h$p*      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~None#> Taxonomy&Datastructure for Gene2Accession tableTaxonomySimple Gene2Accession tableTaxonomy>Datastructure for entries of Taxonomy database dump nodes file$Taxonomy7Taxonomic ranks: NCBI uses the uncommon SpeciessubgroupOTaxonomy>Datastructure for entries of Taxonomy database dump names fileUTaxonomyDatastructure for entries of Taxonomy database dump mergednodes fileYTaxonomyDatastructure for entries of Taxonomy database dump gencode file`TaxonomyDatastructure for entries of Taxonomy database dump division filefTaxonomyDatastructure for entries of Taxonomy database dump deleted nodes fileiTaxonomyDatastructure for entries of Taxonomy database dump citations filerTaxonomyNCBI Taxonomy database dump hierachichal data structure as defined in 6ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt{TaxonomyLineage Taxons denote all parent Taxonomy nodes of a node retrieved by Entrez fetchTaxonomyLineage Taxons denote all parent Taxonomy nodes of a node retrieved by Entrez fetchTaxonomy/Data structure for Entrez taxonomy fetch resultTaxonomy"Datastructure for tree comparisonsTaxonomySimpleTaxon only contains the most relevant fields of a taxonomy entry. For all annotaded fields use the Taxon datatype and its associated functions #"! $NMLKJIHGFEDBA@?>=<:9876543210/-,+*)('&%;.COPTSRQUVXWYZ_^]\[`aedcbfghijqonmlkprszyxwvut{|~}{|~}rszyxwvutijqonmlkpfgh`aedcbYZ_^]\[UVXWOPTSRQ$NMLKJIHGFEDBA@?>=<:9876543210/-,+*)('&%;.C#"!  NoneTaxonomyNCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree with scientific names for each node is generated.TaxonomyNCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated.TaxonomyNCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated.Taxonomy(parse NCBITaxCitations from input stringTaxonomy*parse NCBITaxCitations from input filePathTaxonomy'parse NCBITaxDelNodes from input stringTaxonomy)parse NCBITaxDelNodes from input filePathTaxonomy'parse NCBITaxDivisons from input stringTaxonomy)parse NCBITaxDivisons from input filePathTaxonomy'parse NCBITaxGenCodes from input stringTaxonomy)parse NCBITaxGenCodes from input filePathTaxonomy*parse NCBITaxMergedNodes from input stringTaxonomy,parse NCBITaxMergedNodes from input filePathTaxonomy$parse NCBITaxNames from input stringTaxonomy&parse NCBITaxNames from input filePathTaxonomy$parse NCBITaxNames from input stringTaxonomy*parse NCBITaxCitations from input filePathTaxonomy*parse NCBISimpleTaxNames from input stringTaxonomy*parse NCBITaxCitations from input filePathTaxonomy#Parse the input as NCBITax datatype #"! $NMLKJIHGFEDBA@?>=<:9876543210/-,+*)('&%;C.OPTSQRUVWXYZ_^][\`aedbcfghijqonmlpkrszyxwvtu{|}~NoneTaxonomyExtract a subtree correpsonding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2TreeCompare tool.TaxonomyExtract a subtree corresponding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2Tree tool.TaxonomyExtract a subtree corresponding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2Tree tool.TaxonomyExtract a subtree corresponding to input node paths to root. If a Rank is provided, all node that are less or equal are omittedTaxonomy'Extract parent node with specified RankTaxonomy>Returns path between 2 maybe nodes. Used in TreeDistance tool. #"! $NMLKJIHGFEDBA@?>=<:9876543210/-,+*)('&%;C.OPTSQRUVWXYZ_^][\`aedbcfghijqonmlpkrszyxwvtu{|}~None!Taxonomy0Draw graph in dot format. Used in Ids2Tree tool.TaxonomyDraw tree comparison graph in dot format. Used in Ids2TreeCompare tool.TaxonomyWrite tree representation either as dot or json to provided file pathTaxonomyWrite tree representation as dot to provided file path. Graphviz tools like dot can be applied to the written .dot file to generate e.g. svg-format images.TaxonomyWrite tree representation as json to provided file path. You can visualize the result for example with 3Djs. #"! $NMLKJIHGFEDBA@?>=<:9876543210/-,+*)('&%;C.OPTSQRUVWXYZ_^][\`aedbcfghijqonmlpkrszyxwvtu{|}~None #"! $NMLKJIHGFEDBA@?>=<:9876543210/-,+*)('&%;C.OPTSQRUVWXYZ_^][\`aedbcfghijqonmlpkrszyxwvtu{|}~      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRRSTUVWWXYZZ[\]^_``abcdeefgghijklmnoopqrstuvwwxyz{{|}~%Taxonomy-2.2.0-Ih28zG6Do796A67Ti4grIABiobase.Taxonomy.TypesBiobase.Taxonomy.ImportBiobase.Taxonomy.UtilsBiobase.Taxonomy.VisualizationBiobase.TaxonomyGene2Accession$sel:taxIdEntry:Gene2Accession$sel:geneID:Gene2Accession$sel:status:Gene2Accession1$sel:rnaNucleotideAccessionVersion:Gene2Accession#$sel:rnaNucleotideGi:Gene2Accession+$sel:proteinAccessionVersion:Gene2Accession$sel:proteinGi:Gene2Accession5$sel:genomicNucleotideAccessionVersion:Gene2Accession'$sel:genomicNucleotideGi:Gene2Accession6$sel:startPositionOnTheGenomicAccession:Gene2Accession4$sel:endPositionOnTheGenomicAccession:Gene2Accession$sel:orientation:Gene2Accession$sel:assembly:Gene2Accession1$sel:maturePeptideAccessionVersion:Gene2Accession#$sel:maturePeptideGi:Gene2AccessionSimpleGene2Accession*$sel:simpleTaxIdEntry:SimpleGene2Accession$sel:simpleGenomicNucleotideAccessionVersion:SimpleGene2AccessionTaxNode$sel:taxId:TaxNode$sel:parentTaxId:TaxNode$sel:rank:TaxNode$sel:emblCode:TaxNode$sel:nodeDivisionId:TaxNode$sel:inheritedDivFlag:TaxNode$sel:nodeGeneticCodeId:TaxNode$sel:inheritedGCFlag:TaxNode'$sel:mitochondrialGeneticCodeId:TaxNode$sel:inheritedMGCFlag:TaxNode$sel:genBankHiddenFlag:TaxNode"$sel:hiddenSubtreeRootFlag:TaxNode$sel:nodeComments:TaxNodeRankNorankFormVariety Infraspecies SubspeciesSpeciessubgroupSpecies Speciesgroup SuperspeciesSeriesSectionSubgenusGenusSubtribeTribe Supertribe SubfamilyFamily Superfamily Parvorder InfraorderSuborderOrder Superorder MagnorderCohortLegion Parvclass InfraclassSubclassClass Superclass Microphylum Infraphylum SubphylumPhylum Superphylum Infrakingdom SubkingdomKingdom SuperkingdomDomainTaxName$sel:nameTaxId:TaxName$sel:nameTxt:TaxName$sel:uniqueName:TaxName$sel:nameClass:TaxName TaxMergedNode$sel:oldTaxId:TaxMergedNode$sel:newTaxId:TaxMergedNode TaxGenCode$sel:geneticCodeId:TaxGenCode$sel:abbreviation:TaxGenCode$sel:geneCodeName:TaxGenCode$sel:cde:TaxGenCode$sel:starts:TaxGenCode TaxDivision$sel:divisionId:TaxDivision$sel:divisionCDE:TaxDivision$sel:divisonName:TaxDivision!$sel:divisionComments:TaxDivision TaxDelNode$sel:delTaxId:TaxDelNode TaxCitation$sel:citId:TaxCitation$sel:citKey:TaxCitation$sel:pubmedId:TaxCitation$sel:medlineId:TaxCitation$sel:url:TaxCitation$sel:text:TaxCitation$sel:taxIdList:TaxCitation NCBITaxDump$sel:taxCitations:NCBITaxDump$sel:taxDelNodes:NCBITaxDump$sel:taxDivisions:NCBITaxDump$sel:taxGenCodes:NCBITaxDump$sel:taxMergedNodes:NCBITaxDump$sel:taxNames:NCBITaxDump$sel:taxNodes:NCBITaxDump LineageTaxon$sel:lineageTaxId:LineageTaxon%$sel:lineageScienticName:LineageTaxon$sel:lineageRank:LineageTaxonLineage$sel:lineageStartTaxId:Lineage%$sel:lineageStartScienticName:Lineage$sel:lineageStartRank:Lineage$sel:lineageTaxons:Lineage TaxonName$sel:classCDE:TaxonName$sel:dispName:TaxonNameTaxon$sel:taxonTaxId:Taxon$sel:taxonScientificName:Taxon$sel:taxonParentTaxId:Taxon$sel:taxonRank:Taxon$sel:division:Taxon$sel:geneticCode:Taxon$sel:mitoGeneticCode:Taxon$sel:lineage:Taxon$sel:lineageEx:Taxon$sel:createDate:Taxon$sel:updateDate:Taxon$sel:pubDate:Taxon CompareTaxon'$sel:compareScientificName:CompareTaxon$sel:compareRank:CompareTaxon$sel:inTree:CompareTaxon SimpleTaxon$sel:simpleTaxId:SimpleTaxon%$sel:simpleScientificName:SimpleTaxon"$sel:simpleParentTaxId:SimpleTaxon$sel:simpleRank:SimpleTaxon readsRanksimpleTaxonJSONValue $fReadRank $fToJSONGr$fShowGene2Accession$fEqGene2Accession$fReadGene2Accession$fShowSimpleGene2Accession$fEqSimpleGene2Accession$fReadSimpleGene2Accession$fShowNCBITaxDump$fReadNCBITaxDump$fEqNCBITaxDump $fShowTaxNode $fReadTaxNode $fEqTaxNode$fShowSimpleTaxon$fReadSimpleTaxon$fEqSimpleTaxon$fShowCompareTaxon$fReadCompareTaxon$fEqCompareTaxon $fShowTaxon $fEqTaxon $fShowLineage $fEqLineage$fShowLineageTaxon$fEqLineageTaxon$fEqRank $fOrdRank $fShowRank $fBoundedRank $fEnumRank $fShowTaxName $fReadTaxName $fEqTaxName$fShowTaxMergedNode$fReadTaxMergedNode$fEqTaxMergedNode$fShowTaxGenCode$fReadTaxGenCode$fEqTaxGenCode$fShowTaxDivision$fReadTaxDivision$fEqTaxDivision$fShowTaxDelNode$fReadTaxDelNode$fEqTaxDelNode$fShowTaxCitation$fReadTaxCitation$fEqTaxCitation$fShowTaxonName $fEqTaxonNamereadNamedTaxonomy readTaxonomy parseTaxonomyparseNCBITaxCitationsreadNCBITaxCitationsparseNCBITaxDelNodesreadNCBITaxDelNodesparseNCBITaxDivisionsreadNCBITaxDivisionsparseNCBITaxGenCodesreadNCBITaxGenCodesparseNCBITaxMergedNodesreadNCBITaxMergedNodesparseNCBITaxNamesreadNCBITaxNamesparseNCBITaxNodesreadNCBITaxNodesparseNCBISimpleTaxonsreadNCBISimpleTaxonsreadNCBITaxonomyDatabasecompareSubTreesextractTaxonomySubTreebyLevel extractTaxonomySubTreebyLevelNewextractTaxonomySubTreebyRankgetParentbyRank safeNodePath drawTaxonomydrawTaxonomyComparison writeTree writeDotTree writeJsonTree