Safe Haskell	None
Language	Haskell2010

Biobase.Taxonomy.Types

Description

This module contains data structures for taxonomy data

Synopsis

data SimpleTaxon = SimpleTaxon {
- simpleTaxId :: Int
- simpleScientificName :: Text
- simpleParentTaxId :: Int
- simpleRank :: Rank
}
data CompareTaxon = CompareTaxon {
- compareScientificName :: Text
- compareRank :: Rank
- inTree :: [Int]
}
data Taxon = Taxon {
- taxonTaxId :: Int
- taxonScientificName :: ByteString
- taxonParentTaxId :: Int
- taxonRank :: Rank
- division :: ByteString
- geneticCode :: TaxGenCode
- mitoGeneticCode :: TaxGenCode
- lineage :: ByteString
- lineageEx :: [LineageTaxon]
- createDate :: ByteString
- updateDate :: ByteString
- pubDate :: ByteString
}
data TaxonName = TaxonName {
- classCDE :: ByteString
- dispName :: ByteString
}
data Lineage = Lineage {
- lineageStartTaxId :: Int
- lineageStartScienticName :: ByteString
- lineageStartRank :: Rank
- lineageTaxons :: [LineageTaxon]
}
data LineageTaxon = LineageTaxon {
- lineageTaxId :: Int
- lineageScienticName :: ByteString
- lineageRank :: Rank
}
data NCBITaxDump = NCBITaxDump {
- taxCitations :: [TaxCitation]
- taxDelNodes :: [TaxDelNode]
- taxDivisions :: [TaxDivision]
- taxGenCodes :: [TaxGenCode]
- taxMergedNodes :: [TaxMergedNode]
- taxNames :: [TaxName]
- taxNodes :: [TaxNode]
}
data TaxCitation = TaxCitation {
- citId :: Int
- citKey :: ByteString
- pubmedId :: Maybe Int
- medlineId :: Maybe Int
- url :: ByteString
- text :: ByteString
- taxIdList :: [Int]
}
data TaxDelNode = TaxDelNode {
- delTaxId :: Int
}
data TaxDivision = TaxDivision {
- divisionId :: Int
- divisionCDE :: ByteString
- divisonName :: ByteString
- divisionComments :: ByteString
}
data TaxGenCode = TaxGenCode {
- geneticCodeId :: Int
- abbreviation :: ByteString
- geneCodeName :: ByteString
- cde :: ByteString
- starts :: ByteString
}
data TaxMergedNode = TaxMergedNode {
- oldTaxId :: Int
- newTaxId :: Int
}
data TaxName = TaxName {
- nameTaxId :: Int
- nameTxt :: Text
- uniqueName :: ByteString
- nameClass :: ByteString
}
data Rank
- = 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
readsRank :: String -> [(Rank, String)]
data TaxNode = TaxNode {
- taxId :: Int
- parentTaxId :: Int
- rank :: Rank
- emblCode :: ByteString
- nodeDivisionId :: Int
- inheritedDivFlag :: Bool
- nodeGeneticCodeId :: Int
- inheritedGCFlag :: Bool
- mitochondrialGeneticCodeId :: Int
- inheritedMGCFlag :: Bool
- genBankHiddenFlag :: Bool
- hiddenSubtreeRootFlag :: Bool
- nodeComments :: ByteString
}
data SimpleGene2Accession = SimpleGene2Accession {
- simpleTaxIdEntry :: Int
- simpleGenomicNucleotideAccessionVersion :: ByteString
}
data Gene2Accession = Gene2Accession {
- taxIdEntry :: Int
- geneID :: Int
- status :: ByteString
- rnaNucleotideAccessionVersion :: ByteString
- rnaNucleotideGi :: ByteString
- proteinAccessionVersion :: ByteString
- proteinGi :: ByteString
- genomicNucleotideAccessionVersion :: ByteString
- genomicNucleotideGi :: ByteString
- startPositionOnTheGenomicAccession :: ByteString
- endPositionOnTheGenomicAccession :: ByteString
- orientation :: ByteString
- assembly :: ByteString
- maturePeptideAccessionVersion :: ByteString
- maturePeptideGi :: ByteString
}
simpleTaxonJSONValue :: Gr SimpleTaxon Double -> Node -> Value

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 #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: SimpleTaxon -> SimpleTaxon -> Bool # (/=) :: SimpleTaxon -> SimpleTaxon -> Bool #
Read SimpleTaxon Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS SimpleTaxon # readList :: ReadS [SimpleTaxon] # readPrec :: ReadPrec SimpleTaxon # readListPrec :: ReadPrec [SimpleTaxon] #
Show SimpleTaxon Source #
Instance details Defined in Biobase.Taxonomy.Types Methods showsPrec :: Int -> SimpleTaxon -> ShowS # show :: SimpleTaxon -> String # showList :: [SimpleTaxon] -> ShowS #
ToJSON (Gr SimpleTaxon Double) Source #
Instance details Defined in Biobase.Taxonomy.Types 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 #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: CompareTaxon -> CompareTaxon -> Bool # (/=) :: CompareTaxon -> CompareTaxon -> Bool #
Read CompareTaxon Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS CompareTaxon # readList :: ReadS [CompareTaxon] # readPrec :: ReadPrec CompareTaxon # readListPrec :: ReadPrec [CompareTaxon] #
Show CompareTaxon Source #
Instance details Defined in Biobase.Taxonomy.Types 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 :: ByteString taxonParentTaxId :: Int taxonRank :: Rank division :: ByteString geneticCode :: TaxGenCode mitoGeneticCode :: TaxGenCode lineage :: ByteString lineageEx :: [LineageTaxon] createDate :: ByteString updateDate :: ByteString pubDate :: ByteString

Instances

Eq Taxon Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: Taxon -> Taxon -> Bool # (/=) :: Taxon -> Taxon -> Bool #
Show Taxon Source #
Instance details Defined in Biobase.Taxonomy.Types Methods showsPrec :: Int -> Taxon -> ShowS # show :: Taxon -> String # showList :: [Taxon] -> ShowS #

data TaxonName Source #

Constructors

TaxonName
Fields classCDE :: ByteString dispName :: ByteString

Instances

Eq TaxonName Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: TaxonName -> TaxonName -> Bool # (/=) :: TaxonName -> TaxonName -> Bool #
Show TaxonName Source #
Instance details Defined in Biobase.Taxonomy.Types Methods showsPrec :: Int -> TaxonName -> ShowS # show :: TaxonName -> String # showList :: [TaxonName] -> ShowS #

data Lineage Source #

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

Constructors

Lineage
Fields lineageStartTaxId :: Int lineageStartScienticName :: ByteString lineageStartRank :: Rank lineageTaxons :: [LineageTaxon]

Instances

Eq Lineage Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: Lineage -> Lineage -> Bool # (/=) :: Lineage -> Lineage -> Bool #
Show Lineage Source #
Instance details Defined in Biobase.Taxonomy.Types Methods showsPrec :: Int -> Lineage -> ShowS # show :: Lineage -> String # showList :: [Lineage] -> ShowS #

data LineageTaxon Source #

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

Constructors

LineageTaxon
Fields lineageTaxId :: Int lineageScienticName :: ByteString lineageRank :: Rank

Instances

Eq LineageTaxon Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: LineageTaxon -> LineageTaxon -> Bool # (/=) :: LineageTaxon -> LineageTaxon -> Bool #
Show LineageTaxon Source #
Instance details Defined in Biobase.Taxonomy.Types 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 #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: NCBITaxDump -> NCBITaxDump -> Bool # (/=) :: NCBITaxDump -> NCBITaxDump -> Bool #
Read NCBITaxDump Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS NCBITaxDump # readList :: ReadS [NCBITaxDump] # readPrec :: ReadPrec NCBITaxDump # readListPrec :: ReadPrec [NCBITaxDump] #
Show NCBITaxDump Source #
Instance details Defined in Biobase.Taxonomy.Types 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 :: ByteString pubmedId :: Maybe Int medlineId :: Maybe Int url :: ByteString text :: ByteString taxIdList :: [Int]

Instances

Eq TaxCitation Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: TaxCitation -> TaxCitation -> Bool # (/=) :: TaxCitation -> TaxCitation -> Bool #
Read TaxCitation Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS TaxCitation # readList :: ReadS [TaxCitation] # readPrec :: ReadPrec TaxCitation # readListPrec :: ReadPrec [TaxCitation] #
Show TaxCitation Source #
Instance details Defined in Biobase.Taxonomy.Types 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 #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: TaxDelNode -> TaxDelNode -> Bool # (/=) :: TaxDelNode -> TaxDelNode -> Bool #
Read TaxDelNode Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS TaxDelNode # readList :: ReadS [TaxDelNode] # readPrec :: ReadPrec TaxDelNode # readListPrec :: ReadPrec [TaxDelNode] #
Show TaxDelNode Source #
Instance details Defined in Biobase.Taxonomy.Types 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 :: ByteString divisonName :: ByteString divisionComments :: ByteString

Instances

Eq TaxDivision Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: TaxDivision -> TaxDivision -> Bool # (/=) :: TaxDivision -> TaxDivision -> Bool #
Read TaxDivision Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS TaxDivision # readList :: ReadS [TaxDivision] # readPrec :: ReadPrec TaxDivision # readListPrec :: ReadPrec [TaxDivision] #
Show TaxDivision Source #
Instance details Defined in Biobase.Taxonomy.Types 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 :: ByteString geneCodeName :: ByteString cde :: ByteString starts :: ByteString

Instances

Eq TaxGenCode Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: TaxGenCode -> TaxGenCode -> Bool # (/=) :: TaxGenCode -> TaxGenCode -> Bool #
Read TaxGenCode Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS TaxGenCode # readList :: ReadS [TaxGenCode] # readPrec :: ReadPrec TaxGenCode # readListPrec :: ReadPrec [TaxGenCode] #
Show TaxGenCode Source #
Instance details Defined in Biobase.Taxonomy.Types 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 #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: TaxMergedNode -> TaxMergedNode -> Bool # (/=) :: TaxMergedNode -> TaxMergedNode -> Bool #
Read TaxMergedNode Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS TaxMergedNode # readList :: ReadS [TaxMergedNode] # readPrec :: ReadPrec TaxMergedNode # readListPrec :: ReadPrec [TaxMergedNode] #
Show TaxMergedNode Source #
Instance details Defined in Biobase.Taxonomy.Types 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 :: ByteString nameClass :: ByteString

Instances

Eq TaxName Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: TaxName -> TaxName -> Bool # (/=) :: TaxName -> TaxName -> Bool #
Read TaxName Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS TaxName # readList :: ReadS [TaxName] # readPrec :: ReadPrec TaxName # readListPrec :: ReadPrec [TaxName] #
Show TaxName Source #
Instance details Defined in Biobase.Taxonomy.Types 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 #
Instance details Defined in Biobase.Taxonomy.Types Methods minBound :: Rank # maxBound :: Rank #
Enum Rank Source #
Instance details Defined in Biobase.Taxonomy.Types 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 #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: Rank -> Rank -> Bool # (/=) :: Rank -> Rank -> Bool #
Ord Rank Source #
Instance details Defined in Biobase.Taxonomy.Types 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 #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS Rank # readList :: ReadS [Rank] # readPrec :: ReadPrec Rank # readListPrec :: ReadPrec [Rank] #
Show Rank Source #
Instance details Defined in Biobase.Taxonomy.Types 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 :: ByteString nodeDivisionId :: Int inheritedDivFlag :: Bool nodeGeneticCodeId :: Int inheritedGCFlag :: Bool mitochondrialGeneticCodeId :: Int inheritedMGCFlag :: Bool genBankHiddenFlag :: Bool hiddenSubtreeRootFlag :: Bool nodeComments :: ByteString

Instances

Eq TaxNode Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: TaxNode -> TaxNode -> Bool # (/=) :: TaxNode -> TaxNode -> Bool #
Read TaxNode Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS TaxNode # readList :: ReadS [TaxNode] # readPrec :: ReadPrec TaxNode # readListPrec :: ReadPrec [TaxNode] #
Show TaxNode Source #
Instance details Defined in Biobase.Taxonomy.Types Methods showsPrec :: Int -> TaxNode -> ShowS # show :: TaxNode -> String # showList :: [TaxNode] -> ShowS #

data SimpleGene2Accession Source #

Simple Gene2Accession table

Constructors

SimpleGene2Accession
Fields simpleTaxIdEntry :: Int simpleGenomicNucleotideAccessionVersion :: ByteString

Instances

Eq SimpleGene2Accession Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: SimpleGene2Accession -> SimpleGene2Accession -> Bool # (/=) :: SimpleGene2Accession -> SimpleGene2Accession -> Bool #
Read SimpleGene2Accession Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS SimpleGene2Accession # readList :: ReadS [SimpleGene2Accession] # readPrec :: ReadPrec SimpleGene2Accession # readListPrec :: ReadPrec [SimpleGene2Accession] #
Show SimpleGene2Accession Source #
Instance details Defined in Biobase.Taxonomy.Types Methods showsPrec :: Int -> SimpleGene2Accession -> ShowS # show :: SimpleGene2Accession -> String # showList :: [SimpleGene2Accession] -> ShowS #

data Gene2Accession Source #

Datastructure for Gene2Accession table

Constructors

Gene2Accession

Instances

Eq Gene2Accession Source #
Instance details Defined in Biobase.Taxonomy.Types Methods (==) :: Gene2Accession -> Gene2Accession -> Bool # (/=) :: Gene2Accession -> Gene2Accession -> Bool #
Read Gene2Accession Source #
Instance details Defined in Biobase.Taxonomy.Types Methods readsPrec :: Int -> ReadS Gene2Accession # readList :: ReadS [Gene2Accession] # readPrec :: ReadPrec Gene2Accession # readListPrec :: ReadPrec [Gene2Accession] #
Show Gene2Accession Source #
Instance details Defined in Biobase.Taxonomy.Types Methods showsPrec :: Int -> Gene2Accession -> ShowS # show :: Gene2Accession -> String # showList :: [Gene2Accession] -> ShowS #

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