[Taxacom] recursive SQL database for taxonomy available?

Roderic Page r.page at bio.gla.ac.uk
Wed Jan 15 03:05:31 CST 2014


Hi Kim,

Regarding your earlier question of “accuracy”, I’m not sure how you would measure this (I regard classifications as navigation tools, not as estimates of something “real”). Perhaps you mean how well it reflects current phylogenetics?

Regarding ranks, GBIF is restricted to typical phylum, class, order, family, genus, species, and subspecies. The NCBI database has more levels, including tribes for some taxa such as insects. It is substantially less complete than GBIF (a consequence of the different goals of the two databases).

Regards

Rod

On 15 Jan 2014, at 01:49, Kim van der Linde <kim at kimvdlinde.com> wrote:

> Rod,
> 
> Does any of the databases include super and sub families, tribes, and 
> other ranks other than regnum, phylum, ordo, familia, genus and (sub) 
> species?
> 
> Kim
> 
> On 1/14/2014 12:02 PM, Roderic Page 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
>>> 
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>> ---------------------------------------------------------
>> 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.
>> 
> 
> 
> _______________________________________________
> 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




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