Here is how to achieve this using Python/pygbif (what else? ;-))
from pprint import pprint from pygbif import species, occurrences
taxon_name = "Plantae" # a kingdom level taxon taxon_rank = "kingdom"
key = species.name_backbone(name=taxon_name, rank=taxon_rank)["usageKey"] n = occurrences.count(taxonKey=key, isGeoreferenced=True) print format(n, ','), " record(s) for ", taxon_name
max = 5 # maximum number of records to retrieve results = occurrences.search(taxonKey=key, basisOfRecord="PRESERVED_SPECIMEN", hasCoordinate=True, limit=max) for x in results["results"]: print pprint(x) # results are returned in JSON format
Hope it helps.
Salud!
2016-09-01 10:28 GMT-03:00 Eduardo Dalcin edalcin@jbrj.org:
Oops: http://www.gbif.org/occurrence/search?taxon_key= Plantae&basis_of_record=PRESERVED_SPECIMEN
*Eduardo Dalcin http://eduardo.dalc.in* Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ Diretoria de Pesquisas e-mail: edalcin@jbrj.org Trabalho / Work: +55 21 3204 2116 WhatsApp / Telegram: +55 21 98393 3344 Portal de Dados do JBRJ/DIPEQ http://dados.jbrj.gov.br/
On Thu, Sep 1, 2016 at 10:27 AM, Eduardo Dalcin edalcin@jbrj.org wrote:
That's it! Thanks!
I don't get this: [image: Inline image 1]
*Eduardo Dalcin http://eduardo.dalc.in* Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ Diretoria de Pesquisas e-mail: edalcin@jbrj.org Trabalho / Work: +55 21 3204 2116 WhatsApp / Telegram: +55 21 98393 3344 Portal de Dados do JBRJ/DIPEQ http://dados.jbrj.gov.br/
On Thu, Sep 1, 2016 at 10:23 AM, Tim Robertson trobertson@gbif.org wrote:
Thanks Eduardo.
No, you can type “Plantae” or any higher taxa in the scientific name filter and it will assist with autocompletion.
I hope this helps, Tim
From: Eduardo Dalcin edalcin@jbrj.org Date: Thursday 1 September 2016 at 15:19
To: Tim Robertson trobertson@gbif.org Cc: "api-users@lists.gbif.org" api-users@lists.gbif.org Subject: Re: [API-users] Changes in GBIF.org and API
Hi Tim, Thanks for the prompt reply. Yes, I'm aware of the KEY parameter. My comment is that at the filter, for humans that are not aware of those "obscure codes", still no way to select upper taxonomic ranks but species, through scientific name. Am I right?
Eduardo
*Eduardo Dalcin http://eduardo.dalc.in* Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ Diretoria de Pesquisas e-mail: edalcin@jbrj.org Trabalho / Work: +55 21 3204 2116 WhatsApp / Telegram: +55 21 98393 3344 Portal de Dados do JBRJ/DIPEQ http://dados.jbrj.gov.br/
On Thu, Sep 1, 2016 at 10:12 AM, Tim Robertson trobertson@gbif.org wrote:
Hi Eduardo,
I hope you are well. I’m not sure I understand your comment I’m afraid. Taxonomic filters have been working in GBIF since 2007 and they can be combined with any other filters. They are the most used search filters, which all species pages link to.
Plants: http://www.gbif.org/occurrence/search?TAXON_KEY=6 or http://api.gbif.org/v1/occurrence/search?TAXON_KEY=6 Animals: http://www.gbif.org/occurrence/search?TAXON_KEY=1 or http://api.gbif.org/v1/occurrence/search?TAXON_KEY=1
I presume you mean something else though - can you please explain and I’ll try and help?
Thanks, Tim
From: Eduardo Dalcin edalcin@jbrj.org Date: Thursday 1 September 2016 at 14:55 To: Tim Robertson trobertson@gbif.org Cc: "api-users@lists.gbif.org" api-users@lists.gbif.org Subject: Re: [API-users] Changes in GBIF.org and API
Congrats folks! Great job!
Still no way to separate plants of animals, or I missing something?
Cheers
Eduardo
*Eduardo Dalcin http://eduardo.dalc.in* Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ Diretoria de Pesquisas e-mail: edalcin@jbrj.org Trabalho / Work: +55 21 3204 2116 WhatsApp / Telegram: +55 21 98393 3344 Portal de Dados do JBRJ/DIPEQ http://dados.jbrj.gov.br/
On Thu, Sep 1, 2016 at 8:55 AM, Tim Robertson trobertson@gbif.org wrote:
Hi folks,
I am very happy to let you know that a new release of GBIF.org went online at lunchtime today with the following enhancements:
*Occurrence search (http://www.gbif.org/occurrence/search http://www.gbif.org/occurrence/search):*
- New locality based filters:
what publishers state nia SIN%2C+RIO+JURUA
- locality, province/state and water body
- These are not interpreted terms, but allow search based on
- A new organismID filter
- Publishing protocol filter
- License filter and facet:
- The occurrence API supports all the filters mentioned above with
the addition of also allowing search by publishing organisation
*Occurrence downloads*:
- The rights.txt file: has been changed to list all the licenses
of datasets included in that download.
- DwC-A based downloads and the Datacite metada (DOIs) use the
most restrictive license of the datasets included in the download defaulting to CC-BY.
- The CSV downloads contain a new column ‘*License*’.
The *Dataset search page* now supports faceted navigation by license: http://www.gbif.org/dataset/search?license=CC_BY_4_0
In the release, we have temporarily broken the “*repatriation*” filter which is being re-enabled now, and will be online again tomorrow. Sorry about this partial outage of that search term.
Many thanks, Tim
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