Hi Christian,

 

I’ve written a small Python script that runs through the DarwinCore archive Markus mentioned, extracts a given list of terms (taxon, vernacular names, but can be extended) and writes bulk files that can be loaded into SQL Server. It’s lacking any documentation (apart from some inline comments), since I’ve only used it internally. But if you’re familiar with Python, it’s probably easy to adapt to MySQL’s format.

Just let me know if you want to give it a try.

 

Cheers,

Jörg

 

Von: API-users [mailto:api-users-bounces@lists.gbif.org] Im Auftrag von Köhler Christian
Gesendet: Mittwoch, 16. November 2016 11:01
An: api-users@lists.gbif.org
Betreff: Re: [API-users] Backbone data as SQL

 

Hi,

I already looked at both of the git project. Looks interesting. Is I am more "pythonic" the idb-backend is easier to adapt for me.
Thanks for showing me. I was hoping that someone already addressed the question as it seemed to me quite obviously to provide the data in a widely used format like sql. I have the feeling I am reenventing the wheel ;-)

The "B-HIT" tool seems to be a reasonable alternative to get a the desired data into an sql data base. In case you are interested, have a look here:
https://www.researchgate.net/publication/283543150_B-HIT_-_A_Tool_for_Harvesting_and_Indexing_Biodiversity_Data
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636251/

Cheers
Chris


Am 14.11.2016 um 17:40 schrieb Scott Chamberlain:

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 Döring

Software 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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-- 
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