New taxonomy files available with lineage, type, and host information


NCBI is now producing a new set of taxonomy files that include the taxonomic lineage of taxa, information on type strains and material, and host information. These files are particularly helpful for people maintaining local installations of NCBI data.

You can download the new archive (new_taxdump.tar.gz) from the taxonomy directory on the FTP site (ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/). The new files are typematerial.dmp, typeoftype.dmp, rankedlineage.dmp, fullnamelineage.dmp,
taxidlineage.dmp, and host.dmp. Please see the readme file for details of the file contents.

The original taxonomy file archive without the new content will remain available under its original name, taxdump.tar.gz. The section below shows the entries for the monkey species Cercopithecus lomamiensis from the new ranked lineage and  type material files.


1191211	|	Cercopithecus lomamiensis	|		|	Cercopithecus	|	Cercopithecidae	|	Primates	|	Mammalia	|	Chordata	|	Metazoa	|	Eukaryota	|

1191211	|	Cercopithecus lomamiensis	|	holotype	|	YPM 14080	|
1191211	|	Cercopithecus lomamiensis	|	holotype	|	YPM MAM 14080	|
1191211	|	Cercopithecus lomamiensis	|	paratype	|	YPM 14189	|
1191211	|	Cercopithecus lomamiensis	|	paratype	|	YPM 14191	|
1191211	|	Cercopithecus lomamiensis	|	paratype	|	YPM 14192	|
1191211	|	Cercopithecus lomamiensis	|	paratype	|	YPM MAM 14189	|
1191211	|	Cercopithecus lomamiensis	|	paratype	|	YPM MAM 14191	|
1191211	|	Cercopithecus lomamiensis	|	paratype	|	YPM MAM 14192	|

Top panel: Ranked lineage for Cercopithecus lomamiensis from rankedlineage.dmp. The ranks are species, genus, family, order, class, phylum, kingdom, and superkingdom. Bottom panel: Type material information from typematerial.dmp. The columns are taxonomy id, name, type designation, collection/repository details.

Tree

 

2 thoughts on “New taxonomy files available with lineage, type, and host information

  1. Pingback: New taxonomy files available with lineage, type, and host information – Science

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