[API-users] Backbone data as SQL

[godfoder]

I convert the backbone to an elasticsearch index for taxon name matching 
at iDigBio. The code is public, but not particularly built for re-use. I 
also pre-process the backbone files to enforce sorting on id/coreid, 
which makes the extension matching code easier to write.

https://github.com/iDigBio/idb-backend/blob/master/idb/data_tables/build_taxon_index.py

It could probably be fairly easily adapted to another search engine or 
NoSQL database that can handle nested JSON structures if SQL is not a 
hard and fast requirement.

- Alex

On 11/14/2016 11:40 AM, Scott Chamberlain wrote:
> Hi Chris, I started something a while back to automate building a 
> SQLite version of the backbone taxonomy 
> (https://github.com/ropensci/gbif-backbone-sql) but it's not quite 
> done yet. Idea is to run on Heroku (e.g., once a day), resulting in a 
> fresh SQLite version of the backbone taxonomy on Amazon S3.
>
> Scott
>
> On Mon, Nov 14, 2016 at 7:50 AM Markus Döring <mdoering at gbif.org 
> <mailto:mdoering at gbif.org>> wrote:
>
>     Hi Chris,
>     the latest GBIF backbone is always available as a Darwin Core
>     archive. This is mostly a collection of tab delimited text files
>     with the accepted and synonym names at its core.
>     You can find the latest and previous, archived versions here:
>     http://rs.gbif.org/datasets/backbone/
>
>     Best,
>     Markus
>
>
>     --
>     Markus Döring
>     Software Developer
>     Global Biodiversity Information Facility (GBIF)
>     mdoering at gbif.org <mailto:mdoering at gbif.org>
>     http://www.gbif.org
>
>
>
>
>
>>     On 14 Nov 2016, at 16:42, Köhler Christian <C.Koehler at zfmk.de
>>     <mailto:C.Koehler at zfmk.de>> wrote:
>>
>>     Hi,
>>
>>     we are developing an application to curate taxonomic and
>>     morphological
>>     data for scientists. At the moment we are evaluating different
>>     taxonomic
>>     backbones to be used within our application. The GIBF taxonomic
>>     backbone
>>     seems to be an good choice in regards to quality, number of
>>     entries and
>>     acceptance.
>>
>>     Due to the nature of our application, a web service to browse the
>>     taxonomy will not fulfil our requirements. A local copy of the
>>     GIBF data
>>     as SQL would be an ideal solution. I looked for this data publicly
>>     available to no avail.  "Harvesting" the GBIF rest api seems not
>>     a good
>>     option. Are there plans to provide current taxonomic backbone data in
>>     the future? Maybe the data is already available, but I failed to
>>     find it
>>     yet.
>>
>>     Regards
>>     Chris
>>
>>     --
>>     Christian Köhler
>>     Tel.: 0228 9122-434
>>
>>     Zoologisches Forschungsmuseum Alexander Koenig
>>     Leibniz-Institut für Biodiversität der Tiere
>>     Adenauerallee 160, 53113 Bonn, Germany
>>     www.zfmk.de <http://www.zfmk.de>
>>
>>     Stiftung des öffentlichen Rechts
>>     Direktor: Prof. J. Wolfgang Wägele
>>     Sitz: Bonn
>>     --
>>     Zoologisches Forschungsmuseum Alexander Koenig
>>     - Leibniz-Institut für Biodiversität der Tiere -
>>     Adenauerallee 160, 53113 Bonn, Germany
>>     www.zfmk.de <http://www.zfmk.de>
>>
>>     Stiftung des öffentlichen Rechts; Direktor: Prof. J. Wolfgang Wägele
>>     Sitz: Bonn
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