[API-users] Some questions from a begginer

Wed Sep 9 18:16:43 CEST 2015

Hi Rod,

The real purpose is to have a list of UUID and the "source web page" for
the data set. Thus, one way to do it is to select those resources that
counts <> 0 for PLANTAE *AND* Brazil.

I don't want to do any stats analysis, but feed up one local harverster /
agregator.

The problem is, considering the reply from Jan Legind at Sep 3, we have to
check one by one (https://goo.gl/3wysaA) to check if it is a Herbarium /
Preserved Specimen (Plantae) or not, from the request
http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN
.

Does it make sense?

Thanks for your curiosity! :)

Cheers,

Eduardo

--------------------------------
*Eduardo Dalcin
<https://mailtrack.io/trace/link/5516ed5e4f903c6ee9bd9fb3876fb65ffffc687c?url=http%3A%2F%2Feduardo.dalc.in&signature=cda9e9bf584a828c>*
Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ
e-mail: edalcin at jbrj.gov.br
Trabalho / Work: +55 21 3204 2116
--------------------------------
*e-mail alternativo / * *alternate email:** edalcin at jbrj.org
<edalcin at jbrj.org>*
--------------------------------
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On Mon, Sep 7, 2015 at 12:33 PM, Roderic Page <Roderic.Page at glasgow.ac.uk>
wrote:

> Hi Eduardo,
>
> I’m curious, is the purpose to get counts by dataset by country, or to get
> all the plant occurrences for Brazil? The later can be obtained by
> downloading all plant occurrences in Brazil
> http://www.gbif.org/occurrence/search?TAXON_KEY=6&COUNTRY=BR (you could
> then compute the per-dataset stats locally). I realise that this isn’t as
> convenient as having GBIF slice the data for you in the API.
>
> Regards
>
> Rod
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email:  Roderic.Page at glasgow.ac.uk
> Tel:  +44 141 330 4778
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> Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> ResearchGate https://www.researchgate.net/profile/Roderic_Page
>
>
> On 4 Sep 2015, at 10:39, Eduardo Dalcin <edalcin at jbrj.org> wrote:
>
> Hi Markus,
>
> Yes, that's a shame I can't have country and "nub" together. There is any
> hope about it?
>
> Eduardo
>
>
> --------------------------------
> *Eduardo Dalcin
> <https://mailtrack.io/trace/link/bac23864202354f3789938ce352a878faa0cd8b8?url=http%3A%2F%2Feduardo.dalc.in&signature=aea58ef6f439535b>*
> Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ
> e-mail: edalcin at jbrj.gov.br
> Trabalho / Work: +55 21 3204 2116
> --------------------------------
> *e-mail alternativo / * *alternate email:** edalcin at jbrj.org
> <edalcin at jbrj.org>*
> --------------------------------
> Agendar reunião / Schedule a meeting: http://agendar.dalc.in
> <https://mailtrack.io/trace/link/db57b837be515d4b7caefe43d55b60467cd7c2c1?url=http%3A%2F%2Fagendar.dalc.in&signature=69b244942739c0f5>
>
> On Thu, Sep 3, 2015 at 4:29 PM, Markus Döring <mdoering at gbif.org> wrote:
>
>> Eduardo,
>>
>> as you might have seen from my issue comment the webservice uses a
>> different parameter name for taxonKey which is a bug we need to fix at some
>> point.
>> Please use nubKey for now to use the service like that:
>>
>> http://api.gbif.org/v1/occurrence/counts/datasets?nubKey=6
>>
>> The real problem for you will be that we do not support the combination
>> of the country and the taxon filter, just one of the two. So you cannot
>> search for plants in Brazil I am afraid, just for datasets about Brazil and
>> datasets with plant records.
>>
>> Markus
>>
>>
>>
>> > On 03 Sep 2015, at 14:12, Eduardo Dalcin <edalcin at jbrj.org> wrote:
>> >
>> > Thanks Jan. I'll keep exploring and I'll be in touch, if I need.
>> >
>> > Best,
>> >
>> > Eduardo
>> >
>> >
>> >
>> > --------------------------------
>> > Eduardo Dalcin
>> > Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ
>> > e-mail: edalcin at jbrj.gov.br
>> > Trabalho / Work: +55 21 3204 2116
>> > --------------------------------
>> > e-mail alternativo /  alternate email: edalcin at jbrj.org
>> > --------------------------------
>> > Agendar reunião / Schedule a meeting: http://agendar.dalc.in
>> <https://mailtrack.io/trace/link/db57b837be515d4b7caefe43d55b60467cd7c2c1?url=http%3A%2F%2Fagendar.dalc.in&signature=69b244942739c0f5>
>> >
>> > On Thu, Sep 3, 2015 at 4:51 AM, Jan Legind [GBIF] <jlegind at gbif.org>
>> wrote:
>> > Dear Eduardo,
>> >
>> >
>> >
>> > Thanks for getting in touch with us about these issues.
>> >
>> >
>> >
>> > The first request
>> http://api.gbif.org/v1/occurrence/count?country=BR&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&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
>> >
>> > Lists occurrence counts for datasets that cover a given taxon or
>> country.
>> >
>> > country, 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, 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&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN
>> >
>> >
>> >
>> > returns 4.982.689 records
>> >
>> >
>> >
>> > And the request:
>> >
>> >
>> >
>> >
>> http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&basisOfRecord=PRESERVED_SPECIMEN
>> >
>> >
>> >
>> > returns (here) 7.406.310 records
>> >
>> >
>> >
>> > Comments?
>> >
>> >
>> >
>> > Second:
>> >
>> >
>> >
>> > The request:
>> >
>> >
>> >
>> >
>> http://api.gbif.org/v1/occurrence/count?country=BR&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&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
>> >
>> >
>> >
>> > Comments?
>> >
>> >
>> >
>> > I think those two questions is a good start. Please, let me know if I'm
>> doing something wrong.
>> >
>> >
>> >
>> > Cheers,
>> >
>> >
>> >
>> > Eduardo
>> >
>> > --------------------------------
>> >
>> > Eduardo Dalcin
>> >
>> > Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ
>> >
>> > e-mail: edalcin at jbrj.gov.br
>> >
>> > Trabalho / Work: +55 21 3204 2116
>> >
>> > --------------------------------
>> >
>> > e-mail alternativo /  alternate email: edalcin at jbrj.org
>> >
>> > --------------------------------
>> >
>> > Agendar reunião / Schedule a meeting: http://agendar.dalc.in
>> <https://mailtrack.io/trace/link/db57b837be515d4b7caefe43d55b60467cd7c2c1?url=http%3A%2F%2Fagendar.dalc.in&signature=69b244942739c0f5>
>> >
>> >
>> >
>> >
>>
>>
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