<div dir="ltr"><div><div><br>Javier,<br><br></div>The problem with these tools (LontraHarvest, OpenRefine, etc.) is that they are just data *retrieval* tools, not providing for data analytical and representation functionalities -- one or more different tools should be used after retrieving the data of interest for plotting maps, charts, tabulation, statistical analyses, etc.<br>This is just where R excels, allowing to perform all these operations in a unified, straightforward workflow.<br><br></div>Salud!<br><div><div class="gmail_extra"><br><div class="gmail_quote">2015-09-09 17:23 GMT-03:00 Javier Otegui <span dir="ltr"><<a href="mailto:javier.otegui@gmail.com" target="_blank">javier.otegui@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Hi Eduardo (et al.),<br><br></div>If I understand correctly,
the list at <a href="https://goo.gl/3wysaA" target="_blank">https://goo.gl/3wysaA</a> shows the resources with data from
Brazil and you want to filter out those with records other than Plants,
am I right? Have you considered using OpenRefine
(<a href="http://openrefine.org/" target="_blank">http://openrefine.org/</a>) for this task? OpenRefine has a service to
fetch URLs built based on data from other columns, which plays very well
with GBIF APIs. You can make the program dinamically build the API
request URL based on the dataset UUID, and fetch and parse the JSON
response, without having to download the data and without having to code
almost anything. The way I would go here is:<br></div><ol><li>Create a column based off of the value in column A of your table, to extract just the dataset UUID</li><li>Create a new column fetching the GBIF API, adding the value in the previous column to a template URL: <span style="font-family:monospace,monospace"><a href="http://api.gbif.org/v1/occurrence/search?TAXON_KEY=6&limit=1&DATASET_KEY=" target="_blank">http://api.gbif.org/v1/occurrence/search?TAXON_KEY=6&limit=1&DATASET_KEY=</a><value></span>. The "limit:1" part makes things faster by avoiding having to show the default 20 records in the column</li><li>Create
yet another column parsing the JSON result from the previous column,
extracting just the value in the field "count". The result is the number
of plant records in that dataset (therefore, resources such as FishBase
will have a value of zero)<br></li></ol><p>Actually, you can add as
many columns as you want, with as many API calls, to fill the rest of
the fields in your table. Using the "registry" API, you can get the
title, external data link and the protocol (IPT, DiGIR...).</p><p>Hope this helps. Let me know if you are interested in this approach and need more help using OpenRefine.</p>Cheers!<div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr">Javier Otegui<br></div><div><a href="http://www.jotegui.com" target="_blank">http://www.jotegui.com</a><br></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Sep 9, 2015 at 8:07 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"><p dir="ltr">Scott, </p>
<p dir="ltr">That's my very point - that using R and rgbif should be the best path to take in this case, both because of the easier access to the GBIF API provided by rgbif and the HUGE data analytical capabilities of R itself. I had been working on a paper discussing this in the context of conservation databases (using R/rgbif and a Red-Listed group of mammals as an exemple), but unfortunately this work has been delayed by unexpected health problems. Hope it can be the light someday, however.</p>
<p dir="ltr">Best regards,</p><div><div>
<div class="gmail_quote">Em 09/09/2015 14:44, "Scott Chamberlain" <<a href="mailto:scott@ropensci.org" target="_blank">scott@ropensci.org</a>> escreveu:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Note that the R client rgbif does interface with the GBIF download API in addition to the search API - making it easier to deal with larger datasets. This works even if you downloaded bulk data from the GBIF GUI. Ignore this if you don't use R :)<div><br></div><div>Best, S</div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Sep 9, 2015 at 10:35 AM Alex Thompson <<a href="mailto:godfoder@acis.ufl.edu" target="_blank">godfoder@acis.ufl.edu</a>> wrote:<br></div><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.</div><div bgcolor="#FFFFFF" text="#000000"><br>
<br>
- Alex</div><div bgcolor="#FFFFFF" text="#000000"><br>
<br>
<div>On 09/09/2015 12:16 PM, Eduardo Dalcin
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>Hi Rod,</div>
<div><br>
</div>
<div>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><br>
</div>
<div>I don't want to do any stats
analysis, but feed up one local harverster / agregator.</div>
<div><br>
</div>
<div>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><br>
</div>
<div>Does it make sense?<br>
</div>
<div><br>
</div>
<div>Thanks for your curiosity! :)</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Eduardo</div>
</div>
</div>
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<div><font face="verdana, sans-serif" size="1"><b><span style="line-height:11.5px"></span></b><span style="line-height:11px">Instituto de
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<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">
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<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>
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<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 style="font-size:small">Hi Markus,</div>
<div style="font-size:small"><br>
</div>
<div 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 style="font-size:small"><br>
</div>
<div style="font-size:small">Eduardo</div>
<img height="0" width="0"></div>
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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
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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 /
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edalcin@jbrj.org</a><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>
</div>
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<fieldset></fieldset>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature">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>
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