Safe Haskell	None
Language	Haskell98

Bio.TaxonomyData

Description

This module contains data structures for taxonomy data

Synopsis

Documentation

data SimpleTaxon Source #

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 Source #
Methods (==) :: SimpleTaxon -> SimpleTaxon -> Bool # (/=) :: SimpleTaxon -> SimpleTaxon -> Bool #
Read SimpleTaxon Source #
Methods readsPrec :: Int -> ReadS SimpleTaxon # readList :: ReadS [SimpleTaxon] # readPrec :: ReadPrec SimpleTaxon # readListPrec :: ReadPrec [SimpleTaxon] #
Show SimpleTaxon Source #
Methods showsPrec :: Int -> SimpleTaxon -> ShowS # show :: SimpleTaxon -> String # showList :: [SimpleTaxon] -> ShowS #
ToJSON (Gr SimpleTaxon Double) Source #
Methods toJSON :: Gr SimpleTaxon Double -> Value # toEncoding :: Gr SimpleTaxon Double -> Encoding # toJSONList :: [Gr SimpleTaxon Double] -> Value # toEncodingList :: [Gr SimpleTaxon Double] -> Encoding #

data CompareTaxon Source #

Datastructure for tree comparisons

Constructors

CompareTaxon
Fields compareScientificName :: Text compareRank :: Rank inTree :: [Int]

Instances

Eq CompareTaxon Source #
Methods (==) :: CompareTaxon -> CompareTaxon -> Bool # (/=) :: CompareTaxon -> CompareTaxon -> Bool #
Read CompareTaxon Source #
Methods readsPrec :: Int -> ReadS CompareTaxon # readList :: ReadS [CompareTaxon] # readPrec :: ReadPrec CompareTaxon # readListPrec :: ReadPrec [CompareTaxon] #
Show CompareTaxon Source #
Methods showsPrec :: Int -> CompareTaxon -> ShowS # show :: CompareTaxon -> String # showList :: [CompareTaxon] -> ShowS #

data Taxon Source #

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 Source #
Methods (==) :: Taxon -> Taxon -> Bool # (/=) :: Taxon -> Taxon -> Bool #
Show Taxon Source #
Methods showsPrec :: Int -> Taxon -> ShowS # show :: Taxon -> String # showList :: [Taxon] -> ShowS #

data TaxonName Source #

Constructors

TaxonName
Fields classCDE :: String dispName :: String

Instances

Eq TaxonName Source #
Methods (==) :: TaxonName -> TaxonName -> Bool # (/=) :: TaxonName -> TaxonName -> Bool #
Show TaxonName Source #
Methods showsPrec :: Int -> TaxonName -> ShowS # show :: TaxonName -> String # showList :: [TaxonName] -> ShowS #

data LineageTaxon Source #

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 Source #
Methods (==) :: LineageTaxon -> LineageTaxon -> Bool # (/=) :: LineageTaxon -> LineageTaxon -> Bool #
Show LineageTaxon Source #
Methods showsPrec :: Int -> LineageTaxon -> ShowS # show :: LineageTaxon -> String # showList :: [LineageTaxon] -> ShowS #

data NCBITaxDump Source #

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 Source #
Methods (==) :: NCBITaxDump -> NCBITaxDump -> Bool # (/=) :: NCBITaxDump -> NCBITaxDump -> Bool #
Read NCBITaxDump Source #
Methods readsPrec :: Int -> ReadS NCBITaxDump # readList :: ReadS [NCBITaxDump] # readPrec :: ReadPrec NCBITaxDump # readListPrec :: ReadPrec [NCBITaxDump] #
Show NCBITaxDump Source #
Methods showsPrec :: Int -> NCBITaxDump -> ShowS # show :: NCBITaxDump -> String # showList :: [NCBITaxDump] -> ShowS #

data TaxCitation Source #

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 Source #
Methods (==) :: TaxCitation -> TaxCitation -> Bool # (/=) :: TaxCitation -> TaxCitation -> Bool #
Read TaxCitation Source #
Methods readsPrec :: Int -> ReadS TaxCitation # readList :: ReadS [TaxCitation] # readPrec :: ReadPrec TaxCitation # readListPrec :: ReadPrec [TaxCitation] #
Show TaxCitation Source #
Methods showsPrec :: Int -> TaxCitation -> ShowS # show :: TaxCitation -> String # showList :: [TaxCitation] -> ShowS #

data TaxDelNode Source #

Datastructure for entries of Taxonomy database dump deleted nodes file

Constructors

TaxDelNode
Fields delTaxId :: Int

Instances

Eq TaxDelNode Source #
Methods (==) :: TaxDelNode -> TaxDelNode -> Bool # (/=) :: TaxDelNode -> TaxDelNode -> Bool #
Read TaxDelNode Source #
Methods readsPrec :: Int -> ReadS TaxDelNode # readList :: ReadS [TaxDelNode] # readPrec :: ReadPrec TaxDelNode # readListPrec :: ReadPrec [TaxDelNode] #
Show TaxDelNode Source #
Methods showsPrec :: Int -> TaxDelNode -> ShowS # show :: TaxDelNode -> String # showList :: [TaxDelNode] -> ShowS #

data TaxDivision Source #

Datastructure for entries of Taxonomy database dump division file

Constructors

TaxDivision
Fields divisionId :: Int divisionCDE :: String divisonName :: String divisionComments :: Maybe String

Instances

Eq TaxDivision Source #
Methods (==) :: TaxDivision -> TaxDivision -> Bool # (/=) :: TaxDivision -> TaxDivision -> Bool #
Read TaxDivision Source #
Methods readsPrec :: Int -> ReadS TaxDivision # readList :: ReadS [TaxDivision] # readPrec :: ReadPrec TaxDivision # readListPrec :: ReadPrec [TaxDivision] #
Show TaxDivision Source #
Methods showsPrec :: Int -> TaxDivision -> ShowS # show :: TaxDivision -> String # showList :: [TaxDivision] -> ShowS #

data TaxGenCode Source #

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 Source #
Methods (==) :: TaxGenCode -> TaxGenCode -> Bool # (/=) :: TaxGenCode -> TaxGenCode -> Bool #
Read TaxGenCode Source #
Methods readsPrec :: Int -> ReadS TaxGenCode # readList :: ReadS [TaxGenCode] # readPrec :: ReadPrec TaxGenCode # readListPrec :: ReadPrec [TaxGenCode] #
Show TaxGenCode Source #
Methods showsPrec :: Int -> TaxGenCode -> ShowS # show :: TaxGenCode -> String # showList :: [TaxGenCode] -> ShowS #

data TaxMergedNode Source #

Datastructure for entries of Taxonomy database dump mergednodes file

Constructors

TaxMergedNode
Fields oldTaxId :: Int newTaxId :: Int

Instances

Eq TaxMergedNode Source #
Methods (==) :: TaxMergedNode -> TaxMergedNode -> Bool # (/=) :: TaxMergedNode -> TaxMergedNode -> Bool #
Read TaxMergedNode Source #
Methods readsPrec :: Int -> ReadS TaxMergedNode # readList :: ReadS [TaxMergedNode] # readPrec :: ReadPrec TaxMergedNode # readListPrec :: ReadPrec [TaxMergedNode] #
Show TaxMergedNode Source #
Methods showsPrec :: Int -> TaxMergedNode -> ShowS # show :: TaxMergedNode -> String # showList :: [TaxMergedNode] -> ShowS #

data TaxName Source #

Datastructure for entries of Taxonomy database dump names file

Constructors

TaxName
Fields nameTaxId :: Int nameTxt :: Text uniqueName :: Text nameClass :: Text

Instances

Eq TaxName Source #
Methods (==) :: TaxName -> TaxName -> Bool # (/=) :: TaxName -> TaxName -> Bool #
Read TaxName Source #
Methods readsPrec :: Int -> ReadS TaxName # readList :: ReadS [TaxName] # readPrec :: ReadPrec TaxName # readListPrec :: ReadPrec [TaxName] #
Show TaxName Source #
Methods showsPrec :: Int -> TaxName -> ShowS # show :: TaxName -> String # showList :: [TaxName] -> ShowS #

data Rank Source #

Taxonomic ranks: NCBI uses the uncommon Speciessubgroup

Instances

Bounded Rank Source #
Methods minBound :: Rank # maxBound :: Rank #
Enum Rank Source #
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 Source #
Methods (==) :: Rank -> Rank -> Bool # (/=) :: Rank -> Rank -> Bool #
Ord Rank Source #
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 Source #
Methods readsPrec :: Int -> ReadS Rank # readList :: ReadS [Rank] # readPrec :: ReadPrec Rank # readListPrec :: ReadPrec [Rank] #
Show Rank Source #
Methods showsPrec :: Int -> Rank -> ShowS # show :: Rank -> String # showList :: [Rank] -> ShowS #

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

data TaxNode Source #

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 Source #
Methods (==) :: TaxNode -> TaxNode -> Bool # (/=) :: TaxNode -> TaxNode -> Bool #
Read TaxNode Source #
Methods readsPrec :: Int -> ReadS TaxNode # readList :: ReadS [TaxNode] # readPrec :: ReadPrec TaxNode # readListPrec :: ReadPrec [TaxNode] #
Show TaxNode Source #
Methods showsPrec :: Int -> TaxNode -> ShowS # show :: TaxNode -> String # showList :: [TaxNode] -> ShowS #

data SimpleGene2Accession Source #

Simple Gene2Accession table

Constructors

SimpleGene2Accession
Fields simpleTaxIdEntry :: Int simpleGenomicNucleotideAccessionVersion :: String

Instances

Eq SimpleGene2Accession Source #
Methods (==) :: SimpleGene2Accession -> SimpleGene2Accession -> Bool # (/=) :: SimpleGene2Accession -> SimpleGene2Accession -> Bool #
Read SimpleGene2Accession Source #
Methods readsPrec :: Int -> ReadS SimpleGene2Accession # readList :: ReadS [SimpleGene2Accession] # readPrec :: ReadPrec SimpleGene2Accession # readListPrec :: ReadPrec [SimpleGene2Accession] #
Show SimpleGene2Accession Source #
Methods showsPrec :: Int -> SimpleGene2Accession -> ShowS # show :: SimpleGene2Accession -> String # showList :: [SimpleGene2Accession] -> ShowS #

data Gene2Accession Source #

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 Source #
Methods (==) :: Gene2Accession -> Gene2Accession -> Bool # (/=) :: Gene2Accession -> Gene2Accession -> Bool #
Read Gene2Accession Source #
Methods readsPrec :: Int -> ReadS Gene2Accession # readList :: ReadS [Gene2Accession] # readPrec :: ReadPrec Gene2Accession # readListPrec :: ReadPrec [Gene2Accession] #
Show Gene2Accession Source #
Methods showsPrec :: Int -> Gene2Accession -> ShowS # show :: Gene2Accession -> String # showList :: [Gene2Accession] -> ShowS #

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

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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
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