[API-users] Changes in GBIF.org and API

Thu Sep 1 15:33:26 CEST 2016

Thanks Mauro and Tim!

Cheers

Eduardo

--------------------------------
*Eduardo Dalcin <http://eduardo.dalc.in>*
Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ
Diretoria de Pesquisas
e-mail: edalcin at 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 10:32 AM, Mauro Cavalcanti <maurobio at gmail.com>
wrote:

> Hi,
>
> Using Python anf the pygbif library, you can do something like this:
>
> from pygbif import species, occurrences
>
> taxon_name = "Myrtales" # an order level taxon
> taxon_rank = "order"
>
> key = species.name_backbone(name=taxon_name, rank=taxon_rank)["usageKey"]
> n = occurrences.count(taxonKey=key, isGeoreferenced=True)
> print n, " record(s) for ", taxon_name
>
> This script allows to retrieve the number of records at a given taxonomic
> level; it can be modified to retrieve the records themselves (or selected
> parts of them).
>
> Hope this helps.
>
> Salud!
>
>
> 2016-09-01 10:19 GMT-03:00 Eduardo Dalcin <edalcin at jbrj.org>:
>
>> 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 at 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 at 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 at jbrj.org>
>>> Date: Thursday 1 September 2016 at 14:55
>>> To: Tim Robertson <trobertson at gbif.org>
>>> Cc: "api-users at lists.gbif.org" <api-users at 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 at 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 at 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:
>>>>       - locality, province/state and water body
>>>>       - These are not interpreted terms, but allow search based on
>>>>       what publishers state
>>>>       - http://www.gbif.org/occurrence/search?STATE_PROVINCE=California
>>>>
>>>>       - http://www.gbif.org/occurrence/search?WATER_BODY=AMAZONAS+BA
>>>>       SIN%2C+RIO+JURUA
>>>>    - A new organismID filter
>>>>       - http://www.gbif.org/occurrence/search?ORGANISM_ID=100
>>>>    - Publishing protocol filter
>>>>       - http://www.gbif.org/occurrence/search?PROTOCOL=TAPIR
>>>>    - License filter and facet:
>>>>       - http://www.gbif.org/occurrence/search?license=CC_BY_4_0
>>>>    - 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
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> API-users mailing list
>>>> API-users at lists.gbif.org
>>>> http://lists.gbif.org/mailman/listinfo/api-users
>>>>
>>>>
>>>
>>
>> _______________________________________________
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>>
>>
>
>
> --
> Dr. Mauro J. Cavalcanti
> E-mail: maurobio at gmail.com
> Web: http://sites.google.com/site/maurobio
>
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