[API-users] Is there any NEO4J or graph-based driver for this API ?

Tue May 31 18:26:22 CEST 2016

Matthew,

As a matter of fact, I have already developed such a tool - it is called
"Feronia" and is a program written in Python that uses several available
software libraries for downloading data from online databases that provided
API's (including, of course, GBIF). This tool downloads data into a
relational database using a generic schema I have devised (
http://sites.google.com/site/acaciadb). Exemples of databases already
implemented using this tool can be found here: http://coralfish.netne.net
and neocop2.biotupe.com

Feronia is not already available but I will make it available on GitHub
ASAP.

Hope this helps.

Best regards,

--
Dr. Mauro J. Cavalcanti
E-mail: maurobio at gmail.com
Web: http://sites.google.com/site/maurobio
Em 31/05/2016 13:02, "Collins, Matthew" <mcollins at acis.ufl.edu> escreveu:

> Jorrit pointed out this thread to us at iDigBio. Downloading and importing
> data into a relational database will work great, especially if as Jan said
> you can cut the data size down to a reasonable amount.
>
>
> Another approach we've been working on in a collaboration called GUODA
> [1] is to build an Apache Spark environment with pre-formatted data frames
> with common data sets in them for researchers to use. This approach would
> offer a remote service where you could write arbitrary Spark code,
> probably in Jupyter notebooks, to iterate over data. Spark does a lot of
> cool stuff including GraphX which might be of interest. This is definitely
> pre-alpha at this point and if anyone is interested, I'd like to hear your
> thoughts. I'll also be at SPNHC talking about this.
>
>
> One thing we've found in working on this is that importing data into a
> structured data format isn't always easy. If you only want a few columns,
> it'll be fine. But getting the data typing, format standardization, and
> column name syntax of the whole width of an iDigBio record right requires
> some code. I looked to see if EcoData Retriever [2] had a GBIF data
> source and they have an eBird one that perhaps you might find useful as a
> starting point if you wanted to try to use someone else's code to download
> and import data.
>
>
> For other data structures like BHL, we're kind of making stuff up since
> we're packaging a relational structure and not something nearly as flat as
> GBIF and DWC stuff.
>
>
> [1] http://guoda.bio/
>
> [2] http://www.ecodataretriever.org/
>
>
> Matthew Collins
> Technical Operations Manager
> Advanced Computing and Information Systems Lab, ECE
> University of Florida
> 352-392-5414 <callto:352-392-5414>
> ------------------------------
> *From:* jorrit poelen <jhpoelen at xs4all.nl>
> *Sent:* Monday, May 30, 2016 11:16 AM
> *To:* Collins, Matthew; Thompson, Alexander M; Hammock, Jennifer
> *Subject:* Fwd: [API-users] Is there any NEO4J or graph-based driver for
> this API ?
>
> Hey y’all:
>
> Interesting request below on the GBIF mailing list - sounds like a perfect
> fit for the GUODA use cases.
>
> Would it be too early to jump onto this thread and share our
> efforts/vision?
>
> thx,
> -jorrit
>
> Begin forwarded message:
>
> *From: *Jan Legind <jlegind at gbif.org>
> *Subject: **Re: [API-users] Is there any NEO4J or graph-based driver for
> this API ?*
> *Date: *May 30, 2016 at 5:48:51 AM PDT
> *To: *Mauro Cavalcanti <maurobio at gmail.com>, "Juan M. Escamilla Molgora" <
> j.escamillamolgora at lancaster.ac.uk>
> *Cc: *"api-users at lists.gbif.org" <api-users at lists.gbif.org>
>
> Dear Juan,
>
> Unfortunately we have no tool for creating these kind of SQL like queries
> to the portal. I am sure you are aware that the filters in the occurrence
> search pages can be applied in combination in numerous ways. The API can go
> even further in this regard[1], but it not well suited for retrieving
> occurrence records since there is a 200.000 records ceiling making it unfit
> for species exceeding this number.
>
> There is going be updates to the pygbif package[2] in the near future that
> will enable you to launch user downloads programmatically where a whole
> list of different species can be used as a query parameter as well as
> adding polygons.[3]
>
> In the meantime, Mauro’s suggestion is excellent. If you can narrow your
> search down until it returns a manageable download (say less than 100
> million records), importing this into a database should be doable. From
> there, you can refine using SQL queries.
>
> Best,
> Jan K. Legind, GBIF Data manager
>
> [1] http://www.gbif.org/developer/occurrence#search
> [2] https://github.com/sckott/pygbif
> [3] https://github.com/jlegind/GBIF-downloads
>
> *From:* API-users [mailto:api-users-bounces at lists.gbif.org
> <api-users-bounces at lists.gbif.org>] *On Behalf Of *Mauro Cavalcanti
> *Sent:* 30. maj 2016 14:06
> *To:* Juan M. Escamilla Molgora
> *Cc:* api-users at lists.gbif.org
> *Subject:* Re: [API-users] Is there any NEO4J or graph-based driver for
> this API ?
>
>
> Hi,
>
> One solution I have successfully adopted for this is to download the
> records (either "manually" via browser or, yet better, using a Python
> script using the fine pygbif library), storing them into a MySQL or SQLite
> database and then perform the relational queries. I can provide examples if
> you are interested.
> Best regards,
>
> 2016-05-30 8:59 GMT-03:00 Juan M. Escamilla Molgora <
> j.escamillamolgora at lancaster.ac.uk>:
> Hola,
>
> Is there any API for making relational queries like taxonomy, location or
> timestamp?
>
> Thank you and best wishes
>
> Juan
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>
>
>
> --
> Dr. Mauro J. Cavalcanti
> E-mail: maurobio at gmail.com
> Web: http://sites.google.com/site/maurobio
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