[Taxacom] recursive SQL database for taxonomy available?

Roderic Page r.page at bio.gla.ac.uk
Tue Jan 14 11:02:21 CST 2014


Hi Kim,

Not sure what you mean by “open source”, do you have a specific license in mind? (licensing data is something of a minefield, none of the options below have an explicit license).

The Catalogue of Life is a MySQL database, the “taxa” table is structured as a list of parent-child relationships (I assume this is what you mean by recursive?). You download the database from http://www.catalogueoflife.org/content/annual-checklist-archive (it’s packaged as a web app, but the data is in a MySQL database).

The GBIF classification is available from http://uat.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c as a Darwin Core Archive (you can import the data into MySQL).

The NCBI taxonomy can also be imported into MySQL (with a little fussing, see http://darwin.zoology.gla.ac.uk/~rpage/tbmap/downloads/ncbi/ for one approach).

Regards

Rod

On 14 Jan 2014, at 16:28, Kim van der Linde <kim at kimvdlinde.com> wrote:

> Hi,
> 
> I am wondering if there is an open source recursive taxonomic SQL (MySQL 
> or other) database available that contains a substantial number of 
> species and higher taxa?
> 
> Kim
> 
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---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
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University of Glasgow
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