NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Taxonomy Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2011-.

Cover of Taxonomy Help

Taxonomy Help [Internet].

Show details

Frequently Asked Questions

Created: ; Last Update: May 10, 2011.

How do I find all of the species in GenBank that belong to a particular group?

You can use Entrez queries to find taxa of a particular rank in a given lineage, e.g.:

Amphibia[subtree] AND species[rank]

You can restrict the output of this list to species with formal Linnaean binomial names:

Amphibia[subtree] AND species[rank] AND specified[prop]

To download the list of species names (1) click ‘Send to’ (2) select ‘File’ (3) switch Format to ‘Taxon name’ and (4) click ‘Create File’. This will create a file named “taxonomy_result” in your download directory.

How can I tell when new species appear in GenBank?

You can register with MyNCBI to get ‘What’s New’ email updates for any Entrez query. For example, if you are interested in amphibian species you can execute the Entrez query:

Amphibia[subtree] AND species[rank] AND specified[prop]

Click the ‘Save search’ hotlink above the Entrez search box to receive email updates whenever this query retrieves something new. There is documentation here –

http://www.ncbi.nlm.nih.gov/books/NBK3843

and some tutorials here –

http://www.nlm.nih.gov/bsd/disted/pubmed.html

http://www.nlm.nih.gov/bsd/viewlet/myncbi/saving_searches.html

How can I track the status of a list of taxa in the GenBank taxonomy?

If you have a list of taxa that are of interest to you, you can upload it (or copy and paste) to the Name/ID Status page – this will tell you which taxa are listed in our database, and whether they are primary or secondary names (synonyms, misspellings, etc.) You can track changes in the GenBank taxonomy by saving a copy of the status report, and comparing it with the status report for the same list of taxa at a later date.

Are taxids stable?

Taxids are assigned sequentially as taxa are added to the taxonomy database, and are never reused for a different taxon once they have been assigned. When two taxa are determined to be synonymous they are merged, and the taxid that disappears becomes a ‘secondary’ taxid for the one that remains. Taxa are occasionally removed from the taxonomy database (particularly internal nodes, during a taxonomic revision) – these taxids are deleted, and are not reused. Lists of merged and deleted taxids are included in the taxonomy dump files on the ftp site.

The public web pages at the NCBI only show taxa that are linked to public sequence entries. If a taxid is linked to a public sequence entry that is later removed, or assigned to a different taxon, the corresponding taxid may disappear from the NCBI web pages without appearing in either the merged or deleted taxid list.

Bookshelf ID: NBK54428

Views

Other titles in this collection

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...