Taxonomy browser

Taxonomy common tree

Taxonomy information

Taxonomy resources

Genetic codes

Taxonomy Statistics

Taxonomy Name/Id Status Report

Taxonomy FTP site

FAQs

How to reference the NCBI taxonomy database

How to create links to the NCBI taxonomy

How to create LinkOut links from the NCBI taxonomy

Extinct organisms

Recent changes to classification

Linking to the NCBI Taxonomy Database

The link with an organism name looks like:

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

The link with a taxonomy id:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7215

The taxonomy browser displays two kinds of pages - pages that show the classification itself, and pages that show only information about a particular taxon. For a classification page, an argument lvl sets the depth of the display. So, if for example you want to display just the immediate descendants for some taxon, then you have to set lvl=1.

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7215&lvl=1

The default value for this argument is 3. The zero value - lvl=0 forces a taxon display page (even for internal nodes)

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7215&lvl=0

If you want to see the various Entrez databases' record counters on a classification page, you have to use argument p with the name of the Entrez database as an argument like p=nucleotide. Currently the following databases are supported:

Entrez database	Argument p value
Nucleotide	nucleotide
Protein	protein
Structure	structure
Genome	genome
PopSet	popset
SNP	snp
3D Domains	domains
Domains	cdd
GEO Datasets	gds
GEO Expressions	geo
UniGene	unigene
UniSTS	unists
PubMed Central	pmc
Gene	gene
Homologene	homologene

Each counter appears as a hotlink to the right of each taxon. The color of each link is the same as the color of the corresponding database check box text in the grey control area at the top of the page.

There are also links to some useful resources that can appear along with these counters. These links are also enabled using argument p and appear as named hotlinks. Currently this set includes:

Hotlink Name	p value	Resource description
MapView	mapview	NCBI Map Viewer presents a graphical view of several types of genomic maps
LinkOut	has_linkout	LinkOut is NCBI external weblink collection that is designed to provide users with links to a wide variety of relevant web-accessible online resources, including full-text publications, biological databases, consumer health information, research tools, and more. A list of NCBI's current non-bibliographic LinkOut providers can be found here.
BLAST	genome_blast	BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases.
TRACE	trace	Trace Archive contains trace data generated by the sequencing centers and ancillary information to identify those traces.

There could be more than one argument p:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7215&p=structure&p=protein&lvl=2

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=Canidae&p=nucleotide&p=has_linkout

The taxon display page shows you a full lineage by default:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7229

To display only an abbreviated lineage you have to use an argument lin=s:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7229&lin=s

And if you want to display the NCBI Taxonomy browser search page, you could use Taxonomy Browser's url without id and name argument (but you can preset other arguments for the users):

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?p=structure&p=nucleotide&lvl=2

There are few parameters that are obsolete and left in place only for compatibility with older versions of Taxonomy Browser. They turn on and off display of some Entrez sequence counters:

Entrez database	Argument name
Nucleotide	nucl
Protein	prot
Structure	struct
Genome	genome

Given value of 1 these arguments turn display of counter on while value 0 turnes it off.

These arguments could be mixed in any combination:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7215&struct=1&prot=1&lvl=2

as well as mixed with p arguments:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7215&struct=1&prot=1&p=mapview&p=has_linkout&lvl=2