[API-users] Backbone data as SQL

[Mauro Cavalcanti]

Dear ALL,

I have developed a tool for harvesting biodiversity data from several
sources (including, of course, GBIF) and consolidating them into a
local database for further analyses. It is probably similar to B-HIT,
although simpler. The tool is a cross-platform desktop application,
written in Python and using the Qt GUI library. Several DBMS other
than MySQL  (Postgres, MariaDB, SQLite, Firebird) are supported. It
currently uses the Acacia database scheme
(http://sites.google.com/site/acaciadb), but could be easily adapted
to any other existing or ad-hoc scheme. It can be found on my GitHub
repository (https://github.com/maurobio/feronia).

Hope this helps.

Best regards,

2016-11-16 8:01 GMT-02:00 Köhler Christian <C.Koehler at zfmk.de>:
> 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 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
>> http://www.gbif.org
>>
>>
>>
>>
>>
>> On 14 Nov 2016, at 16:42, Köhler Christian <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
>>
>> 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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>> API-users at lists.gbif.org
>> http://lists.gbif.org/mailman/listinfo/api-users
>>
>>
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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
>
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>



-- 
Dr. Mauro J. Cavalcanti
E-mail: maurobio at gmail.com
Web: http://sites.google.com/site/maurobio
"Life is complex. It consists of real and imaginary parts."