wrap"> </span><a href="http://orcid.org/0000-0002-7101-9767" target="_blank">http://orcid.org/0000-0002-7101-9767</a></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">Citations: <span style="white-space:pre-wrap"> </span><a href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ" target="_blank">http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ</a></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">ResearchGate<span style="white-space:pre-wrap"> </span><a href="https://www.researchgate.net/profile/Roderic_Page" target="_blank">https://www.researchgate.net/profile/Roderic_Page</a><br>
<br>
</div>
</div>
</div>
</div>
</div>
<br>
<div>
<blockquote type="cite">
<div>
<div>
<div>On 4 Sep 2015, at 10:39, Eduardo Dalcin
<<a href="mailto:edalcin@jbrj.org" target="_blank">edalcin@jbrj.org</a>>
wrote:</div>
<br>
</div>
</div>
<div>
<div>
<div>
<div dir="ltr">
<div class="gmail_default" style="font-size:small">Hi Markus,</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small">Yes, that's a
shame I can't have country and "nub"
together. There is any hope about it?</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small">Eduardo</div>
<img height="0" width="0"></div>
<div class="gmail_extra"><br clear="all">
<div>
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr"><font face="verdana, sans-serif"><br>
</font><font face="verdana,
sans-serif"><font size="1">--------------------------------</font></font>
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Dalcin</a></font></span></b></div>
<div><font size="1" face="verdana,
sans-serif"><b><span style="line-height:11.5px"></span></b><span style="line-height:11px">Instituto de Pesquisas Jardim Botânico do Rio
de Janeiro - JBRJ</span></font></div>
<div><span style="font-size:x-small">e-mail: </span><a href="mailto:edalcin@jbrj.gov.br" style="font-size:x-small" target="_blank">edalcin@jbrj.gov.br</a><br>
</div>
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sans-serif"><b>e-mail
alternativo / </b></font><span style="color:rgb(68,68,68);line-height:16px"> </span><b><span style="line-height:16px"><font size="1" color="#ff0000">alternate
email</font></span><span style="font-size:x-small;color:rgb(255,0,0)">:</span></b><b style="font-size:x-small;color:rgb(255,0,0)"> <a href="mailto:edalcin@jbrj.org" target="_blank">edalcin@jbrj.org</a></b></div>
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<br>
<div class="gmail_quote">On Thu, Sep 3,
2015 at 4:29 PM, Markus Döring <span dir="ltr">
<<a href="mailto:mdoering@gbif.org" target="_blank">mdoering@gbif.org</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Eduardo,<br>
<br>
as you might have seen from my issue
comment the webservice uses a
different parameter name for taxonKey
which is a bug we need to fix at some
point.<br>
Please use nubKey for now to use the
service like that:<br>
<br>
<a href="http://api.gbif.org/v1/occurrence/counts/datasets?nubKey=6" rel="noreferrer" target="_blank">http://api.gbif.org/v1/occurrence/counts/datasets?nubKey=6</a><br>
<br>
The real problem for you will be that
we do not support the combination of
the country and the taxon filter, just
one of the two. So you cannot search
for plants in Brazil I am afraid, just
for datasets about Brazil and datasets
with plant records.<br>
<span><font color="#888888"><br>
Markus<br>
</font></span><span><br>
<br>
<br>
> On 03 Sep 2015, at 14:12,
Eduardo Dalcin <<a href="mailto:edalcin@jbrj.org" target="_blank">edalcin@jbrj.org</a>>
wrote:<br>
><br>
> Thanks Jan. I'll keep exploring
and I'll be in touch, if I need.<br>
><br>
> Best,<br>
><br>
> Eduardo<br>
><br>
><br>
><br>
</span>
<div>
<div>>
--------------------------------<br>
> Eduardo Dalcin<br>
> Instituto de Pesquisas Jardim
Botânico do Rio de Janeiro - JBRJ<br>
> e-mail: <a href="mailto:edalcin@jbrj.gov.br" target="_blank">edalcin@jbrj.gov.br</a><br>
> Trabalho / Work: <a href="tel:%2B55%2021%203204%202116" value="+552132042116" target="_blank">
+55 21 3204 2116</a><br>
>
--------------------------------<br>
> e-mail alternativo /
alternate email: <a href="mailto:edalcin@jbrj.org" target="_blank">
edalcin@jbrj.org</a><br>
>
--------------------------------<br>
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http://agendar.dalc.in</a><br>
><br>
> On Thu, Sep 3, 2015 at 4:51
AM, Jan Legind [GBIF] <<a href="mailto:jlegind@gbif.org" target="_blank">jlegind@gbif.org</a>>
wrote:<br>
> Dear Eduardo,<br>
><br>
><br>
><br>
> Thanks for getting in touch
with us about these issues.<br>
><br>
><br>
><br>
> The first request <a href="http://api.gbif.org/v1/occurrence/count?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN" rel="noreferrer" target="_blank">
http://api.gbif.org/v1/occurrence/count?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN</a>
returns the number of records
located in Brazil for the facets
in the request.<br>
><br>
> The second query <a href="http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN" rel="noreferrer" target="_blank">
http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN</a>
uses the Occurrence Inventories
web service
<a href="http://www.gbif.org/developer/occurrence#inventories" rel="noreferrer" target="_blank">
http://www.gbif.org/developer/occurrence#inventories</a> which does not
support the basis-of-record facet
in the /datasets request. I
understand that it would be better
if the API response yielded an
error message in this instance.<br>
><br>
><br>
><br>
> Concerning the other issues –
you are indeed right that the
counts do not make sense in the
context of taxon key 6 which is
Plantae. Actually the API does not
handle the taxonKey search at all,
contrary to what the documentation
states:<br>
><br>
><br>
><br>
> /occurrence/counts/datasets<br>
><br>
> GET<br>
><br>
> Counts<br>
><br>
> Lists occurrence counts for
datasets that cover a given taxon
or country.<br>
><br>
> country, taxonKey<br>
><br>
><br>
><br>
> As you can see here, <a href="http://api.gbif.org/v1/occurrence/counts/datasets?taxonKey=6" rel="noreferrer" target="_blank">
http://api.gbif.org/v1/occurrence/counts/datasets?taxonKey=6</a> , this
request doesn’t return anything.<br>
><br>
><br>
><br>
> The GBIF developers will
handle this issue in due time.<br>
><br>
> You can follow the issue in
our bug tracking service here: <a href="http://dev.gbif.org/issues/browse/POR-2828" rel="noreferrer" target="_blank">
http://dev.gbif.org/issues/browse/POR-2828</a><br>
><br>
><br>
><br>
><br>
><br>
> With best regards,<br>
><br>
><br>
><br>
> Jan K. Legind<br>
><br>
> Data manager, GBIF
Secretariat<br>
><br>
><br>
><br>
><br>
><br>
> From: API-users [mailto:<a href="mailto:api-users-bounces@lists.gbif.org" target="_blank">api-users-bounces@lists.gbif.org</a>]
On Behalf Of Eduardo Dalcin<br>
> Sent: 2. september 2015 20:06<br>
> To: <a href="mailto:api-users@lists.gbif.org" target="_blank">api-users@lists.gbif.org</a>;
<a href="mailto:dev@gbif.org" target="_blank">dev@gbif.org</a><br>
> Cc: João Monnerat Lanna;
Natália Queiroz; Diogo Silva;
Laura; Ricardo Avancini<br>
> Subject: [API-users] Some
questions from a begginer<br>
><br>
><br>
><br>
> Hi folks,<br>
><br>
><br>
><br>
> This is my first message to
the list. So, please, be nice :)<br>
><br>
><br>
><br>
> I'm working here at Rio de
Janeiro Botanical Garden, together
with the guys at the National
Center for Flora Conservation. We
are doing the risk assessment of
the Brazilian flora to the
government. We assess, so far, the
risk of ca. 6.000 species, but we
still have to assess ca. 35.000.
Access occurrence records for
Brazil is crucial, and every
occurrence is important.<br>
><br>
><br>
><br>
> That means that we have to
put together occurrence data from
different sources and, after the
first batch of the risk
assessment, we realize that we
need to build up our aggregator.
We are planning to do this with
the Lontra-harvester, with the
help of the guys at Brazilian GBIF
Node.<br>
><br>
><br>
><br>
> So, the one of the firsts
steps was to list the available
resources to understand the
dimension of the task and, that
brings me to my questions.<br>
><br>
><br>
><br>
> First:<br>
><br>
><br>
><br>
> The request:<br>
><br>
><br>
><br>
> <a href="http://api.gbif.org/v1/occurrence/count?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN" rel="noreferrer" target="_blank">
http://api.gbif.org/v1/occurrence/count?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN</a><br>
><br>
><br>
><br>
> returns 4.982.689 records<br>
><br>
><br>
><br>
> And the request:<br>
><br>
><br>
><br>
> <a href="http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN" rel="noreferrer" target="_blank">
http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN</a><br>
><br>
><br>
><br>
> returns (here) 7.406.310
records<br>
><br>
><br>
><br>
> Comments?<br>
><br>
><br>
><br>
> Second:<br>
><br>
><br>
><br>
> The request:<br>
><br>
><br>
><br>
> <a href="http://api.gbif.org/v1/occurrence/count?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN" rel="noreferrer" target="_blank">
http://api.gbif.org/v1/occurrence/count?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN</a><br>
><br>
><br>
><br>
> return things like this:<br>
><br>
><br>
><br>
>
"197908d0-5565-11d8-b290-b8a03c50a862":27629<br>
><br>
><br>
> But the consult of the same
dataset:<br>
><br>
><br>
><br>
> <a href="http://www.gbif.org/occurrence/search?TAXON_KEY=6&DATASET_KEY=197908d0-5565-11d8-b290-b8a03c50a862" rel="noreferrer" target="_blank">
http://www.gbif.org/occurrence/search?TAXON_KEY=6&DATASET_KEY=197908d0-5565-11d8-b290-b8a03c50a862</a><br>
><br>
><br>
><br>
> Returns "null" (of course, is
a FishBase!)<br>
><br>
><br>
><br>
> I have plenty of examples
like this, on yellow here (not
finished!):<br>
><br>
><br>
><br>
> <a href="https://docs.google.com/spreadsheets/d/1msUjwMLoKwnXxJFzF20SeN_C65RIkGLbwaYyj459VTc/edit?usp=sharing" rel="noreferrer" target="_blank">
https://docs.google.com/spreadsheets/d/1msUjwMLoKwnXxJFzF20SeN_C65RIkGLbwaYyj459VTc/edit?usp=sharing</a><br>
><br>
><br>
><br>
> Comments?<br>
><br>
><br>
><br>
> I think those two questions
is a good start. Please, let me
know if I'm doing something wrong.<br>
><br>
><br>
><br>
> Cheers,<br>
><br>
><br>
><br>
> Eduardo<br>
><br>
>
--------------------------------<br>
><br>
> Eduardo Dalcin<br>
><br>
> Instituto de Pesquisas Jardim
Botânico do Rio de Janeiro - JBRJ<br>
><br>
> e-mail: <a href="mailto:edalcin@jbrj.gov.br" target="_blank">edalcin@jbrj.gov.br</a><br>
><br>
> Trabalho / Work: <a href="tel:%2B55%2021%203204%202116" value="+552132042116" target="_blank">
+55 21 3204 2116</a><br>
><br>
>
--------------------------------<br>
><br>
> e-mail alternativo /
alternate email: <a href="mailto:edalcin@jbrj.org" target="_blank">
edalcin@jbrj.org</a><br>
><br>
>
--------------------------------<br>
><br>
> Agendar reunião / Schedule a
meeting: <a href="https://mailtrack.io/trace/link/db57b837be515d4b7caefe43d55b60467cd7c2c1?url=http%3A%2F%2Fagendar.dalc.in&signature=69b244942739c0f5" rel="noreferrer" target="_blank">
http://agendar.dalc.in</a><br>
><br>
><br>
><br>
><br>
<br>
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<fieldset></fieldset>
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