[API-users] Some questions from a begginer

Eduardo Dalcin edalcin at jbrj.org
Wed Sep 9 20:02:08 CEST 2015


Thanks Alex. Food for thought.

Best,

Eduardo


--------------------------------
*Eduardo Dalcin
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Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ
e-mail: edalcin at jbrj.gov.br
Trabalho / Work: +55 21 3204 2116
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<edalcin at jbrj.org>*
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On Wed, Sep 9, 2015 at 2:28 PM, Alex Thompson <godfoder at acis.ufl.edu> wrote:

> I'm kind of seconding Rod here.
>
> It might make more sense, depending on your use case and local computer
> resources, to just get a download of Plantae *AND* Brazil from GBIF
> periodically, then process that to exclude existing Brazilian datasets. You
> could then use something like Apache hadoop / spark to efficiently split
> the file by dataset or by institution code.
>
> This would greatly simplify your interactions with GBIF (down to just
> periodically generating a download programmatically) and you would have an
> easy place to insert any additional data transformations you want. This is
> the path i take for my work at least - the incremental cost of a couple
> million more records is worth the reduction in complexity overall.
>
> - Alex
>
>
> On 09/09/2015 12:16 PM, Eduardo Dalcin wrote:
>
> 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>*
> --------------------------------
> Agendar reunião / Schedule a meeting: http://agendar.dalc.in
> <https://mailtrack.io/trace/link/3a5eaa1df56016285886497766577e5357ddc6c1?url=http%3A%2F%2Fagendar.dalc.in&signature=c4e8d8113c34937f>
>
> 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 <%2B44%20141%20330%204778>
>> Skype:  rdmpage
>> Facebook:  http://www.facebook.com/rdmpage
>> LinkedIn:  http://uk.linkedin.com/in/rdmpage
>> Twitter:  http://twitter.com/rdmpage
>> Blog:  http://iphylo.blogspot.com
>> ORCID:  http://orcid.org/0000-0002-7101-9767
>> 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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