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ktym/taxdump2owl.rb

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INSDC (NCBI) taxdump to OWL converter
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taxdump2owl.rb
#!/usr/bin/env ruby
#
# Taxonomy ontology generator
#
# Copyright (C) 2013, 2014 Toshiaki Katayama <ktym@dbcls.jp>
#
# Version: Jan 29, 2014
#
# Usage:
#
# % wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
# % mkdir taxdump
# % tar --directory=taxdump -xvf taxdump.tar.gz
# % ruby taxdump2owl.rb > taxdump.owl 2> taxcite.ttl
#
module TurtleHelper
def quote(str)
return str.gsub('\\', '\\\\').gsub("\e", '\\e').gsub("\b", '\\b').gsub("\f", '\\f').gsub("\t", '\\t').gsub("\n", '\\n').gsub("\r", '\\r').gsub('"', '\\"').inspect
end
def triple(s, p, o)
return [s, p, o].join("\t") + " ."
end
end
module TaxonomyOntology
PREFIX = [
"@base <http://ddbj.nig.ac.jp/ontologies/taxonomy/> .",
"@prefix : <> .",
"@prefix owl: <http://www.w3.org/2002/07/owl#> .",
"@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .",
"@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .",
"@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .",
#"@prefix dcterms: <http://purl.org/dc/terms/> .",
#"@prefix sio: <http://semanticscience.org/resource#> .",
#"@prefix so: <http://purl.org/obo/owl/SO#> .",
#"@prefix obo: <http://purl.obolibrary.org/obo/> .",
#"@prefix faldo: <http://biohackathon.org/resource/faldo#> .",
#"@prefix taxo: <http://taxonomyontology.org/ontology#> .",
#"@prefix taxo: <http://insdc.org/owl/taxonomy#> .",
"@prefix taxid: <http://identifiers.org/taxonomy/> .",
"@prefix taxncbi: <http://www.ncbi.nlm.nih.gov/taxonomy/> .",
#"@prefix codon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#> .",
#"@prefix pmid: <http://pubmed.org/> .",
"@prefix pubmed: <http://identifiers.org/pubmed/> .",
]
ONTOLOGY = <<"END_OF_ONTOLOGY"
# Taxonomy ontology
<>
a owl:Ontology ;
rdfs:comment "Taxonomy ontology generated from NCBI taxdump files" ;
owl:versionInfo "#{Time.now.strftime('%Y-%m-%d')}"^^xsd:date .
# properties
:rank
a owl:ObjectProperty, owl:FunctionalProperty ;
rdfs:label "Taxonomy rank" ;
rdfs:domain :Taxon ;
rdfs:range :Rank .
:merged
a owl:ObjectProperty ;
rdfs:label "Previous taxon ID" ;
rdfs:domain :Taxon ;
rdfs:range :Taxon .
:citation
a owl:ObjectProperty ;
rdfs:label "Citation node" ;
rdfs:domain :Taxon ;
rdfs:range rdfs:Resource .
:citationPubMed
a owl:ObjectProperty ;
rdfs:label "Citation PubMed ID" ;
rdfs:domain :Taxon ;
rdfs:range rdfs:Resource .
:citationURL
a owl:DatatypeProperty ;
rdfs:label "Citation URL" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:citationKey
a owl:DatatypeProperty ;
rdfs:label "Citation key" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:citationText
a owl:DatatypeProperty ;
rdfs:label "Citation text" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:geneticCode
a owl:ObjectProperty, owl:FunctionalProperty ;
rdfs:label "Genetic code" ;
rdfs:domain :Taxon ;
rdfs:range :GeneticCode .
:geneticCodeMt
a owl:ObjectProperty, owl:FunctionalProperty ;
rdfs:label "Mitochondrial genetic code" ;
rdfs:domain :Taxon ;
rdfs:range :GeneticCode .
# properties (taxdump/names.dmp)
:name
a owl:DatatypeProperty ;
rdfs:label "name" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:scientificName
a owl:DatatypeProperty, owl:FunctionalProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "scientific name" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:authority
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "authority" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:synonym
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "synonym" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:preferredSynonym
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "preferred synonym" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:acronym
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "acronym" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:preferredAcronym
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "preferred acronym" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:anamorph
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "anamorph" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:teleomorph
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "teleomorph" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:misnomer
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "misnomer" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:commonName
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "common name" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:preferredCommonName
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "preferred common name" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:inPart
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "in-part" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:includes
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "includes" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:equivalentName
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "equivalent name" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:misspelling
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "misspelling" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:typeMaterial
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "type material" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:genbankAcronym
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "genbank acronym" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:genbankAnamorph
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "genbank anamorph" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:genbankCommonName
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "genbank common name" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:genbankSynonym
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "genbank synonym" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:blastName
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "blast name" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
:uniqueName
a owl:DatatypeProperty ;
rdfs:subPropertyOf :name ;
rdfs:label "unique name" ;
rdfs:domain :Taxon ;
rdfs:range xsd:string .
# classes (taxdump/nodes.dmp)
:Taxon
a owl:Class ;
rdfs:label "taxon" .
:Rank
a owl:Class ;
rdfs:label "rank" .
:Class
a :Rank ;
rdfs:label "class" .
:Family
a :Rank ;
rdfs:label "family" .
:Forma
a :Rank ;
rdfs:label "forma" .
:Genus
a :Rank ;
rdfs:label "genus" .
:Infraclass
a :Rank ;
rdfs:label "infraclass" .
:Infraorder
a :Rank ;
rdfs:label "infraorder" .
:Kingdom
a :Rank ;
rdfs:label "kingdom" .
:NoRank
a :Rank ;
rdfs:label "no rank" .
:Order
a :Rank ;
rdfs:label "order" .
:Parvorder
a :Rank ;
rdfs:label "parvorder" .
:Phylum
a :Rank ;
rdfs:label "phylum" .
:Species
a :Rank ;
rdfs:label "species" .
:SpeciesGroup
a :Rank ;
rdfs:label "species group" .
:SpeciesSubgroup
a :Rank ;
rdfs:label "species subgroup" .
:Subclass
a :Rank ;
rdfs:label "subclass" .
:Subfamily
a :Rank ;
rdfs:label "subfamily" .
:Subgenus
a :Rank ;
rdfs:label "subgenus" .
:Subkingdom
a :Rank ;
rdfs:label "subkingdom" .
:Suborder
a :Rank ;
rdfs:label "suborder" .
:Subphylum
a :Rank ;
rdfs:label "subphylum" .
:Subspecies
a :Rank ;
rdfs:label "subspecies" .
:Subtribe
a :Rank ;
rdfs:label "subtribe" .
:Superclass
a :Rank ;
rdfs:label "superclass" .
:Superfamily
a :Rank ;
rdfs:label "superfamily" .
:Superkingdom
a :Rank ;
rdfs:label "superkingdom" .
:Superorder
a :Rank ;
rdfs:label "superorder" .
:Superphylum
a :Rank ;
rdfs:label "superphylum" .
:Tribe
a :Rank ;
rdfs:label "tribe" .
:Varietas
a :Rank ;
rdfs:label "varietas" .
# classes (taxdump/gencode.dmp)
:GeneticCode
a owl:Class ;
rdfs:label "Genetic code" .
:GeneticCode0
a :GeneticCode ;
rdfs:label "Unspecified" .
:GeneticCode1
a :GeneticCode ;
rdfs:label "Standard" .
:GeneticCode2
a :GeneticCode ;
rdfs:label "Vertebrate Mitochondrial" .
:GeneticCode3
a :GeneticCode ;
rdfs:label "Yeast Mitochondrial" .
:GeneticCode4
a :GeneticCode ;
rdfs:label "Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma" .
:GeneticCode5
a :GeneticCode ;
rdfs:label "Invertebrate Mitochondrial" .
:GeneticCode6
a :GeneticCode ;
rdfs:label "Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear" .
:GeneticCode9
a :GeneticCode ;
rdfs:label "Echinoderm Mitochondrial; Flatworm Mitochondrial" .
:GeneticCode10
a :GeneticCode ;
rdfs:label "Euplotid Nuclear" .
:GeneticCode11
a :GeneticCode ;
rdfs:label "Bacterial, Archaeal and Plant Plastid" .
:GeneticCode12
a :GeneticCode ;
rdfs:label "Alternative Yeast Nuclear" .
:GeneticCode13
a :GeneticCode ;
rdfs:label "Ascidian Mitochondrial" .
:GeneticCode14
a :GeneticCode ;
rdfs:label "Alternative Flatworm Mitochondrial" .
:GeneticCode15
a :GeneticCode ;
rdfs:label "Blepharisma Macronuclear" .
:GeneticCode16
a :GeneticCode ;
rdfs:label "Chlorophycean Mitochondrial" .
:GeneticCode21
a :GeneticCode ;
rdfs:label "Trematode Mitochondrial" .
:GeneticCode22
a :GeneticCode ;
rdfs:label "Scenedesmus obliquus Mitochondrial" .
:GeneticCode23
a :GeneticCode ;
rdfs:label "Thraustochytrium Mitochondrial" .
:GeneticCode24
a :GeneticCode ;
rdfs:label "Pterobranchia Mitochondrial" .
:GeneticCode25
a :GeneticCode ;
rdfs:label "Candidate Division SR1 and Gracilibacteria" .
# taxonomy
END_OF_ONTOLOGY
NAME_PROPERTY = {
"scientific name" => "scientificName",
"authority" => "authority",
"synonym" => "synonym",
"preferred synonym" => "preferredSynonym",
"acronym" => "acronym",
"preferred acronym" => "preferredAcronym",
"anamorph" => "anamorph",
"teleomorph" => "teleomorph",
"misnomer" => "misnomer",
"common name" => "commonName",
"preferred common name" => "preferredCommonName",
"in-part" => "inPart",
"includes" => "includes",
"equivalent name" => "equivalentName",
"misspelling" => "misspelling",
"type material" => "typeMaterial",
"genbank acronym" => "genbankAcronym",
"genbank anamorph" => "genbankAnamorph",
"genbank common name" => "genbankCommonName",
"genbank synonym" => "genbankSynonym",
"blast name" => "blastName",
}
RANK_CLASS = {
"class" => "Class",
"family" => "Family",
"forma" => "Forma",
"genus" => "Genus",
"infraclass" => "Infraclass", # Not defined in UniProt
"infraorder" => "Infraorder", # Not defined in UniProt
"kingdom" => "Kingdom",
"no rank" => "NoRank", # Not defined in UniProt
"order" => "Order",
"parvorder" => "Parvorder",
"phylum" => "Phylum",
"species" => "Species",
"species group" => "SpeciesGroup", # Species_Group in UniProt
"species subgroup" => "SpeciesSubgroup", # Species_Subgroup in UniProt
"subclass" => "Subclass",
"subfamily" => "Subfamily",
"subgenus" => "Subgenus",
"subkingdom" => "Subkingdom",
"suborder" => "Suborder",
"subphylum" => "Subphylum",
"subspecies" => "Subspecies",
"subtribe" => "Subtribe",
"superclass" => "Superclass",
"superfamily" => "Superfamily",
"superkingdom" => "Superkingdom",
"superorder" => "Superorder",
"superphylum" => "Superphylum",
"tribe" => "Tribe",
"varietas" => "Varietas",
}
class Name
attr_reader :name, :unique_name, :name_class
def initialize(name, unique_name, name_class)
@name = name
@unique_name = unique_name
@name_class = name_class
end
def property
NAME_PROPERTY[@name_class]
end
def scientific_name?
@name_class == "scientific name"
end
def unique_variant?
@unique_name.length > 0
end
end
class Citation
attr_reader :pmid, :url, :key, :text
def initialize(pmid, url, key, text)
@pmid = pmid.to_i > 0 ? pmid : nil
@url = url.length > 0 ? url : nil
@key = key.length > 0 ? key : nil
@text = text.length > 0 ? text : nil
end
end
class Parser
def initialize(filename)
$stderr.puts "Loading #{filename} ..." if $DEBUG
@filename = filename
@hash = {}
parse
end
def [](key)
@hash[key]
end
def dmp_split(str)
str.encode!("UTF-8", "CP1250", :invalid => :replace, :undef => :replace, :replace => "?")
ary = str.sub(/\|$/, '').split(/\t\|\t/)
return ary.map{|x| x.strip}
end
end
## taxdump/citations.dmp
class CitationsParser < Parser
def parse
File.open(@filename).each do |line|
cit_id, cit_key, pubmed_id, medline_id, url, text, taxid_list, = *dmp_split(line)
next if (pubmed_id + url + cit_key + text).empty?
citation = Citation.new(pubmed_id, url, cit_key, text)
taxid_list.split(/\s+/).each do |tax_id|
@hash[tax_id] ||= []
@hash[tax_id] << citation
end
end
end
end
## taxdump/merged.dmp
class MergedParser < Parser
def parse
File.open(@filename).each do |line|
old_tax_id, new_tax_id, = *dmp_split(line)
@hash[new_tax_id] ||= []
@hash[new_tax_id] << old_tax_id
end
end
end
## taxdump/names.dmp
class NamesParser < Parser
def parse
File.open(@filename).each do |line|
tax_id, name_txt, unique_name, name_class, = *dmp_split(line)
name = Name.new(name_txt, unique_name, name_class)
@hash[tax_id] ||= []
if name.scientific_name?
@hash[tax_id].unshift name
else
@hash[tax_id] << name
end
end
end
end
## taxdump/nodes.dmp
class TaxdumpParser < Parser
include TurtleHelper
def initialize(hash = {:nodes => "nodes.dmp", :names => "names.dmp", :merged => "merged.dmp", :citations => "citations.dmp"})
output_header
@citations = CitationsParser.new(hash[:citations])
@merged = MergedParser.new(hash[:merged])
@names = NamesParser.new(hash[:names])
super(hash[:nodes])
end
def output_header
$stderr.puts "@prefix : <http://ddbj.nig.ac.jp/ontologies/taxonomy#> ."
$stderr.puts "@prefix taxid: <http://identifiers.org/taxonomy/> .",
$stderr.puts
puts PREFIX
puts ONTOLOGY
end
def parse
File.open(@filename).each do |line|
tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, = *dmp_split(line)
tax = "taxid:#{tax_id}"
puts triple(tax, "a", ":Taxon")
puts triple(tax, "rdfs:subClassOf", "taxid:#{parent_tax_id}") if tax_id != parent_tax_id
puts triple(tax, "rdfs:seeAlso", "taxncbi:#{tax_id}")
puts triple(tax, ":rank", ":#{RANK_CLASS[rank]}")
puts triple(tax, ":geneticCode", ":GeneticCode#{genetic_code_id}")
puts triple(tax, ":geneticCodeMt", ":GeneticCode#{mitochondrial_genetic_code_id}")
if @names[tax_id]
@names[tax_id].each do |name|
if name.scientific_name?
puts triple(tax, "rdfs:label", quote(name.name))
end
puts triple(tax, ":#{NAME_PROPERTY[name.name_class]}", quote(name.name))
if name.unique_variant?
puts triple(tax, ":uniqueName", quote(name.unique_name))
end
end
end
if @citations[tax_id]
@citations[tax_id].each do |citation|
pairs = []
pairs << ":citationPubMed pubmed:#{citation.pmid}" if citation.pmid
pairs << ":citationURL #{quote(citation.url)}" if citation.url
pairs << ":citationKey #{quote(citation.key)}" if citation.key
pairs << ":citationText #{quote(citation.text)}" if citation.text
#puts triple(tax, ":citation", "[ #{pairs.join(' ; ')} ]")
$stderr.puts triple(tax, ":citation", "[ #{pairs.join(' ; ')} ]")
end
end
if @merged[tax_id]
@merged[tax_id].each do |old_tax_id|
puts triple(tax, ":merged", "taxid:#{old_tax_id}")
end
end
end
end
end
end
nodes_dmp = ARGV.shift || "taxdump/nodes.dmp"
names_dmp = ARGV.shift || "taxdump/names.dmp"
merged_dmp = ARGV.shift || "taxdump/merged.dmp"
citations_dmp = ARGV.shift || "taxdump/citations.dmp"
TaxonomyOntology::TaxdumpParser.new(
:nodes => nodes_dmp,
:names => names_dmp,
:merged => merged_dmp,
:citations => citations_dmp
)
=begin
* NCBI (taxdump.tar.gz)
nodes.dmp file consists of 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 (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
1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
562 | 561 | species | EC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
511145 | 83333 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
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, ...)
1 | all | | synonym |
1 | root | | scientific name |
562 | "Bacillus coli" Migula 1895 | | authority |
562 | "Bacterium coli commune" Escherich 1885 | | authority |
562 | "Bacterium coli" (Migula 1895) Lehmann and Neumann 1896 | | authority |
562 | ATCC 11775 | | type material |
562 | Bacillus coli | | synonym |
562 | Bacterium coli | | synonym |
562 | Bacterium coli commune | | synonym |
562 | CCUG 24 | | type material |
562 | CCUG 29300 | | type material |
562 | CIP 54.8 | | type material |
562 | DSM 30083 | | type material |
562 | Enterococcus coli | | synonym |
562 | Escherchia coli | | misspelling |
562 | Escherichia coli | | scientific name |
562 | Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | | authority |
562 | Escherichia coli retron Ec107 | | includes |
562 | Escherichia coli retron Ec67 | | includes |
562 | Escherichia coli retron Ec79 | | includes |
562 | Escherichia coli retron Ec86 | | includes |
562 | Eschericia coli | | misspelling |
562 | JCM 1649 | | type material |
562 | LMG 2092 | | type material |
562 | NBRC 102203 | | type material |
562 | NCCB 54008 | | type material |
562 | NCTC 9001 | | type material |
562 | bacterium 10a | | includes |
562 | bacterium E3 | | synonym |
511145 | Escherichia coli MG1655 | | synonym |
511145 | Escherichia coli str. K-12 substr. MG1655 | | scientific name |
511145 | Escherichia coli str. K12 substr. MG1655 | | equivalent name |
511145 | Escherichia coli str. MG1655 | | equivalent name |
511145 | Escherichia coli strain MG1655 | | equivalent name |
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
9620 | Martinez-Murcia AJ et al. (1999) | 0 | 10319482 | | Martinez-Murcia, A.J., Anton, A.I., Rodriguez-Valera, F. \"Patterns of sequence variation in two regions of the 16S rRNA multigene family of Escherichia coli.\" Int. J. Syst. Bacteriol. (1999) 49:601-610. | 562 |
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
662101 | 562 |
662104 | 562 |
Genetic codes file (gencode.dmp):
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
* EBI (taxonomy.dat)
ID : 1
PARENT ID : 0
RANK : no rank
GC ID : 1
SCIENTIFIC NAME : root
SYNONYM : all
//
ID : 562
PARENT ID : 561
RANK : species
GC ID : 11
SCIENTIFIC NAME : Escherichia coli
SYNONYM : bacterium E3
SYNONYM : Bacterium coli
SYNONYM : Bacterium coli commune
SYNONYM : Enterococcus coli
SYNONYM : Bacillus coli
INCLUDES : bacterium 10a
INCLUDES : Escherichia coli retron Ec86
INCLUDES : Escherichia coli retron Ec79
INCLUDES : Escherichia coli retron Ec67
INCLUDES : Escherichia coli retron Ec107
MISSPELLING : Eschericia coli
MISSPELLING : Escherchia coli
//
ID : 511145
PARENT ID : 83333
RANK : no rank
GC ID : 11
SCIENTIFIC NAME : Escherichia coli str. K-12 substr. MG1655
SYNONYM : Escherichia coli MG1655
EQUIVALENT NAME : Escherichia coli str. K12 substr. MG1655
EQUIVALENT NAME : Escherichia coli strain MG1655
EQUIVALENT NAME : Escherichia coli str. MG1655
//
* OBO (ncbitaxon.obo)
format-version: 1.2
data-version: 2013-01-24
synonymtypedef: acronym "acronym"
synonymtypedef: anamorph "anamorph"
synonymtypedef: blast_name "blast name"
synonymtypedef: common_name "common name"
synonymtypedef: equivalent_name "equivalent name"
synonymtypedef: genbank_acronym "genbank acronym"
synonymtypedef: genbank_anamorph "genbank anamorph"
synonymtypedef: genbank_common_name "genbank common name"
synonymtypedef: genbank_synonym "genbank synonym"
synonymtypedef: in_part "in-part"
synonymtypedef: misnomer "misnomer"
synonymtypedef: misspelling "misspelling"
synonymtypedef: scientific_name "scientific name"
synonymtypedef: synonym "synonym"
synonymtypedef: teleomorph "teleomorph"
remark: Autogenerated by OWLTools-NCBIConverter.
ontology: ncbitaxon
[Term]
id: NCBITaxon:1
name: root
namespace: ncbi_taxonomy
synonym: "all" RELATED synonym []
xref: GC_ID:1
[Term]
id: NCBITaxon:562
name: Escherichia coli
namespace: ncbi_taxonomy
alt_id: NCBITaxon:662101
alt_id: NCBITaxon:662104
synonym: "Bacillus coli" RELATED synonym []
synonym: "Bacterium coli" RELATED synonym []
synonym: "Bacterium coli commune" RELATED synonym []
synonym: "bacterium E3" RELATED synonym []
synonym: "Enterococcus coli" RELATED synonym []
synonym: "Escherchia coli" RELATED misspelling []
synonym: "Eschericia coli" RELATED misspelling []
xref: GC_ID:11
xref: PMID:10319482
is_a: NCBITaxon:561 ! Escherichia
property_value: has_rank NCBITaxon:species
[Term]
id: NCBITaxon:511145
name: Escherichia coli str. K-12 substr. MG1655
namespace: ncbi_taxonomy
synonym: "Escherichia coli MG1655" RELATED synonym []
synonym: "Escherichia coli str. K12 substr. MG1655" EXACT equivalent_name []
synonym: "Escherichia coli str. MG1655" EXACT equivalent_name []
synonym: "Escherichia coli strain MG1655" EXACT equivalent_name []
xref: GC_ID:11
is_a: NCBITaxon:83333 ! Escherichia coli K-12
* OBO2OWL (ncbitaxon.owl)
<!-- http://purl.obolibrary.org/obo/NCBITaxon_1 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_1">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">root</rdfs:label>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GC_ID:1</oboInOwl:hasDbXref>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">all</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ncbi_taxonomy</oboInOwl:hasOBONamespace>
</owl:Class>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">all</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_1"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#synonym"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_562 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_562">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_561"/>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bacillus coli</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bacterium coli</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bacterium coli commune</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Enterococcus coli</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherchia coli</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eschericia coli</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GC_ID:11</oboInOwl:hasDbXref>
<oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NCBITaxon:662101</oboInOwl:hasAlternativeId>
<oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NCBITaxon:662104</oboInOwl:hasAlternativeId>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:10319482</oboInOwl:hasDbXref>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">bacterium E3</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ncbi_taxonomy</oboInOwl:hasOBONamespace>
<ncbitaxon:has_rank rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_species"/>
</owl:Class>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bacillus coli</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_562"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#synonym"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bacterium coli</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_562"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#synonym"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherchia coli</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_562"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#misspelling"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eschericia coli</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_562"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#misspelling"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">bacterium E3</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_562"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#synonym"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bacterium coli commune</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_562"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#synonym"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Enterococcus coli</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_562"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#synonym"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_511145 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_511145">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli str. K-12 substr. MG1655</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_83333"/>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli MG1655</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli str. K12 substr. MG1655</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli str. MG1655</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli strain MG1655</oboInOwl:hasExactSynonym>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GC_ID:11</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ncbi_taxonomy</oboInOwl:hasOBONamespace>
</owl:Class>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli MG1655</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_511145"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#synonym"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli strain MG1655</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_511145"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli str. MG1655</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_511145"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Escherichia coli str. K12 substr. MG1655</owl:annotatedTarget>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_511145"/>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
</owl:Axiom>
* Turtle (draft version; final version will be generated by this script)
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
#@prefix taxo: <http://taxonomyontology.org/ontology#> .
@prefix taxo: <http://insdc.org/ontology/taxonomy#> .
@prefix taxid: <http://identifiers.org/taxonomy/> .
@prefix taxncbi: <http://www.ncbi.nlm.nih.gov/taxonomy/> .
@prefix codon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#> .
@prefix pmid: <http://pubmed.org/> .
<>
a owl:Ontology ;
rdfs:comment "Ontology for NCBI taxonomy converted from NCBI's taxdump files" ;
owl:versionIRI <http://taxonomyontology.org/version/2013-08-21> .
taxid:1
rdfs:seeAlso taxncbi:1 ;
a owl:Class ;
rdfs:label "root" ;
taxo:codonTable codon:SG1 ;
taxo:hasRelatedSynonym "all" .
[]
a owl:Axiom ;
owl:annotatedProperty taxo:hasRelatedSynonym ;
owl:annotatedSource taxid:1 ;
owl:annotatedTarget "all" .
taxid:562
rdfs:seeAlso taxncbi:562 ;
a owl:Class ;
rdfs:label "Escherichia coli" ;
rdfs:subClassOf taxid:561 ;
taxo:hasRelatedSynonym "Bacillus coli" ;
taxo:hasRelatedSynonym "Bacterium coli" ;
taxo:hasRelatedSynonym "Bacterium coli commune" ;
taxo:hasRelatedSynonym "Enterococcus coli" ;
taxo:hasRelatedSynonym "Escherchia coli" ;
taxo:hasRelatedSynonym "Eschericia coli" ;
taxo:hasRelatedSynonym "bacterium E3" ;
taxo:codonTable codon:SG11 ;
taxo:hasAlternativeId taxid:662101 ;
taxo:hasAlternativeId taxid:662104 ;
taxo:reference pmid:10319482 ;
taxo:rank taxo:Species .
[]
a owl:Axiom ;
owl:annotatedProperty taxo:hasRelatedSynonym ;
owl:annotatedSource taxid:562 ;
owl:annotatedTarget "Bacillus coli" ;
taxo:hasSynonymType taxo:synonym .
[]
a owl:Axiom ;
owl:annotatedProperty taxo:hasRelatedSynonym ;
owl:annotatedSource taxid:562 ;
owl:annotatedTarget "Escherchia coli" ;
taxo:hasSynonymType taxo:misspelling .
taxid:511145
rdfs:seeAlso taxncbi:511145 ;
a owl:Class ;
rdfs:label "Escherichia coli str. K-12 substr. MG1655" ;
rdfs:subClassOf taxid:83333 ;
taxo:hasRelatedSynonym "Escherichia coli MG1655" ;
taxo:hasExactSynonym "Escherichia coli MG1655" ;
taxo:hasExactSynonym "Escherichia coli str. K12 substr. MG1655" ;
taxo:hasExactSynonym "Escherichia coli str. MG1655" ;
taxo:hasExactSynonym "Escherichia coli strain MG1655" ;
taxo:codonTable codon:SG11 ;
taxo:rank taxo:NoRank . # missing in OBO2OWL
[]
a owl:Axiom ;
owl:annotatedSource taxid:511145 ;
owl:annotatedTarget "Escherichia coli MG1655" ;
owl:annotatedProperty taxo:hasRelatedSynonym ;
taxo:hasSynonymType taxo:synonym .
[]
a owl:Axiom ;
owl:annotatedSource taxid:511145 ;
owl:annotatedTarget "Escherichia coli str.MG1655" ;
owl:annotatedProperty taxo:hasExactSynonym ;
taxo:hasSynonymType taxo:equivalent_name .
* Taxon name types
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245000/table/gkr1178-T2/
http://www.ebi.ac.uk/ena/about/taxonomy_name_types
% cut -f 4 -d '|' taxdump/names.dmp | s | u -c
919 acronym
441 anamorph
178894 authority
224 blast name
13429 common name
18928 equivalent name
342 genbank acronym
144 genbank anamorph
23282 genbank common name
1947 genbank synonym
415 in-part
16200 includes
1193 misnomer
19980 misspelling
1060921 scientific name
178108 synonym
171 teleomorph
49212 type material
* Taxon ranks
% cut -f 3 -d '|' taxdump/nodes.dmp | s | u -c
258 class
7607 family
393 forma
66644 genus
14 infraclass
76 infraorder
3 kingdom
138971 no rank
1229 order
6 parvorder
102 phylum
817572 species
318 species group
123 species subgroup
129 subclass
2433 subfamily
1111 subgenus
1 subkingdom
354 suborder
24 subphylum
15564 subspecies
321 subtribe
5 superclass
793 superfamily
5 superkingdom
48 superorder
5 superphylum
1635 tribe
5177 varietas
* Uniprot taxon ranks
<rdf:Description>
<rdf:type rdf:resource="&owl;AllDifferent"/>
<owl:distinctMembers rdf:parseType="Collection">
<rdf:Description rdf:about="&core;Class"/>
<rdf:Description rdf:about="&core;Family"/>
<rdf:Description rdf:about="&core;Forma"/>
<rdf:Description rdf:about="&core;Genus"/>
<rdf:Description rdf:about="&core;Kingdom"/>
<rdf:Description rdf:about="&core;Order"/>
<rdf:Description rdf:about="&core;Parvorder"/>
<rdf:Description rdf:about="&core;Phylum"/>
<rdf:Description rdf:about="&core;Species"/>
<rdf:Description rdf:about="&core;Species_Group"/>
<rdf:Description rdf:about="&core;Species_Subgroup"/>
<rdf:Description rdf:about="&core;Subclass"/>
<rdf:Description rdf:about="&core;Subfamily"/>
<rdf:Description rdf:about="&core;Subgenus"/>
<rdf:Description rdf:about="&core;Subkingdom"/>
<rdf:Description rdf:about="&core;Suborder"/>
<rdf:Description rdf:about="&core;Subphylum"/>
<rdf:Description rdf:about="&core;Subspecies"/>
<rdf:Description rdf:about="&core;Subtribe"/>
<rdf:Description rdf:about="&core;Superclass"/>
<rdf:Description rdf:about="&core;Superfamily"/>
<rdf:Description rdf:about="&core;Superkingdom"/>
<rdf:Description rdf:about="&core;Superorder"/>
<rdf:Description rdf:about="&core;Superphylum"/>
<rdf:Description rdf:about="&core;Tribe"/>
<rdf:Description rdf:about="&core;Varietas"/>
</owl:distinctMembers>
</rdf:Description>
=end
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