[Taxacom] recursive SQL database for taxonomy available?

Kim van der Linde kim at kimvdlinde.com
Tue Jan 14 12:03:46 CST 2014


Hi Rod,

Thank you very helpful. Yes, each taxon has a code, and a parent code.

Which of the databases would you say is the most accurate?

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/ 
> <http://darwin.zoology.gla.ac.uk/%7Erpage/tbmap/downloads/ncbi/> for 
> one approach).
>
> Regards
>
> Rod
>
> On 14 Jan 2014, at 16:28, Kim van der Linde <kim at kimvdlinde.com 
> <mailto: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 <mailto:r.page at bio.gla.ac.uk>
> Tel:+44 141 330 4778
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> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
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> ORCID:http://orcid.org/0000-0002-7101-9767
>




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