Commit 3789dd5b authored by David Trudgian's avatar David Trudgian
Browse files

Project specific readme.txt - replace accidental NCBI taxonomy readme

parent f7316f49
*.dmp files are bcp-like dump from GenBank taxonomy database. Slopetree from Raquel Bromberg - Repo for BioHPC web service project
General information. Some fixes / optimizations added by DCT
Field terminator is "\t|\t" \ No newline at end of file
Row terminator is "\t|\n"
nodes.dmp file consists of taxonomy nodes. The description for each node includes the following
tax_id -- node id in GenBank taxonomy database
parent tax_id -- parent node id in GenBank taxonomy database
rank -- rank of this node (superkingdom, 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
Taxonomy names file (names.dmp):
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, ...)
Divisions file (division.dmp):
division id -- taxonomy database division id
division cde -- GenBank division code (three characters)
division name -- e.g. BCT, PLN, VRT, MAM, PRI...
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
Deleted nodes file (delnodes.dmp):
tax_id -- deleted node id
Merged nodes file (merged.dmp):
old_tax_id -- id of nodes which has been merged
new_tax_id -- id of nodes which is result of merging
Citations file (citations.dmp):
cit_id -- the unique id of citation
cit_key -- citation key
pubmed_id -- unique id in PubMed database (0 if not in PubMed)
medline_id -- unique id in MedLine database (0 if not in MedLine)
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
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