[API-users] Some questions from a begginer

Thu Sep 3 09:51:52 CEST 2015

Dear Eduardo,

Thanks for getting in touch with us about these issues.

The first request http://api.gbif.org/v1/occurrence/count?country=BR <https://mailtrack.io/trace/link/a74c129abf8bbfa4b19b1e189b34df8e0487feca?url=http%3A%2F%2Fapi.gbif.org%2Fv1%2Foccurrence%2Fcount%3Fcountry%3DBR%26taxonKey%3D6%26basisOfRecord%3DPRESERVED_SPECIMEN&signature=135dde174fa6c96e> &taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN returns the number of records located in Brazil for the facets in the request. 

The second query http://api.gbif.org/v1/occurrence/counts/datasets?country=BR <https://mailtrack.io/trace/link/9d992e7b6733894b7f83de11d178c1437080224b?url=http%3A%2F%2Fapi.gbif.org%2Fv1%2Foccurrence%2Fcounts%2Fdatasets%3Fcountry%3DBR%26taxonKey%3D6%26basisOfRecord%3DPRESERVED_SPECIMEN&signature=8b9c03790290e0ba> &taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN uses the Occurrence Inventories web service http://www.gbif.org/developer/occurrence#inventories 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.

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: 

/occurrence/counts/datasets

GET

Counts <http://api.gbif.org/v1/occurrence/counts/datasets?country=DE> 

Lists occurrence counts for datasets that cover a given taxon or country.

country <http://www.gbif.org/developer/occurrence#p_country> , taxonKey <http://www.gbif.org/developer/occurrence#p_taxonKey> 

As you can see here, http://api.gbif.org/v1/occurrence/counts/datasets?taxonKey=6 , this request doesn’t return anything.

The GBIF developers will handle this issue in due time.

You can follow the issue in our bug tracking service here: http://dev.gbif.org/issues/browse/POR-2828 

With best regards,

Jan K. Legind

Data manager, GBIF Secretariat

From: API-users [mailto:api-users-bounces at lists.gbif.org] On Behalf Of Eduardo Dalcin
Sent: 2. september 2015 20:06
To: api-users at lists.gbif.org; dev at gbif.org
Cc: João Monnerat Lanna; Natália Queiroz; Diogo Silva; Laura; Ricardo Avancini
Subject: [API-users] Some questions from a begginer

Hi folks,

This is my first message to the list. So, please, be nice :)

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 <https://mailtrack.io/trace/link/453c7d453a2da4e332a97aeca082eb5547d8191b?url=http%3A%2F%2Fcncflora.jbrj.gov.br%2Farquivos%2Farquivos%2Fpdfs%2FLivroVermelho.pdf&signature=500078d211c9dfde> , but we still have to assess ca. 35.000. Access occurrence records for Brazil is crucial, and every occurrence is important.

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.

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.

First:

The request:

http://api.gbif.org/v1/occurrence/count?country=BR <https://mailtrack.io/trace/link/a74c129abf8bbfa4b19b1e189b34df8e0487feca?url=http%3A%2F%2Fapi.gbif.org%2Fv1%2Foccurrence%2Fcount%3Fcountry%3DBR%26taxonKey%3D6%26basisOfRecord%3DPRESERVED_SPECIMEN&signature=135dde174fa6c96e> &taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN

returns 4.982.689 records

And the request:

http://api.gbif.org/v1/occurrence/counts/datasets?country=BR <https://mailtrack.io/trace/link/9d992e7b6733894b7f83de11d178c1437080224b?url=http%3A%2F%2Fapi.gbif.org%2Fv1%2Foccurrence%2Fcounts%2Fdatasets%3Fcountry%3DBR%26taxonKey%3D6%26basisOfRecord%3DPRESERVED_SPECIMEN&signature=8b9c03790290e0ba> &taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN

returns (here <https://mailtrack.io/trace/link/f15b92c6e49e193b58c96df93026b672d630a4fd?url=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1msUjwMLoKwnXxJFzF20SeN_C65RIkGLbwaYyj459VTc%2Fedit%3Fusp%3Dsharing&signature=c9883058799925fd> ) 7.406.310 records

Comments?

Second:

The request:

http://api.gbif.org/v1/occurrence/count?country=BR <https://mailtrack.io/trace/link/a74c129abf8bbfa4b19b1e189b34df8e0487feca?url=http%3A%2F%2Fapi.gbif.org%2Fv1%2Foccurrence%2Fcount%3Fcountry%3DBR%26taxonKey%3D6%26basisOfRecord%3DPRESERVED_SPECIMEN&signature=135dde174fa6c96e> &taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN

return things like this:

"197908d0-5565-11d8-b290-b8a03c50a862":27629

But the consult of the same dataset:

http://www.gbif.org/occurrence/search?TAXON_KEY=6 <https://mailtrack.io/trace/link/6b3dbf4bfc7f45d67d05057979f1e72e2617ca68?url=http%3A%2F%2Fwww.gbif.org%2Foccurrence%2Fsearch%3FTAXON_KEY%3D6%26DATASET_KEY%3D197908d0-5565-11d8-b290-b8a03c50a862&signature=b7f33a6c62020571> &DATASET_KEY=197908d0-5565-11d8-b290-b8a03c50a862

Returns "null" (of course, is a FishBase!)

I have plenty of examples like this, on yellow here (not finished!):

https://docs.google.com/spreadsheets/d/1msUjwMLoKwnXxJFzF20SeN_C65RIkGLbwaYyj459VTc/edit?usp=sharing <https://mailtrack.io/trace/link/21008349e3704f943677730af8f5afdc6cd3cc7b?url=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1msUjwMLoKwnXxJFzF20SeN_C65RIkGLbwaYyj459VTc%2Fedit%3Fusp%3Dsharing&signature=b9533d9cc7784c04> 

Comments?

I think those two questions is a good start. Please, let me know if I'm doing something wrong.

Cheers,

Eduardo

--------------------------------

Eduardo Dalcin <https://mailtrack.io/trace/link/0013f9d54db6dace53d2df17834b697a7abd50cc?url=http%3A%2F%2Feduardo.dalc.in&signature=d1933ed6341a6234> 

Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ

e-mail:  <mailto:edalcin at jbrj.gov.br> edalcin at jbrj.gov.br

Trabalho / Work: +55 21 3204 2116 <tel:%2B55%2021%203204%202116> 

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e-mail alternativo /  alternate email: edalcin at jbrj.org

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Agendar reunião / Schedule a meeting: http://agendar.dalc.in <https://mailtrack.io/trace/link/0307534e3500b69d419aa6594a8e7baed96be03e?url=http%3A%2F%2Fagendar.dalc.in&signature=8525294e2422d17d> 

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