Difference between revisions of "NCBI Taxonomy Information"

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== Overview ==
 
== Overview ==
  
NCBI's organismal taxonomy is extensive and widely used.  In the early days this was very crude and systematists used to make fun of it.  But by the later 1990's NCBI had committed itself to a serious taxonomy effort and had recruited systematists to its staff.
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NCBI's organismal taxonomy is extensive and widely used.  In the early days this was very crude and systematists used to make fun of it.  But by the later 1990's NCBI had committed itself to a serious taxonomy effort and had recruited systematists to its staff.
  
 
According to recent [http://www.ncbi.nlm.nih.gov/Taxonomy/txstat.cgi statistics] there are over 43 000 genera and over 170 000 species, assigned to over 15 000 higher taxa.
 
According to recent [http://www.ncbi.nlm.nih.gov/Taxonomy/txstat.cgi statistics] there are over 43 000 genera and over 170 000 species, assigned to over 15 000 higher taxa.
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== Scope and applications ==
 
== Scope and applications ==
  
The NCBI taxonomy covers the taxonomy for cellular organisms (eukaryotes, eubacteria and archaebacteria), as well as viruses.
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The NCBI taxonomy covers the taxonomy for cellular organisms (eukaryotes, eubacteria and archaebacteria), as well as viruses.
  
It includes some ranks (e.g., phylum, class, etc). I think some categories are not ranked.
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It includes some ranks (e.g., phylum, class, etc). I think some categories are not ranked.
  
It also includes information about genetic codes used in different organisms (by cellular compartment, as appropriate).  The distribution (see below) includes the definitions of genetic codes.  
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It also includes information about genetic codes used in different organisms (by cellular compartment, as appropriate).  The distribution (see below) includes the definitions of genetic codes.
  
 
== Representation, availability, status, etc ==
 
== Representation, availability, status, etc ==
  
The entire taxonomy can be downloaded as a relational database dump from NCBI's [ftp://ftp.ncbi.nih.gov/pub/taxonomy/ taxonomy ftp site].
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The entire taxonomy can be downloaded as a relational database dump from NCBI's [ftp://ftp.ncbi.nih.gov/pub/taxonomy/ taxonomy ftp site].
  
The taxonomy is updated continually by a team of researchers at NCBI.  
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The taxonomy is updated continually by a team of researchers at NCBI.
  
The taxonomy is updated only by NCBI, though of course you can write to them if you have an issue.
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The taxonomy is updated only by NCBI, though of course you can write to them if you have an issue.
  
 
== What we can use ==
 
== What we can use ==
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[[Category:Data Resources]]

Latest revision as of 01:25, 3 March 2009

Overview

NCBI's organismal taxonomy is extensive and widely used. In the early days this was very crude and systematists used to make fun of it. But by the later 1990's NCBI had committed itself to a serious taxonomy effort and had recruited systematists to its staff.

According to recent statistics there are over 43 000 genera and over 170 000 species, assigned to over 15 000 higher taxa.

Its easy to link into the taxonomy directly via the web, for instance:

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=drosophila+miranda

Scope and applications

The NCBI taxonomy covers the taxonomy for cellular organisms (eukaryotes, eubacteria and archaebacteria), as well as viruses.

It includes some ranks (e.g., phylum, class, etc). I think some categories are not ranked.

It also includes information about genetic codes used in different organisms (by cellular compartment, as appropriate). The distribution (see below) includes the definitions of genetic codes.

Representation, availability, status, etc

The entire taxonomy can be downloaded as a relational database dump from NCBI's taxonomy ftp site.

The taxonomy is updated continually by a team of researchers at NCBI.

The taxonomy is updated only by NCBI, though of course you can write to them if you have an issue.

What we can use