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

Eduardo Dalcin edalcin at jbrj.org
Thu Sep 1 16:20:05 CEST 2016


Thanks Mauro.

The point is that I want to use the web interface provided by GBIF.

Best

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 11:16 AM, Mauro Cavalcanti <maurobio at gmail.com>
wrote:

> 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 at jbrj.org>:
>
>> Oops: http://www.gbif.org/occurrence/search?taxon_key=Planta
>> e&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 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 10:27 AM, Eduardo Dalcin <edalcin at 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 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 10:23 AM, Tim Robertson <trobertson at 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 at jbrj.org>
>>>> Date: Thursday 1 September 2016 at 15:19
>>>>
>>>> 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
>>>>
>>>> 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=Califor
>>>>>>       nia
>>>>>>       - 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>> _______________________________________________
>> API-users mailing list
>> API-users at lists.gbif.org
>> http://lists.gbif.org/mailman/listinfo/api-users
>>
>>
>
>
> --
> Dr. Mauro J. Cavalcanti
> E-mail: maurobio at gmail.com
> Web: http://sites.google.com/site/maurobio
>
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