Linking to the NCBI Taxonomy Database

You can make the links to NCBI taxonomy browser using either organism name or taxonomy id.

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

Comments and questions to [email protected]

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