[API-users] Some questions from a begginer

Wed Sep 9 23:27:42 CEST 2015

Javier,

Without some kind of empirical benchmark, a faithful comparison between R
and one of these other tools cannot be stated so clearly. In my own
experience, using R/rgbif to retrieve *and* locally database about 20,000
records from GBIF took less than 15 minutes. And all subsequent processing
(counting, tabulating, plotting, etc.) is done on the local machine, by
means of R, so this is dependent upon the performance of said machine. I
understand that the dataset under discussion is much larger than the one I
have been working with, but I cannot say that R would be an "overkill" in
any instance -- after all, why would anyone just want to retrieve records
from GBIF? For doing what with them? A conservation monitoring center is
supposed to generate *products*, in the form of charts, tables, maps,
statistcs, and therefore some kind of specializaed tool will be required at
some point in the process. So, why not using an integrated package (like R)
from the start for this?

Salud!

2015-09-09 18:16 GMT-03:00 Javier Otegui <javier.otegui at gmail.com>:

> Mauro,
>
> Agreed 100% (I'm actually a regular R user), but according to Eduardo's
> needs (or my understanding of his needs), I think that might be an overkill
> here. I have replicated and completed Eduardo's table in less than 30
> minutes with OpenRefine, while using R would probably take a larger amount
> of time just to get the data. But again, for more serious analytics, few
> things (if any) beat R.
>
> Cheers!
>
> El mié 09/09/2015, 22:59, Mauro Cavalcanti <maurobio at gmail.com> escribió:
>
>>
>> Javier,
>>
>> The problem with these tools (LontraHarvest, OpenRefine, etc.) is that
>> they are just data *retrieval* tools, not providing for data analytical and
>> representation functionalities -- one or more different tools should be
>> used after retrieving the data of interest for plotting maps, charts,
>> tabulation, statistical analyses, etc.
>> This is just where R excels, allowing to perform all these operations in
>> a unified, straightforward workflow.
>>
>> Salud!
>>
>> 2015-09-09 17:23 GMT-03:00 Javier Otegui <javier.otegui at gmail.com>:
>>
>>> Hi Eduardo (et al.),
>>>
>>> If I understand correctly, the list at https://goo.gl/3wysaA shows the
>>> resources with data from Brazil and you want to filter out those with
>>> records other than Plants, am I right? Have you considered using OpenRefine
>>> (http://openrefine.org/) for this task? OpenRefine has a service to
>>> fetch URLs built based on data from other columns, which plays very well
>>> with GBIF APIs. You can make the program dinamically build the API request
>>> URL based on the dataset UUID, and fetch and parse the JSON response,
>>> without having to download the data and without having to code almost
>>> anything. The way I would go here is:
>>>
>>>    1. Create a column based off of the value in column A of your table,
>>>    to extract just the dataset UUID
>>>    2. Create a new column fetching the GBIF API, adding the value in
>>>    the previous column to a template URL:
>>>    http://api.gbif.org/v1/occurrence/search?TAXON_KEY=6&limit=1&DATASET_KEY=
>>>    <value>. The "limit:1" part makes things faster by avoiding having
>>>    to show the default 20 records in the column
>>>    3. Create yet another column parsing the JSON result from the
>>>    previous column, extracting just the value in the field "count". The result
>>>    is the number of plant records in that dataset (therefore, resources such
>>>    as FishBase will have a value of zero)
>>>
>>> Actually, you can add as many columns as you want, with as many API
>>> calls, to fill the rest of the fields in your table. Using the "registry"
>>> API, you can get the title, external data link and the protocol (IPT,
>>> DiGIR...).
>>>
>>> Hope this helps. Let me know if you are interested in this approach and
>>> need more help using OpenRefine.
>>> Cheers!
>>>
>>> Javier Otegui
>>> http://www.jotegui.com
>>>
>>> On Wed, Sep 9, 2015 at 8:07 PM, Mauro Cavalcanti <maurobio at gmail.com>
>>> wrote:
>>>
>>>> Scott,
>>>>
>>>> That's my very point - that using R and rgbif should be the best path
>>>> to take in this case, both because of the easier access to the GBIF API
>>>> provided by rgbif and the HUGE data analytical capabilities of R itself. I
>>>> had been working on a paper discussing this in the context of conservation
>>>> databases (using R/rgbif and a Red-Listed group of mammals as an exemple),
>>>> but unfortunately this work has been delayed by unexpected health problems.
>>>> Hope it can be the light someday, however.
>>>>
>>>> Best regards,
>>>> Em 09/09/2015 14:44, "Scott Chamberlain" <scott at ropensci.org> escreveu:
>>>>
>>>>> Note that the R client rgbif does interface with the GBIF download API
>>>>> in addition to the search API - making it easier to deal with larger
>>>>> datasets. This works even if you downloaded bulk data from the GBIF GUI.
>>>>> Ignore this if you don't use R :)
>>>>>
>>>>> Best, S
>>>>>
>>>>> On Wed, Sep 9, 2015 at 10:35 AM 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>
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> API-users mailing list
>>>>>>> API-users at lists.gbif.org
>>>>>>> http://lists.gbif.org/mailman/listinfo/api-users
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>>
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>>>>>>
>>>>>
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>>>>>
>>>>>
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>>>>
>>>>
>>>
>>
>>
>> --
>> 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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