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*.dmp files are bcp-like dump from GenBank taxonomy database.
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General information.
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Field terminator is "\t|\t"
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Row terminator is "\t|\n"
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nodes.dmp file consists of taxonomy nodes. The description for each node includes the following
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fields:
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tax_id -- node id in GenBank taxonomy database
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parent tax_id -- parent node id in GenBank taxonomy database
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rank -- rank of this node (superkingdom, kingdom, ...)
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embl code -- locus-name prefix; not unique
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division id -- see division.dmp file
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inherited div flag (1 or 0) -- 1 if node inherits division from parent
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genetic code id -- see gencode.dmp file
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inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent
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mitochondrial genetic code id -- see gencode.dmp file
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inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent
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GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage
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hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet
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comments -- free-text comments and citations
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Taxonomy names file (names.dmp):
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tax_id -- the id of node associated with this name
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name_txt -- name itself
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unique name -- the unique variant of this name if name not unique
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name class -- (synonym, common name, ...)
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Divisions file (division.dmp):
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division id -- taxonomy database division id
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division cde -- GenBank division code (three characters)
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division name -- e.g. BCT, PLN, VRT, MAM, PRI...
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comments
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Genetic codes file:
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genetic code id -- GenBank genetic code id
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abbreviation -- genetic code name abbreviation
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name -- genetic code name
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cde -- translation table for this genetic code
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starts -- start codons for this genetic code
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Deleted nodes file (delnodes.dmp):
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tax_id -- deleted node id
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Merged nodes file (merged.dmp):
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old_tax_id -- id of nodes which has been merged
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new_tax_id -- id of nodes which is result of merging
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Citations file (citations.dmp):
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cit_id -- the unique id of citation
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cit_key -- citation key
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pubmed_id -- unique id in PubMed database (0 if not in PubMed)
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medline_id -- unique id in MedLine database (0 if not in MedLine)
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url -- URL associated with citation
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text -- any text (usually article name and authors).
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-- The following characters are escaped in this text by a backslash:
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-- newline (appear as "\n"),
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-- tab character ("\t"),
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-- double quotes ('\"'),
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-- backslash character ("\\").
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taxid_list -- list of node ids separated by a single space
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