<div dir="ltr"><div class="gmail_default" style="font-size:small">Thanks Mauro.</div><img width="0" height="0" class="mailtrack-img" src="https://mailtrack.io/trace/mail/b6bafee62f65ec6228518b1df2de2f9f44a6f59c.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/260ddb67a47f62cce404e06d766c44c4739f1ede?url=http%3A%2F%2Feduardo.dalc.in&signature=e4530308d2563fc1" 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/437dcf6445c1d03972f4089a557db31363205d94?url=http%3A%2F%2Fagendar.dalc.in&signature=392fac43ed8d3965" 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 Mon, Sep 7, 2015 at 7:21 PM, Mauro Cavalcanti <span dir="ltr"><<a href="mailto:maurobio@gmail.com" target="_blank">maurobio@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Dalcin,<br><br></div>For retrieving, counting, performing statistical analyses, databasing, plotting charts and maps, of GBIF data I have been using quite successfully the R oftware environment for statistical computing and graphics (<a href="https://www.r-project.org/" target="_blank">https://www.r-project.org/</a>) with the rgbif package (<a href="https://github.com/ropensci/rgbif" target="_blank">https://github.com/ropensci/rgbif</a>) written by Scott Chamberlain, which makes direct calls to the GBIF API. The advantages of R as a data retrieval and analytical tool are overwhelming and would be worth exploring in your case.<br><br></div>Hope this helps.<br><br></div>Salud!<br></div><div class="gmail_extra"><div><div class="h5"><br><div class="gmail_quote">2015-09-07 12:33 GMT-03:00 Roderic Page <span dir="ltr"><<a href="mailto:Roderic.Page@glasgow.ac.uk" target="_blank">Roderic.Page@glasgow.ac.uk</a>></span>:<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>
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---------------------------------------------------------<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>
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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>
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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>
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<blockquote type="cite">
<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 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 src="data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7" height="0" width="0"></div>
<div class="gmail_extra"><br clear="all">
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<div dir="ltr">
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<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/bac23864202354f3789938ce352a878faa0cd8b8?url=http%3A%2F%2Feduardo.dalc.in&signature=aea58ef6f439535b" 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: <a href="tel:%2B55%2021%203204%202116" value="+552132042116" target="_blank">+55 21 3204 2116</a></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 style="font-size:x-small" face="verdana, sans-serif" color="#ff0000" size="1"><b>e-mail alternativo / </b></font><span style="color:rgb(68,68,68);line-height:16px"> </span><b><span style="line-height:16px"><font color="#ff0000" size="1">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/db57b837be515d4b7caefe43d55b60467cd7c2c1?url=http%3A%2F%2Fagendar.dalc.in&signature=69b244942739c0f5" target="_blank">http://agendar.dalc.in</a></font></div>
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<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>
> 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>
> 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>
</div>
</div>
</blockquote>
</div>
<br>
</div>
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<br>_______________________________________________<br>
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<br></blockquote></div><br><br clear="all"><br></div></div><span class="HOEnZb"><font color="#888888">-- <br><div>Dr. Mauro J. Cavalcanti<br>E-mail: <a href="mailto:maurobio@gmail.com" target="_blank">maurobio@gmail.com</a><br>Web: <a href="http://sites.google.com/site/maurobio" target="_blank">http://sites.google.com/site/maurobio</a></div>
</font></span></div>
</blockquote></div><br></div>