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 :: ByteString simpleParentTaxId :: Int simpleRank :: Rank

Instances

Eq SimpleTaxon
Read SimpleTaxon
Show SimpleTaxon
ToJSON (Gr SimpleTaxon Double)

data CompareTaxon Source

Datastructure for tree comparisons

Constructors

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

Instances

Eq CompareTaxon
Read CompareTaxon
Show CompareTaxon

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
Show Taxon

data TaxonName Source

Constructors

TaxonName
Fields classCDE :: String dispName :: String

Instances

Eq TaxonName
Show TaxonName

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
Show LineageTaxon

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
Read NCBITaxDump
Show NCBITaxDump

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
Read TaxCitation
Show TaxCitation

data TaxDelNode Source

Datastructure for entries of Taxonomy database dump deleted nodes file

Constructors

TaxDelNode
Fields delTaxId :: Int

Instances

Eq TaxDelNode
Read TaxDelNode
Show TaxDelNode

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
Read TaxDivision
Show TaxDivision

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
Read TaxGenCode
Show TaxGenCode

data TaxMergedNode Source

Datastructure for entries of Taxonomy database dump mergednodes file

Constructors

TaxMergedNode
Fields oldTaxId :: Int newTaxId :: Int

Instances

Eq TaxMergedNode
Read TaxMergedNode
Show TaxMergedNode

data TaxName Source

Datastructure for entries of Taxonomy database dump names file

Constructors

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

Instances

Eq TaxName
Read TaxName
Show TaxName

data Rank Source

Taxonomic ranks: NCBI uses the uncommon Speciessubgroup

Instances

Bounded Rank
Enum Rank
Eq Rank
Ord Rank
Read Rank
Show Rank

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
Read TaxNode
Show TaxNode

data SimpleGene2Accession Source

Simple Gene2Accession table

Constructors

SimpleGene2Accession
Fields simpleTaxIdEntry :: Int simpleGenomicNucleotideAccessionVersion :: String

Instances

Eq SimpleGene2Accession
Read SimpleGene2Accession
Show SimpleGene2Accession

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
Read Gene2Accession
Show Gene2Accession

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

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