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

Mauro Cavalcanti maurobio at gmail.com
Thu Sep 1 16:39:37 CEST 2016 

Dalcin,

As you can see, the web interface does not work the way you expect.

Salud!

2016-09-01 11:20 GMT-03:00 Eduardo Dalcin <edalcin at jbrj.org>:

> 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
>>
>
>


-- 
Dr. Mauro J. Cavalcanti
E-mail: maurobio at gmail.com
Web: http://sites.google.com/site/maurobio
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