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
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@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:
Best,Markus
--
Markus DöringSoftware Developer
Global Biodiversity Information Facility (GBIF)
_______________________________________________
On 14 Nov 2016, at 16:42, Köhler Christian <C.Koehler@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
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
Stiftung des öffentlichen Rechts; Direktor: Prof. J. Wolfgang Wägele
Sitz: Bonn
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