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 > _______________________________________________ > API-users mailing list > API-users at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/api-users > > > > -- > Dr. Mauro J. Cavalcanti > E-mail: maurobio at gmail.com > Web: http://sites.google.com/site/maurobio > _______________________________________________ > API-users mailing list > API-users at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/api-users > > > > _______________________________________________ > API-users mailing list > API-users at lists.gbif.org > http://lists.gbif.org/mailman/listinfo/api-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.gbif.org/pipermail/api-users/attachments/20160531/419cec00/attachment.html>
