Bio.TaxonomyData

This module contains data structures for taxonomy data

Documentation

data SimpleTaxon

SimpleTaxon only contains the most relevant fields of a taxonomy entry. For all annotaded fields use the Taxon datatype and its associated functions

Constructors

SimpleTaxon

Fields

• simpleTaxId :: Int
• simpleScientificName :: Text
• simpleParentTaxId :: Int
• simpleRank :: Rank

Instances

Eq SimpleTaxon

Methods

(==) :: SimpleTaxon -> SimpleTaxon -> Bool

(/=) :: SimpleTaxon -> SimpleTaxon -> Bool

Read SimpleTaxon

Methods

readsPrec :: Int -> ReadS SimpleTaxon

readList :: ReadS [SimpleTaxon]

readPrec :: ReadPrec SimpleTaxon

readListPrec :: ReadPrec [SimpleTaxon]

Show SimpleTaxon

Methods

showsPrec :: Int -> SimpleTaxon -> ShowS

show :: SimpleTaxon -> String

showList :: [SimpleTaxon] -> ShowS

ToJSON (Gr SimpleTaxon Double)

Methods

toJSON :: Gr SimpleTaxon Double -> Value

toEncoding :: Gr SimpleTaxon Double -> Encoding

toJSONList :: [Gr SimpleTaxon Double] -> Value

toEncodingList :: [Gr SimpleTaxon Double] -> Encoding

data CompareTaxon

Datastructure for tree comparisons

Constructors

CompareTaxon

Fields

• compareScientificName :: Text
• compareRank :: Rank
• inTree :: [Int]

Instances

Eq CompareTaxon

Methods

(==) :: CompareTaxon -> CompareTaxon -> Bool

(/=) :: CompareTaxon -> CompareTaxon -> Bool

Read CompareTaxon

Methods

readsPrec :: Int -> ReadS CompareTaxon

readList :: ReadS [CompareTaxon]

readPrec :: ReadPrec CompareTaxon

readListPrec :: ReadPrec [CompareTaxon]

Show CompareTaxon

Methods

showsPrec :: Int -> CompareTaxon -> ShowS

show :: CompareTaxon -> String

showList :: [CompareTaxon] -> ShowS

data Taxon

Data structure for Entrez taxonomy fetch result

Constructors

Taxon

Fields

• taxonTaxId :: Int
• taxonScientificName :: String
• taxonParentTaxId :: Int
• taxonRank :: Rank
• division :: String
• geneticCode :: TaxGenCode
• mitoGeneticCode :: TaxGenCode
• lineage :: String
• lineageEx :: [LineageTaxon]
• createDate :: String
• updateDate :: String
• pubDate :: String

Instances

Eq Taxon

Methods

(==) :: Taxon -> Taxon -> Bool

(/=) :: Taxon -> Taxon -> Bool

Show Taxon

Methods

showsPrec :: Int -> Taxon -> ShowS

show :: Taxon -> String

showList :: [Taxon] -> ShowS

data TaxonName

Constructors

TaxonName

Fields

• classCDE :: String
• dispName :: String

Instances

Eq TaxonName

Methods

(==) :: TaxonName -> TaxonName -> Bool

(/=) :: TaxonName -> TaxonName -> Bool

Show TaxonName

Methods

showsPrec :: Int -> TaxonName -> ShowS

show :: TaxonName -> String

showList :: [TaxonName] -> ShowS

data LineageTaxon

Lineage Taxons denote all parent Taxonomy nodes of a node retrieved by Entrez fetch

Constructors

LineageTaxon

Fields

• lineageTaxId :: Int
• lineageScienticName :: String
• lineageRank :: Rank

Instances

Eq LineageTaxon

Methods

(==) :: LineageTaxon -> LineageTaxon -> Bool

(/=) :: LineageTaxon -> LineageTaxon -> Bool

Show LineageTaxon

Methods

showsPrec :: Int -> LineageTaxon -> ShowS

show :: LineageTaxon -> String

showList :: [LineageTaxon] -> ShowS

data NCBITaxDump

NCBI Taxonomy database dump hierachichal data structure as defined in ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt

Constructors

NCBITaxDump

Fields

• taxCitations :: [TaxCitation]
• taxDelNodes :: [TaxDelNode]
• taxDivisions :: [TaxDivision]
• taxGenCodes :: [TaxGenCode]
• taxMergedNodes :: [TaxMergedNode]
• taxNames :: [TaxName]
• taxNodes :: [TaxNode]

Instances

Eq NCBITaxDump

Methods

(==) :: NCBITaxDump -> NCBITaxDump -> Bool

(/=) :: NCBITaxDump -> NCBITaxDump -> Bool

Read NCBITaxDump

Methods

readsPrec :: Int -> ReadS NCBITaxDump

readList :: ReadS [NCBITaxDump]

readPrec :: ReadPrec NCBITaxDump

readListPrec :: ReadPrec [NCBITaxDump]

Show NCBITaxDump

Methods

showsPrec :: Int -> NCBITaxDump -> ShowS

show :: NCBITaxDump -> String

showList :: [NCBITaxDump] -> ShowS

data TaxCitation

Datastructure for entries of Taxonomy database dump citations file

Constructors

TaxCitation

Fields

• citId :: Int
• citKey :: Maybe String
• pubmedId :: Maybe Int
• medlineId :: Maybe Int
• url :: Maybe String
• text :: Maybe String
• taxIdList :: Maybe [Int]

Instances

Eq TaxCitation

Methods

(==) :: TaxCitation -> TaxCitation -> Bool

(/=) :: TaxCitation -> TaxCitation -> Bool

Read TaxCitation

Methods

readsPrec :: Int -> ReadS TaxCitation

readList :: ReadS [TaxCitation]

readPrec :: ReadPrec TaxCitation

readListPrec :: ReadPrec [TaxCitation]

Show TaxCitation

Methods

showsPrec :: Int -> TaxCitation -> ShowS

show :: TaxCitation -> String

showList :: [TaxCitation] -> ShowS

data TaxDelNode

Datastructure for entries of Taxonomy database dump deleted nodes file

Constructors

TaxDelNode

Fields

• delTaxId :: Int

Instances

Eq TaxDelNode

Methods

(==) :: TaxDelNode -> TaxDelNode -> Bool

(/=) :: TaxDelNode -> TaxDelNode -> Bool

Read TaxDelNode

Methods

readsPrec :: Int -> ReadS TaxDelNode

readList :: ReadS [TaxDelNode]

readPrec :: ReadPrec TaxDelNode

readListPrec :: ReadPrec [TaxDelNode]

Show TaxDelNode

Methods

showsPrec :: Int -> TaxDelNode -> ShowS

show :: TaxDelNode -> String

showList :: [TaxDelNode] -> ShowS

data TaxDivision

Datastructure for entries of Taxonomy database dump division file

Constructors

TaxDivision

Fields

• divisionId :: Int
• divisionCDE :: String
• divisonName :: String
• divisionComments :: Maybe String

Instances

Eq TaxDivision

Methods

(==) :: TaxDivision -> TaxDivision -> Bool

(/=) :: TaxDivision -> TaxDivision -> Bool

Read TaxDivision

Methods

readsPrec :: Int -> ReadS TaxDivision

readList :: ReadS [TaxDivision]

readPrec :: ReadPrec TaxDivision

readListPrec :: ReadPrec [TaxDivision]

Show TaxDivision

Methods

showsPrec :: Int -> TaxDivision -> ShowS

show :: TaxDivision -> String

showList :: [TaxDivision] -> ShowS

data TaxGenCode

Datastructure for entries of Taxonomy database dump gencode file

Constructors

TaxGenCode

Fields

• geneticCodeId :: Int
• abbreviation :: Maybe String
• geneCodeName :: String
• cde :: String
• starts :: String

Instances

Eq TaxGenCode

Methods

(==) :: TaxGenCode -> TaxGenCode -> Bool

(/=) :: TaxGenCode -> TaxGenCode -> Bool

Read TaxGenCode

Methods

readsPrec :: Int -> ReadS TaxGenCode

readList :: ReadS [TaxGenCode]

readPrec :: ReadPrec TaxGenCode

readListPrec :: ReadPrec [TaxGenCode]

Show TaxGenCode

Methods

showsPrec :: Int -> TaxGenCode -> ShowS

show :: TaxGenCode -> String

showList :: [TaxGenCode] -> ShowS

data TaxMergedNode

Datastructure for entries of Taxonomy database dump mergednodes file

Constructors

TaxMergedNode

Fields

• oldTaxId :: Int
• newTaxId :: Int

Instances

Eq TaxMergedNode

Methods

(==) :: TaxMergedNode -> TaxMergedNode -> Bool

(/=) :: TaxMergedNode -> TaxMergedNode -> Bool

Read TaxMergedNode

Methods

readsPrec :: Int -> ReadS TaxMergedNode

readList :: ReadS [TaxMergedNode]

readPrec :: ReadPrec TaxMergedNode

readListPrec :: ReadPrec [TaxMergedNode]

Show TaxMergedNode

Methods

showsPrec :: Int -> TaxMergedNode -> ShowS

show :: TaxMergedNode -> String

showList :: [TaxMergedNode] -> ShowS

data TaxName

Datastructure for entries of Taxonomy database dump names file

Constructors

TaxName

Fields

• nameTaxId :: Int
• nameTxt :: Text
• uniqueName :: Text
• nameClass :: Text

Instances

Eq TaxName

Methods

(==) :: TaxName -> TaxName -> Bool

(/=) :: TaxName -> TaxName -> Bool

Read TaxName

Methods

readsPrec :: Int -> ReadS TaxName

readList :: ReadS [TaxName]

readPrec :: ReadPrec TaxName

readListPrec :: ReadPrec [TaxName]

Show TaxName

Methods

showsPrec :: Int -> TaxName -> ShowS

show :: TaxName -> String

showList :: [TaxName] -> ShowS

data Rank

Taxonomic ranks: NCBI uses the uncommon Speciessubgroup

Constructors

Norank

Form

Variety

Infraspecies

Subspecies

Speciessubgroup

Species

Speciesgroup

Superspecies

Series

Section

Subgenus

Genus

Subtribe

Tribe

Supertribe

Subfamily

Family

Superfamily

Parvorder

Infraorder

Suborder

Order

Superorder

Magnorder

Cohort

Legion

Parvclass

Infraclass

Subclass

Class

Superclass

Microphylum

Infraphylum

Subphylum

Phylum

Superphylum

Infrakingdom

Subkingdom

Kingdom

Superkingdom

Domain

Instances

Bounded Rank

Methods

minBound :: Rank

maxBound :: Rank

Enum Rank

Methods

succ :: Rank -> Rank

pred :: Rank -> Rank

toEnum :: Int -> Rank

fromEnum :: Rank -> Int

enumFrom :: Rank -> [Rank]

enumFromThen :: Rank -> Rank -> [Rank]

enumFromTo :: Rank -> Rank -> [Rank]

enumFromThenTo :: Rank -> Rank -> Rank -> [Rank]

Eq Rank

Methods

(==) :: Rank -> Rank -> Bool

(/=) :: Rank -> Rank -> Bool

Ord Rank

Methods

compare :: Rank -> Rank -> Ordering

(<) :: Rank -> Rank -> Bool

(<=) :: Rank -> Rank -> Bool

(>) :: Rank -> Rank -> Bool

(>=) :: Rank -> Rank -> Bool

max :: Rank -> Rank -> Rank

min :: Rank -> Rank -> Rank

Read Rank

Methods

readsPrec :: Int -> ReadS Rank

readList :: ReadS [Rank]

readPrec :: ReadPrec Rank

readListPrec :: ReadPrec [Rank]

Show Rank

Methods

showsPrec :: Int -> Rank -> ShowS

show :: Rank -> String

showList :: [Rank] -> ShowS

readsRank :: String -> [(Rank, String)]

data TaxNode

Datastructure for entries of Taxonomy database dump nodes file

Constructors

TaxNode

Fields

• taxId :: Int
• parentTaxId :: Int
• rank :: Rank
• emblCode :: Maybe String
• nodeDivisionId :: String
• inheritedDivFlag :: Bool
• nodeGeneticCodeId :: String
• inheritedGCFlag :: Bool
• mitochondrialGeneticCodeId :: String
• inheritedMGCFlag :: Bool
• genBankHiddenFlag :: Bool
• hiddenSubtreeRootFlag :: Bool
• nodeComments :: Maybe String

Instances

Eq TaxNode

Methods

(==) :: TaxNode -> TaxNode -> Bool

(/=) :: TaxNode -> TaxNode -> Bool

Read TaxNode

Methods

readsPrec :: Int -> ReadS TaxNode

readList :: ReadS [TaxNode]

readPrec :: ReadPrec TaxNode

readListPrec :: ReadPrec [TaxNode]

Show TaxNode

Methods

showsPrec :: Int -> TaxNode -> ShowS

show :: TaxNode -> String

showList :: [TaxNode] -> ShowS

data SimpleGene2Accession

Simple Gene2Accession table

Constructors

SimpleGene2Accession

Fields

• simpleTaxIdEntry :: Int
• simpleGenomicNucleotideAccessionVersion :: String

Instances

Eq SimpleGene2Accession

Methods

(==) :: SimpleGene2Accession -> SimpleGene2Accession -> Bool

(/=) :: SimpleGene2Accession -> SimpleGene2Accession -> Bool

Read SimpleGene2Accession

Methods

readsPrec :: Int -> ReadS SimpleGene2Accession

readList :: ReadS [SimpleGene2Accession]

readPrec :: ReadPrec SimpleGene2Accession

readListPrec :: ReadPrec [SimpleGene2Accession]

Show SimpleGene2Accession

Methods

showsPrec :: Int -> SimpleGene2Accession -> ShowS

show :: SimpleGene2Accession -> String

showList :: [SimpleGene2Accession] -> ShowS

data Gene2Accession

Datastructure for Gene2Accession table

Constructors

Gene2Accession

Fields

• taxIdEntry :: Int
• geneID :: Int
• status :: String
• rnaNucleotideAccessionVersion :: String
• rnaNucleotideGi :: String
• proteinAccessionVersion :: String
• proteinGi :: String
• genomicNucleotideAccessionVersion :: String
• genomicNucleotideGi :: String
• startPositionOnTheGenomicAccession :: String
• endPositionOnTheGenomicAccession :: String
• orientation :: String
• assembly :: String
• maturePeptideAccessionVersion :: String
• maturePeptideGi :: String

Instances

Eq Gene2Accession

Methods

(==) :: Gene2Accession -> Gene2Accession -> Bool

(/=) :: Gene2Accession -> Gene2Accession -> Bool

Read Gene2Accession

Methods

readsPrec :: Int -> ReadS Gene2Accession

readList :: ReadS [Gene2Accession]

readPrec :: ReadPrec Gene2Accession

readListPrec :: ReadPrec [Gene2Accession]

Show Gene2Accession

Methods

showsPrec :: Int -> Gene2Accession -> ShowS

show :: Gene2Accession -> String

showList :: [Gene2Accession] -> ShowS

simpleTaxonJSONValue :: Gr SimpleTaxon Double -> Node -> Value