This directory contains the following NCBI Taxonomy database dump files: new_taxdump.zip new_taxdump.tar.Z new_taxdump.tar.gz All these files containes exactly the same information and are arranged so for the convenience of unpacking them on various operating environments. In addition there are files: new_taxdump.zip.md5 new_taxdump.tar.Z.md5 new_taxdump.tar.gz.md5 which contain MD5 sums for the corresponding archive files. These files might be used to check correctness of the download of corresponding archive file. new_taxdump.zip --------------- Is intended for zip-capable utilities such as pkunzip, unzip, and WinZip. These utilities are widely available in almost all operating environments. To unpack it command-line pkunzip and unzip: pkunzip new_taxdump.zip or unzip new_taxdump.zip Note: pkunzip and/or unzip executables must be in the executable search path and new_taxdump.zip must be in the current directory. Files will be unzipped into current directory. For desired dump files placement and more please refer to the manual and/or option descriptions of pkunzip and unzip utilities. new_taxdump.tar.Z ----------------- This file is to be unpacked by uncompress utility and subsequent tar archiver. These utilities are usually used in UNIX-like environment. Unpacking instructions follows: uncompress -c new_taxdump.tar.Z | tar xf - new_taxdump.tar.gz ------------------ This file is to be unpacked by GNU unzip utility and subsequent tar archiver. These utilities are usually used in UNIX-like environment. Unpacking instructions follows: gunzip -c new_taxdump.tar.gz | tar xf - The content of the archive -------------------------- It may look like this: citations.dmp delnodes.dmp division.dmp gencode.dmp typeoftype.dmp merged.dmp names.dmp nodes.dmp host.dmp typematerial.dmp rankedlineage.dmp fullnamelineage.dmp taxidlineage.dmp excludedfromtype.dmp images.dmp readme.txt The readme.txt file gives a brief description of *.dmp files. These files contain taxonomic information and are briefly described below. Each of the files store one record in the single line that are delimited by "\t|\n" (tab, vertical bar, and newline) characters. Each record consists of one or more fields delimited by "\t|\t" (tab, vertical bar, and tab) characters. The brief description of field position and meaning for each file follows. nodes.dmp --------- This file represents taxonomy nodes. The description for each node includes the following fields: tax_id -- node id in GenBank taxonomy database parent tax_id -- parent node id in GenBank taxonomy database rank -- rank of this node (domain, kingdom, ...) embl code -- locus-name prefix; not unique division id -- see division.dmp file inherited div flag (1 or 0) -- 1 if node inherits division from parent genetic code id -- see gencode.dmp file inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent mitochondrial genetic code id -- see gencode.dmp file inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet comments -- free-text comments and citations plastid genetic code id -- see gencode.dmp file inherited PGC flag (1 or 0) -- 1 if node inherits plastid gencode from parent specified_species -- 1 if species in the node's lineage has formal name hydrogenosome genetic code id -- see gencode.dmp file inherited HGC flag (1 or 0) -- 1 if node inherits hydrogenosome gencode from parent names.dmp --------- Taxonomy names file has these fields: tax_id -- the id of node associated with this name name_txt -- name itself unique name -- the unique variant of this name if name not unique name class -- (synonym, common name, ...) division.dmp ------------ Divisions file has these fields: division id -- taxonomy database division id division cde -- GenBank division code (three characters) division name -- e.g. BCT, PLN, VRT, MAM, PRI... comments gencode.dmp ----------- Genetic codes file: genetic code id -- GenBank genetic code id abbreviation -- genetic code name abbreviation name -- genetic code name cde -- translation table for this genetic code starts -- start codons for this genetic code delnodes.dmp ------------ Deleted nodes (nodes that existed but were deleted) file field: tax_id -- deleted node id merged.dmp ---------- Merged nodes file fields: old_tax_id -- id of nodes which has been merged new_tax_id -- id of nodes which is result of merging citations.dmp ------------- Citations file fields: cit_id -- the unique id of citation cit_key -- citation key medline_id -- unique id in MedLine database (0 if not in MedLine) pubmed_id -- unique id in PubMed database (0 if not in PubMed) url -- URL associated with citation text -- any text (usually article name and authors) -- The following characters are escaped in this text by a backslash: -- newline (appear as "\n"), -- tab character ("\t"), -- double quotes ('\"'), -- backslash character ("\\"). taxid_list -- list of node ids separated by a single space typeoftype.dmp -------------- Type material types file fields: type_name -- name of type material type synonyms -- alternative names for type material type nomenclature -- Taxonomic Code of Nomenclature coded by a single letter: -- B - International Code for algae, fungi and plants (ICN), previously Botanical Code, -- P - International Code of Nomenclature of Prokaryotes (ICNP), -- Z - International Code of Zoological Nomenclature (ICZN), -- V - International Committee on Taxonomy of Viruses (ICTV) virus classification. description -- descriptive text host.dmp -------- Theoretical host for organism file fields: tax_id -- node id potential_hosts -- theoretical host list separated by comma ',' typematerial.dmp ---------------- Type material information file fields: tax_id -- node id tax_name -- organism name type material is assigned to type -- type material type (see typeoftype.dmp) identifier -- identifier in type material collection rankedlineage.dmp ----------------- Select ancestor names for well-established taxonomic ranks (species, genus, family, order, class, phylum, kingdom, domain/realm) file fields: tax_id -- node id tax_name -- scientific name of the organism species -- name of a species (coincide with organism name for species-level nodes) genus -- genus name when available family -- family name when available order -- order name when available class -- class name when available phylum -- phylum name when available kingdom -- kingdom name when available domain/realm -- domain/realm name when available fullnamelineage.dmp ---------------- Full name lineage file fields: tax_id -- node id tax_name -- scientific name of the organism lineage -- sequence of sncestor names separated by semicolon ';' denoting nodes' ancestors starting from the most distant one and ending with the immediate one taxidlineage.dmp ---------------- Taxonomy id lineage file fields: tax_id -- node id lineage -- sequence of node ids separated by space denoting nodes' ancestors starting from the most distant one and ending with the immediate one excludedfromtype.dmp -------------------- A set of strains or vouchers determined not be from type material: tax_id -- node id tax_name -- organism name type material is assigned to property -- "not considered type" for strains/vouchers determined to be wrongly assigned -- "not verified as type" for strains/vouchers of uncertain provenance voucher_strain -- strain or voucher id string Organism images file (images.dmp): image_id -- the unique id of image image_key -- image key url -- image URL associated with citation license -- image license attribution -- image attribution source -- source of the image properties -- various image properties separated by semicolon taxid_list -- list of node ids separated by a single space