[Taxacom] recursive SQL database for taxonomy available?

Markus Döring mdoering at gbif.org
Tue Jan 14 18:20:03 CST 2014


Hi Kim,
if useful I could also provide a postgresql dump of the GBIF backbone in addition to the dwc archive already available.
We use a parent child relationship in GBIF with an additional nested set index to support quick descendants queries.

best,
Markus



--
Markus Döring
Software Developer
Global Biodiversity Information Facility (GBIF)
mdoering at gbif.org
http://www.gbif.org





On 14 Jan 2014, at 18:02, Roderic Page <r.page at bio.gla.ac.uk> wrote:

> 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
>> 
>> _______________________________________________
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom Archive back to 1992 may be searched with either of these methods:
>> 
>> (1) by visiting http://taxacom.markmail.org
>> 
>> (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>> 
>> Celebrating 26 years of Taxacom in 2013.
>> 
> 
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
> 
> Email: 		r.page at bio.gla.ac.uk
> Tel: 			+44 141 330 4778
> Fax: 		+44 141 330 2792
> Skype: 		rdmpage
> Facebook: 	http://www.facebook.com/rdmpage
> LinkedIn: 	http://uk.linkedin.com/in/rdmpage
> Twitter: 		http://twitter.com/rdmpage
> Blog: 		http://iphylo.blogspot.com
> Home page: 	http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Wikipedia: 	http://en.wikipedia.org/wiki/Roderic_D._M._Page
> Citations: 	http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> ORCID: 		http://orcid.org/0000-0002-7101-9767
> 
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom Archive back to 1992 may be searched with either of these methods:
> 
> (1) by visiting http://taxacom.markmail.org
> 
> (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> Celebrating 26 years of Taxacom in 2013.
> 




More information about the Taxacom mailing list