Safe Haskell	Safe
Language	Haskell2010

Bio.Uniprot.Type

Synopsis

data Kingdom
- = Archea
- | Bacteria
- | Eukaryota
- | Virus
- | Other
data Organism = Organism {
- code :: Text
- kingdom :: Kingdom
- officialName :: Text
- commonName :: Maybe Text
- synonym :: Maybe Text
}
data Status
- = Reviewed
- | Unreviewed
data ID = ID {
- entryName :: Text
- status :: Status
- seqLength :: Int
}
newtype AC = AC {
- accessionNumbers :: [Text]
}
data DT = DT {
- dbIntegrationDate :: Text
- dbName :: Text
- seqVersionDate :: Text
- seqVersion :: Int
- entryVersionDate :: Text
- entryVersion :: Int
}
data Name = Name {
- fullName :: Text
- shortName :: [Text]
- ecNumber :: [Text]
}
data AltName
- = Simple Name
- | Allergen Text
- | Biotech Text
- | CDAntigen Text
- | INN Text
data Flag
- = Fragment
- | Fragments
- | Precursor
data DE = DE {
- recName :: Maybe Name
- altNames :: [AltName]
- subNames :: [Name]
- includes :: [DE]
- contains :: [DE]
- flags :: [Flag]
}
data GN = GN {
- geneName :: Maybe Text
- synonyms :: [Text]
- orderedLocusNames :: [Text]
- orfNames :: [Text]
}
newtype OS = OS {
- specie :: Text
}
data Plastid
- = PlastidSimple
- | PlastidApicoplast
- | PlastidChloroplast
- | PlastidOrganellarChromatophore
- | PlastidCyanelle
- | PlastidNonPhotosynthetic
data OG
- = Hydrogenosome
- | Mitochondrion
- | Nucleomorph
- | Plasmid [Text]
- | Plastid Plastid
newtype OC = OC {
- nodes :: [Text]
}
data OX = OX {
- databaseQualifier :: Text
- taxonomicCode :: Text
}
data OH = OH {
- taxId :: Text
- hostName :: Text
}
data Token
- = STRAIN
- | PLASMID
- | TRANSPOSON
- | TISSUE
data BibliographicDB
- = MEDLINE
- | PubMed
- | DOI
- | AGRICOLA
data RN = RN {
- number :: Int
- evidence :: [Text]
}
data Reference = Reference {
- rn :: Int
- rp :: Text
- rc :: [(Token, Text)]
- rx :: [(BibliographicDB, Text)]
- rg :: [Text]
- ra :: [Text]
- rt :: Maybe Text
- rl :: Text
}
type Topic = Text
data CC = CC {
- topic :: Topic
- comment :: Text
}
data DR = DR {
- resourceAbbr :: Text
- resourceId :: Text
- optionalInfo :: [Text]
}
data PE
- = EvidenceAtProteinLevel
- | EvidenceAtTranscriptLevel
- | InferredFromHomology
- | Predicted
- | Uncertain
newtype KW = KW {
- keywords :: [Text]
}
data Endpoint
- = ExactEP Int
- | NTerminalEP Int
- | CTerminalEP Int
- | UncertainEP Int
- | UnknownEP
data FT = FT {
- keyName :: Text
- fromEP :: Endpoint
- toEP :: Endpoint
- description :: [Text]
}
data SQ = SQ {
- length :: Int
- molWeight :: Int
- crc64 :: Text
- sequence :: Text
}
data Record = Record {
- id :: ID
- ac :: AC
- dt :: DT
- de :: DE
- gn :: [GN]
- os :: OS
- og :: [OG]
- oc :: OC
- ox :: OX
- oh :: [OH]
- refs :: [Reference]
- cc :: [CC]
- dr :: [DR]
- pe :: PE
- kw :: Maybe KW
- ft :: [FT]
- sq :: SQ
}

Documentation

data Kingdom #

Which taxonomic kingdom an organism belongs to.

Constructors

Archea	`A` for archaea (=archaebacteria)
Bacteria	`B` for bacteria (=prokaryota or eubacteria)
Eukaryota	`E` for eukaryota (=eukarya)
Virus	`V` for viruses and phages (=viridae)
Other	`O` for others (such as artificial sequences)

Instances

Bounded Kingdom #
Instance details Defined in Bio.Uniprot.Type Methods minBound :: Kingdom # maxBound :: Kingdom #
Enum Kingdom #
Instance details Defined in Bio.Uniprot.Type Methods succ :: Kingdom -> Kingdom # pred :: Kingdom -> Kingdom # toEnum :: Int -> Kingdom # fromEnum :: Kingdom -> Int # enumFrom :: Kingdom -> [Kingdom] # enumFromThen :: Kingdom -> Kingdom -> [Kingdom] # enumFromTo :: Kingdom -> Kingdom -> [Kingdom] # enumFromThenTo :: Kingdom -> Kingdom -> Kingdom -> [Kingdom] #
Eq Kingdom #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Kingdom -> Kingdom -> Bool # (/=) :: Kingdom -> Kingdom -> Bool #
Ord Kingdom #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Kingdom -> Kingdom -> Ordering # (<) :: Kingdom -> Kingdom -> Bool # (<=) :: Kingdom -> Kingdom -> Bool # (>) :: Kingdom -> Kingdom -> Bool # (>=) :: Kingdom -> Kingdom -> Bool # max :: Kingdom -> Kingdom -> Kingdom # min :: Kingdom -> Kingdom -> Kingdom #
Show Kingdom #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Kingdom -> ShowS # show :: Kingdom -> String # showList :: [Kingdom] -> ShowS #
Generic Kingdom #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Kingdom :: Type -> Type # Methods from :: Kingdom -> Rep Kingdom x # to :: Rep Kingdom x -> Kingdom #
type Rep Kingdom #
Instance details Defined in Bio.Uniprot.Type type Rep Kingdom = D1 (MetaData "Kingdom" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) ((C1 (MetaCons "Archea" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Bacteria" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "Eukaryota" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "Virus" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Other" PrefixI False) (U1 :: Type -> Type))))

data Organism #

Controlled vocabulary of species

Constructors

Organism
Fields code :: Text Code of organism (up to 5 symbols) kingdom :: Kingdom Kingdom of organism officialName :: Text Official (scientific) name commonName :: Maybe Text Common name synonym :: Maybe Text Synonym name

Instances

Eq Organism #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Organism -> Organism -> Bool # (/=) :: Organism -> Organism -> Bool #
Ord Organism #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Organism -> Organism -> Ordering # (<) :: Organism -> Organism -> Bool # (<=) :: Organism -> Organism -> Bool # (>) :: Organism -> Organism -> Bool # (>=) :: Organism -> Organism -> Bool # max :: Organism -> Organism -> Organism # min :: Organism -> Organism -> Organism #
Show Organism #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Organism -> ShowS # show :: Organism -> String # showList :: [Organism] -> ShowS #
Generic Organism #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Organism :: Type -> Type # Methods from :: Organism -> Rep Organism x # to :: Rep Organism x -> Organism #
type Rep Organism #
Instance details Defined in Bio.Uniprot.Type type Rep Organism = D1 (MetaData "Organism" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "Organism" PrefixI True) ((S1 (MetaSel (Just "code") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: S1 (MetaSel (Just "kingdom") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Kingdom)) :: (S1 (MetaSel (Just "officialName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: (S1 (MetaSel (Just "commonName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe Text)) :: S1 (MetaSel (Just "synonym") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe Text))))))

data Status #

To distinguish the fully annotated entries in the Swiss-Prot section of the UniProt Knowledgebase from the computer-annotated entries in the TrEMBL section, the status of each entry is indicated in the first (ID) line of each entry

Constructors

Reviewed	Entries that have been manually reviewed and annotated by UniProtKB curators
Unreviewed	Computer-annotated entries that have not been reviewed by UniProtKB curators

Instances

Bounded Status #
Instance details Defined in Bio.Uniprot.Type Methods minBound :: Status # maxBound :: Status #
Enum Status #
Instance details Defined in Bio.Uniprot.Type Methods succ :: Status -> Status # pred :: Status -> Status # toEnum :: Int -> Status # fromEnum :: Status -> Int # enumFrom :: Status -> [Status] # enumFromThen :: Status -> Status -> [Status] # enumFromTo :: Status -> Status -> [Status] # enumFromThenTo :: Status -> Status -> Status -> [Status] #
Eq Status #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Status -> Status -> Bool # (/=) :: Status -> Status -> Bool #
Ord Status #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Status -> Status -> Ordering # (<) :: Status -> Status -> Bool # (<=) :: Status -> Status -> Bool # (>) :: Status -> Status -> Bool # (>=) :: Status -> Status -> Bool # max :: Status -> Status -> Status # min :: Status -> Status -> Status #
Show Status #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Status -> ShowS # show :: Status -> String # showList :: [Status] -> ShowS #
Generic Status #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Status :: Type -> Type # Methods from :: Status -> Rep Status x # to :: Rep Status x -> Status #
type Rep Status #
Instance details Defined in Bio.Uniprot.Type type Rep Status = D1 (MetaData "Status" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "Reviewed" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Unreviewed" PrefixI False) (U1 :: Type -> Type))

data ID #

IDentification

Constructors

ID
Fields entryName :: Text This name is a useful means of identifying a sequence, but it is not a stable identifier as is the accession number. status :: Status The status of the entry seqLength :: Int The length of the molecule, which is the total number of amino acids in the sequence. This number includes the positions reported to be present but which have not been determined (coded as `X`).

Instances

Eq ID #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: ID -> ID -> Bool # (/=) :: ID -> ID -> Bool #
Ord ID #
Instance details Defined in Bio.Uniprot.Type Methods compare :: ID -> ID -> Ordering # (<) :: ID -> ID -> Bool # (<=) :: ID -> ID -> Bool # (>) :: ID -> ID -> Bool # (>=) :: ID -> ID -> Bool # max :: ID -> ID -> ID # min :: ID -> ID -> ID #
Show ID #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> ID -> ShowS # show :: ID -> String # showList :: [ID] -> ShowS #
Generic ID #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep ID :: Type -> Type # Methods from :: ID -> Rep ID x # to :: Rep ID x -> ID #
type Rep ID #
Instance details Defined in Bio.Uniprot.Type type Rep ID = D1 (MetaData "ID" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "ID" PrefixI True) (S1 (MetaSel (Just "entryName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: (S1 (MetaSel (Just "status") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Status) :: S1 (MetaSel (Just "seqLength") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int))))

newtype AC #

ACcession numbers. The purpose of accession numbers is to provide a stable way of identifying entries from release to release. It is sometimes necessary for reasons of consistency to change the names of the entries, for example, to ensure that related entries have similar names. However, an accession number is always conserved, and therefore allows unambiguous citation of entries. Researchers who wish to cite entries in their publications should always cite the first accession number. This is commonly referred to as the 'primary accession number'. 'Secondary accession numbers' are sorted alphanumerically.

Constructors

AC
Fields accessionNumbers :: [Text]

Instances

Eq AC #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: AC -> AC -> Bool # (/=) :: AC -> AC -> Bool #
Ord AC #
Instance details Defined in Bio.Uniprot.Type Methods compare :: AC -> AC -> Ordering # (<) :: AC -> AC -> Bool # (<=) :: AC -> AC -> Bool # (>) :: AC -> AC -> Bool # (>=) :: AC -> AC -> Bool # max :: AC -> AC -> AC # min :: AC -> AC -> AC #
Show AC #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> AC -> ShowS # show :: AC -> String # showList :: [AC] -> ShowS #
Generic AC #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep AC :: Type -> Type # Methods from :: AC -> Rep AC x # to :: Rep AC x -> AC #
type Rep AC #
Instance details Defined in Bio.Uniprot.Type type Rep AC = D1 (MetaData "AC" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" True) (C1 (MetaCons "AC" PrefixI True) (S1 (MetaSel (Just "accessionNumbers") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text])))

data DT #

DaTe: the date of creation and last modification of the database entry.

Constructors

DT

Fields

dbIntegrationDate :: Text
Indicates when the entry first appeared in the database.
dbName :: Text
Indicates in which section of UniProtKB, Swiss-Prot or TrEMBL, the entry can be found.
seqVersionDate :: Text
Indicates when the sequence data was last modified.
seqVersion :: Int
The sequence version number of an entry is incremented by one when the amino acid sequence shown in the sequence record is modified.
entryVersionDate :: Text
Indicates when data other than the sequence was last modified.
entryVersion :: Int
The entry version number is incremented by one whenever any data in the flat file representation of the entry is modified.

Instances

Eq DT #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: DT -> DT -> Bool # (/=) :: DT -> DT -> Bool #
Ord DT #
Instance details Defined in Bio.Uniprot.Type Methods compare :: DT -> DT -> Ordering # (<) :: DT -> DT -> Bool # (<=) :: DT -> DT -> Bool # (>) :: DT -> DT -> Bool # (>=) :: DT -> DT -> Bool # max :: DT -> DT -> DT # min :: DT -> DT -> DT #
Show DT #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> DT -> ShowS # show :: DT -> String # showList :: [DT] -> ShowS #
Generic DT #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep DT :: Type -> Type # Methods from :: DT -> Rep DT x # to :: Rep DT x -> DT #
type Rep DT #
Instance details Defined in Bio.Uniprot.Type type Rep DT = D1 (MetaData "DT" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "DT" PrefixI True) ((S1 (MetaSel (Just "dbIntegrationDate") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: (S1 (MetaSel (Just "dbName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: S1 (MetaSel (Just "seqVersionDate") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text))) :: (S1 (MetaSel (Just "seqVersion") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :: (S1 (MetaSel (Just "entryVersionDate") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :*: S1 (MetaSel (Just "entryVersion") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))))

data Name #

Constructors

Name
Fields fullName :: Text The full name. shortName :: [Text] A set of abbreviations of the full name or acronyms. ecNumber :: [Text] A set of Enzyme Commission numbers.

Instances

Eq Name #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Name -> Name -> Bool # (/=) :: Name -> Name -> Bool #
Ord Name #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Name -> Name -> Ordering # (<) :: Name -> Name -> Bool # (<=) :: Name -> Name -> Bool # (>) :: Name -> Name -> Bool # (>=) :: Name -> Name -> Bool # max :: Name -> Name -> Name # min :: Name -> Name -> Name #
Show Name #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Name -> ShowS # show :: Name -> String # showList :: [Name] -> ShowS #
Generic Name #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Name :: Type -> Type # Methods from :: Name -> Rep Name x # to :: Rep Name x -> Name #
type Rep Name #
Instance details Defined in Bio.Uniprot.Type type Rep Name = D1 (MetaData "Name" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "Name" PrefixI True) (S1 (MetaSel (Just "fullName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: (S1 (MetaSel (Just "shortName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text]) :: S1 (MetaSel (Just "ecNumber") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text]))))

data AltName #

Constructors

Simple Name
Allergen Text
Biotech Text
CDAntigen Text
INN Text

Instances

Eq AltName #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: AltName -> AltName -> Bool # (/=) :: AltName -> AltName -> Bool #
Ord AltName #
Instance details Defined in Bio.Uniprot.Type Methods compare :: AltName -> AltName -> Ordering # (<) :: AltName -> AltName -> Bool # (<=) :: AltName -> AltName -> Bool # (>) :: AltName -> AltName -> Bool # (>=) :: AltName -> AltName -> Bool # max :: AltName -> AltName -> AltName # min :: AltName -> AltName -> AltName #
Show AltName #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> AltName -> ShowS # show :: AltName -> String # showList :: [AltName] -> ShowS #
Generic AltName #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep AltName :: Type -> Type # Methods from :: AltName -> Rep AltName x # to :: Rep AltName x -> AltName #
type Rep AltName #
Instance details Defined in Bio.Uniprot.Type type Rep AltName = D1 (MetaData "AltName" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) ((C1 (MetaCons "Simple" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Name)) :+: C1 (MetaCons "Allergen" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text))) :+: (C1 (MetaCons "Biotech" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)) :+: (C1 (MetaCons "CDAntigen" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)) :+: C1 (MetaCons "INN" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))))

data Flag #

Constructors

Fragment	The complete sequence is not determined.
Fragments	The complete sequence is not determined.
Precursor	The sequence displayed does not correspond to the mature form of the protein.

Instances

Bounded Flag #
Instance details Defined in Bio.Uniprot.Type Methods minBound :: Flag # maxBound :: Flag #
Enum Flag #
Instance details Defined in Bio.Uniprot.Type Methods succ :: Flag -> Flag # pred :: Flag -> Flag # toEnum :: Int -> Flag # fromEnum :: Flag -> Int # enumFrom :: Flag -> [Flag] # enumFromThen :: Flag -> Flag -> [Flag] # enumFromTo :: Flag -> Flag -> [Flag] # enumFromThenTo :: Flag -> Flag -> Flag -> [Flag] #
Eq Flag #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Flag -> Flag -> Bool # (/=) :: Flag -> Flag -> Bool #
Ord Flag #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Flag -> Flag -> Ordering # (<) :: Flag -> Flag -> Bool # (<=) :: Flag -> Flag -> Bool # (>) :: Flag -> Flag -> Bool # (>=) :: Flag -> Flag -> Bool # max :: Flag -> Flag -> Flag # min :: Flag -> Flag -> Flag #
Read Flag #
Instance details Defined in Bio.Uniprot.Type Methods readsPrec :: Int -> ReadS Flag # readList :: ReadS [Flag] # readPrec :: ReadPrec Flag # readListPrec :: ReadPrec [Flag] #
Show Flag #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Flag -> ShowS # show :: Flag -> String # showList :: [Flag] -> ShowS #
Generic Flag #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Flag :: Type -> Type # Methods from :: Flag -> Rep Flag x # to :: Rep Flag x -> Flag #
type Rep Flag #
Instance details Defined in Bio.Uniprot.Type type Rep Flag = D1 (MetaData "Flag" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "Fragment" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "Fragments" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Precursor" PrefixI False) (U1 :: Type -> Type)))

data DE #

DEscription - general descriptive information about the sequence stored.

Constructors

DE

Fields

recName :: Maybe Name
The name recommended by the UniProt consortium.
altNames :: [AltName]
A synonym of the recommended name.
subNames :: [Name]
A name provided by the submitter of the underlying nucleotide sequence.
includes :: [DE]
A protein is known to include multiple functional domains each of which is described by a different name.
contains :: [DE]
The functional domains of an enzyme are cleaved, but the catalytic activity can only be observed, when the individual chains reorganize in a complex.
flags :: [Flag]
Flags whether the entire is a precursor or/and a fragment.

Instances

Eq DE #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: DE -> DE -> Bool # (/=) :: DE -> DE -> Bool #
Ord DE #
Instance details Defined in Bio.Uniprot.Type Methods compare :: DE -> DE -> Ordering # (<) :: DE -> DE -> Bool # (<=) :: DE -> DE -> Bool # (>) :: DE -> DE -> Bool # (>=) :: DE -> DE -> Bool # max :: DE -> DE -> DE # min :: DE -> DE -> DE #
Show DE #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> DE -> ShowS # show :: DE -> String # showList :: [DE] -> ShowS #
Generic DE #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep DE :: Type -> Type # Methods from :: DE -> Rep DE x # to :: Rep DE x -> DE #
type Rep DE #
Instance details Defined in Bio.Uniprot.Type type Rep DE = D1 (MetaData "DE" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "DE" PrefixI True) ((S1 (MetaSel (Just "recName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe Name)) :: (S1 (MetaSel (Just "altNames") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [AltName]) :: S1 (MetaSel (Just "subNames") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Name]))) :: (S1 (MetaSel (Just "includes") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [DE]) :: (S1 (MetaSel (Just "contains") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [DE]) :*: S1 (MetaSel (Just "flags") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Flag])))))

data GN #

Gene Name - the name(s) of the gene(s) that code for the stored protein sequence.

Constructors

GN
Fields geneName :: Maybe Text The name used to represent a gene. synonyms :: [Text] Other (unofficial) names of a gene. orderedLocusNames :: [Text] A name used to represent an ORF in a completely sequenced genome or chromosome. orfNames :: [Text] A name temporarily attributed by a sequencing project to an open reading frame.

Instances

Eq GN #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: GN -> GN -> Bool # (/=) :: GN -> GN -> Bool #
Ord GN #
Instance details Defined in Bio.Uniprot.Type Methods compare :: GN -> GN -> Ordering # (<) :: GN -> GN -> Bool # (<=) :: GN -> GN -> Bool # (>) :: GN -> GN -> Bool # (>=) :: GN -> GN -> Bool # max :: GN -> GN -> GN # min :: GN -> GN -> GN #
Show GN #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> GN -> ShowS # show :: GN -> String # showList :: [GN] -> ShowS #
Generic GN #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep GN :: Type -> Type # Methods from :: GN -> Rep GN x # to :: Rep GN x -> GN #
type Rep GN #
Instance details Defined in Bio.Uniprot.Type type Rep GN = D1 (MetaData "GN" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "GN" PrefixI True) ((S1 (MetaSel (Just "geneName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe Text)) :: S1 (MetaSel (Just "synonyms") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text])) :: (S1 (MetaSel (Just "orderedLocusNames") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text]) :*: S1 (MetaSel (Just "orfNames") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text]))))

newtype OS #

Organism Species - the organism which was the source of the stored sequence.

Constructors

OS
Fields specie :: Text

Instances

Eq OS #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: OS -> OS -> Bool # (/=) :: OS -> OS -> Bool #
Ord OS #
Instance details Defined in Bio.Uniprot.Type Methods compare :: OS -> OS -> Ordering # (<) :: OS -> OS -> Bool # (<=) :: OS -> OS -> Bool # (>) :: OS -> OS -> Bool # (>=) :: OS -> OS -> Bool # max :: OS -> OS -> OS # min :: OS -> OS -> OS #
Show OS #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> OS -> ShowS # show :: OS -> String # showList :: [OS] -> ShowS #
Generic OS #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep OS :: Type -> Type # Methods from :: OS -> Rep OS x # to :: Rep OS x -> OS #
type Rep OS #
Instance details Defined in Bio.Uniprot.Type type Rep OS = D1 (MetaData "OS" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" True) (C1 (MetaCons "OS" PrefixI True) (S1 (MetaSel (Just "specie") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))

data Plastid #

A enum of possible plastid types, based on either taxonomic lineage or photosynthetic capacity.

Constructors

PlastidSimple	The term Plastid is used when the capacities of the organism are unclear; for example in the parasitic plants of the Cuscuta lineage, where sometimes young tissue is photosynthetic.
PlastidApicoplast	Apicoplasts are the plastids found in Apicocomplexa parasites such as Eimeria, Plasmodium and Toxoplasma; they are not photosynthetic.
PlastidChloroplast	Chloroplasts are the plastids found in all land plants and algae with the exception of the glaucocystophyte algae (see below). Chloroplasts in green tissue are photosynthetic; in other tissues they may not be photosynthetic and then may also have secondary information relating to subcellular location (e.g. amyloplasts, chromoplasts).
PlastidOrganellarChromatophore	Chloroplasts are the plastids found in all land plants and algae with the exception of the glaucocystophyte algae (see below). Chloroplasts in green tissue are photosynthetic; in other tissues they may not be photosynthetic and then may also have secondary information relating to subcellular location (e.g. amyloplasts, chromoplasts).
PlastidCyanelle	Cyanelles are the plastids found in the glaucocystophyte algae. They are also photosynthetic but their plastid has a vestigial cell wall between the 2 envelope membranes.
PlastidNonPhotosynthetic	Non-photosynthetic plastid is used when the plastid in question derives from a photosynthetic lineage but the plastid in question is missing essential genes. Some examples are Aneura mirabilis, Epifagus virginiana, Helicosporidium (a liverwort, higher plant and green alga respectively).

Instances

Bounded Plastid #
Instance details Defined in Bio.Uniprot.Type Methods minBound :: Plastid # maxBound :: Plastid #
Enum Plastid #
Instance details Defined in Bio.Uniprot.Type Methods succ :: Plastid -> Plastid # pred :: Plastid -> Plastid # toEnum :: Int -> Plastid # fromEnum :: Plastid -> Int # enumFrom :: Plastid -> [Plastid] # enumFromThen :: Plastid -> Plastid -> [Plastid] # enumFromTo :: Plastid -> Plastid -> [Plastid] # enumFromThenTo :: Plastid -> Plastid -> Plastid -> [Plastid] #
Eq Plastid #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Plastid -> Plastid -> Bool # (/=) :: Plastid -> Plastid -> Bool #
Ord Plastid #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Plastid -> Plastid -> Ordering # (<) :: Plastid -> Plastid -> Bool # (<=) :: Plastid -> Plastid -> Bool # (>) :: Plastid -> Plastid -> Bool # (>=) :: Plastid -> Plastid -> Bool # max :: Plastid -> Plastid -> Plastid # min :: Plastid -> Plastid -> Plastid #
Show Plastid #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Plastid -> ShowS # show :: Plastid -> String # showList :: [Plastid] -> ShowS #
Generic Plastid #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Plastid :: Type -> Type # Methods from :: Plastid -> Rep Plastid x # to :: Rep Plastid x -> Plastid #
type Rep Plastid #
Instance details Defined in Bio.Uniprot.Type type Rep Plastid = D1 (MetaData "Plastid" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) ((C1 (MetaCons "PlastidSimple" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "PlastidApicoplast" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "PlastidChloroplast" PrefixI False) (U1 :: Type -> Type))) :+: (C1 (MetaCons "PlastidOrganellarChromatophore" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "PlastidCyanelle" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "PlastidNonPhotosynthetic" PrefixI False) (U1 :: Type -> Type))))

data OG #

OrGanelle - indicates if the gene coding for a protein originates from mitochondria, a plastid, a nucleomorph or a plasmid.

Constructors

Hydrogenosome	Hydrogenosomes are membrane-enclosed redox organelles found in some anaerobic unicellular eukaryotes which contain hydrogenase and produce hydrogen and ATP by glycolysis. They are thought to have evolved from mitochondria; most hydrogenosomes lack a genome, but some like (e.g. the anaerobic ciliate Nyctotherus ovalis) have retained a rudimentary genome.
Mitochondrion	Mitochondria are redox-active membrane-bound organelles found in the cytoplasm of most eukaryotic cells. They are the site of sthe reactions of oxidative phosphorylation, which results in the formation of ATP.
Nucleomorph	Nucleomorphs are reduced vestigal nuclei found in the plastids of cryptomonad and chlorachniophyte algae. The plastids originate from engulfed eukaryotic phototrophs.
Plasmid [Text]	Plasmid with a specific name. If an entry reports the sequence of a protein identical in a number of plasmids, the names of these plasmids will all be listed.
Plastid Plastid	Plastids are classified based on either their taxonomic lineage or in some cases on their photosynthetic capacity.

Instances

Eq OG #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: OG -> OG -> Bool # (/=) :: OG -> OG -> Bool #
Ord OG #
Instance details Defined in Bio.Uniprot.Type Methods compare :: OG -> OG -> Ordering # (<) :: OG -> OG -> Bool # (<=) :: OG -> OG -> Bool # (>) :: OG -> OG -> Bool # (>=) :: OG -> OG -> Bool # max :: OG -> OG -> OG # min :: OG -> OG -> OG #
Show OG #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> OG -> ShowS # show :: OG -> String # showList :: [OG] -> ShowS #
Generic OG #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep OG :: Type -> Type # Methods from :: OG -> Rep OG x # to :: Rep OG x -> OG #
type Rep OG #
Instance details Defined in Bio.Uniprot.Type type Rep OG = D1 (MetaData "OG" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) ((C1 (MetaCons "Hydrogenosome" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Mitochondrion" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "Nucleomorph" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "Plasmid" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text])) :+: C1 (MetaCons "Plastid" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Plastid)))))

newtype OC #

Organism Classification - the taxonomic classification of the source organism.

Constructors

OC
Fields nodes :: [Text]

Instances

Eq OC #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: OC -> OC -> Bool # (/=) :: OC -> OC -> Bool #
Ord OC #
Instance details Defined in Bio.Uniprot.Type Methods compare :: OC -> OC -> Ordering # (<) :: OC -> OC -> Bool # (<=) :: OC -> OC -> Bool # (>) :: OC -> OC -> Bool # (>=) :: OC -> OC -> Bool # max :: OC -> OC -> OC # min :: OC -> OC -> OC #
Show OC #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> OC -> ShowS # show :: OC -> String # showList :: [OC] -> ShowS #
Generic OC #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep OC :: Type -> Type # Methods from :: OC -> Rep OC x # to :: Rep OC x -> OC #
type Rep OC #
Instance details Defined in Bio.Uniprot.Type type Rep OC = D1 (MetaData "OC" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" True) (C1 (MetaCons "OC" PrefixI True) (S1 (MetaSel (Just "nodes") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text])))

data OX #

Organism taxonomy cross-reference indicates the identifier of a specific organism in a taxonomic database.

Constructors

OX
Fields databaseQualifier :: Text Taxonomy database Qualifier taxonomicCode :: Text Taxonomic code

Instances

Eq OX #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: OX -> OX -> Bool # (/=) :: OX -> OX -> Bool #
Ord OX #
Instance details Defined in Bio.Uniprot.Type Methods compare :: OX -> OX -> Ordering # (<) :: OX -> OX -> Bool # (<=) :: OX -> OX -> Bool # (>) :: OX -> OX -> Bool # (>=) :: OX -> OX -> Bool # max :: OX -> OX -> OX # min :: OX -> OX -> OX #
Show OX #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> OX -> ShowS # show :: OX -> String # showList :: [OX] -> ShowS #
Generic OX #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep OX :: Type -> Type # Methods from :: OX -> Rep OX x # to :: Rep OX x -> OX #
type Rep OX #
Instance details Defined in Bio.Uniprot.Type type Rep OX = D1 (MetaData "OX" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "OX" PrefixI True) (S1 (MetaSel (Just "databaseQualifier") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :*: S1 (MetaSel (Just "taxonomicCode") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))

data OH #

Organism Host - indicates the host organism(s) that are susceptible to be infected by a virus. Appears only in viral entries.

Constructors

OH
Fields taxId :: Text hostName :: Text

Instances

Eq OH #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: OH -> OH -> Bool # (/=) :: OH -> OH -> Bool #
Ord OH #
Instance details Defined in Bio.Uniprot.Type Methods compare :: OH -> OH -> Ordering # (<) :: OH -> OH -> Bool # (<=) :: OH -> OH -> Bool # (>) :: OH -> OH -> Bool # (>=) :: OH -> OH -> Bool # max :: OH -> OH -> OH # min :: OH -> OH -> OH #
Show OH #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> OH -> ShowS # show :: OH -> String # showList :: [OH] -> ShowS #
Generic OH #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep OH :: Type -> Type # Methods from :: OH -> Rep OH x # to :: Rep OH x -> OH #
type Rep OH #
Instance details Defined in Bio.Uniprot.Type type Rep OH = D1 (MetaData "OH" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "OH" PrefixI True) (S1 (MetaSel (Just "taxId") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :*: S1 (MetaSel (Just "hostName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))

data Token #

Reference comment token.

Constructors

STRAIN
PLASMID
TRANSPOSON
TISSUE

Instances

Bounded Token #
Instance details Defined in Bio.Uniprot.Type Methods minBound :: Token # maxBound :: Token #
Enum Token #
Instance details Defined in Bio.Uniprot.Type Methods succ :: Token -> Token # pred :: Token -> Token # toEnum :: Int -> Token # fromEnum :: Token -> Int # enumFrom :: Token -> [Token] # enumFromThen :: Token -> Token -> [Token] # enumFromTo :: Token -> Token -> [Token] # enumFromThenTo :: Token -> Token -> Token -> [Token] #
Eq Token #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Token -> Token -> Bool # (/=) :: Token -> Token -> Bool #
Ord Token #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Token -> Token -> Ordering # (<) :: Token -> Token -> Bool # (<=) :: Token -> Token -> Bool # (>) :: Token -> Token -> Bool # (>=) :: Token -> Token -> Bool # max :: Token -> Token -> Token # min :: Token -> Token -> Token #
Show Token #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Token -> ShowS # show :: Token -> String # showList :: [Token] -> ShowS #
Generic Token #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Token :: Type -> Type # Methods from :: Token -> Rep Token x # to :: Rep Token x -> Token #
type Rep Token #
Instance details Defined in Bio.Uniprot.Type type Rep Token = D1 (MetaData "Token" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) ((C1 (MetaCons "STRAIN" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "PLASMID" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "TRANSPOSON" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "TISSUE" PrefixI False) (U1 :: Type -> Type)))

data BibliographicDB #

Bibliographic database names.

Constructors

MEDLINE
PubMed
DOI
AGRICOLA

Instances

Bounded BibliographicDB #
Instance details Defined in Bio.Uniprot.Type Methods minBound :: BibliographicDB # maxBound :: BibliographicDB #
Enum BibliographicDB #
Instance details Defined in Bio.Uniprot.Type Methods succ :: BibliographicDB -> BibliographicDB # pred :: BibliographicDB -> BibliographicDB # toEnum :: Int -> BibliographicDB # fromEnum :: BibliographicDB -> Int # enumFrom :: BibliographicDB -> [BibliographicDB] # enumFromThen :: BibliographicDB -> BibliographicDB -> [BibliographicDB] # enumFromTo :: BibliographicDB -> BibliographicDB -> [BibliographicDB] # enumFromThenTo :: BibliographicDB -> BibliographicDB -> BibliographicDB -> [BibliographicDB] #
Eq BibliographicDB #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: BibliographicDB -> BibliographicDB -> Bool # (/=) :: BibliographicDB -> BibliographicDB -> Bool #
Ord BibliographicDB #
Instance details Defined in Bio.Uniprot.Type Methods compare :: BibliographicDB -> BibliographicDB -> Ordering # (<) :: BibliographicDB -> BibliographicDB -> Bool # (<=) :: BibliographicDB -> BibliographicDB -> Bool # (>) :: BibliographicDB -> BibliographicDB -> Bool # (>=) :: BibliographicDB -> BibliographicDB -> Bool # max :: BibliographicDB -> BibliographicDB -> BibliographicDB # min :: BibliographicDB -> BibliographicDB -> BibliographicDB #
Show BibliographicDB #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> BibliographicDB -> ShowS # show :: BibliographicDB -> String # showList :: [BibliographicDB] -> ShowS #
Generic BibliographicDB #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep BibliographicDB :: Type -> Type # Methods from :: BibliographicDB -> Rep BibliographicDB x # to :: Rep BibliographicDB x -> BibliographicDB #
type Rep BibliographicDB #
Instance details Defined in Bio.Uniprot.Type type Rep BibliographicDB = D1 (MetaData "BibliographicDB" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) ((C1 (MetaCons "MEDLINE" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "PubMed" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "DOI" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "AGRICOLA" PrefixI False) (U1 :: Type -> Type)))

data RN #

Reference Number - a sequential number to each reference citation in an entry.

Constructors

RN
Fields number :: Int evidence :: [Text]

Instances

Eq RN #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: RN -> RN -> Bool # (/=) :: RN -> RN -> Bool #
Ord RN #
Instance details Defined in Bio.Uniprot.Type Methods compare :: RN -> RN -> Ordering # (<) :: RN -> RN -> Bool # (<=) :: RN -> RN -> Bool # (>) :: RN -> RN -> Bool # (>=) :: RN -> RN -> Bool # max :: RN -> RN -> RN # min :: RN -> RN -> RN #
Show RN #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> RN -> ShowS # show :: RN -> String # showList :: [RN] -> ShowS #
Generic RN #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep RN :: Type -> Type # Methods from :: RN -> Rep RN x # to :: Rep RN x -> RN #
type Rep RN #
Instance details Defined in Bio.Uniprot.Type type Rep RN = D1 (MetaData "RN" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "RN" PrefixI True) (S1 (MetaSel (Just "number") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :*: S1 (MetaSel (Just "evidence") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text])))

data Reference #

Reference lines.

Constructors

Reference

Fields

rn :: Int
Reference Number - a sequential number to each reference citation in an entry.
rp :: Text
Reference Position - the extent of the work relevant to the entry carried out by the authors.
rc :: [(Token, Text)]
Reference Comment - comments relevant to the reference cited.
rx :: [(BibliographicDB, Text)]
Reference cross-reference - the identifier assigned to a specific reference in a bibliographic database.
rg :: [Text]
Reference Group - the consortium name associated with a given citation.
ra :: [Text]
Reference Author - authors of the paper (or other work) cited.
rt :: Maybe Text
Reference Title - the title of the paper (or other work) cited as exactly as possible given the limitations of the computer character set.
rl :: Text
Reference Location - he conventional citation information for the reference.

Instances

Eq Reference #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Reference -> Reference -> Bool # (/=) :: Reference -> Reference -> Bool #
Ord Reference #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Reference -> Reference -> Ordering # (<) :: Reference -> Reference -> Bool # (<=) :: Reference -> Reference -> Bool # (>) :: Reference -> Reference -> Bool # (>=) :: Reference -> Reference -> Bool # max :: Reference -> Reference -> Reference # min :: Reference -> Reference -> Reference #
Show Reference #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Reference -> ShowS # show :: Reference -> String # showList :: [Reference] -> ShowS #
Generic Reference #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Reference :: Type -> Type # Methods from :: Reference -> Rep Reference x # to :: Rep Reference x -> Reference #
type Rep Reference #
Instance details Defined in Bio.Uniprot.Type type Rep Reference = D1 (MetaData "Reference" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "Reference" PrefixI True) (((S1 (MetaSel (Just "rn") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :: S1 (MetaSel (Just "rp") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)) :: (S1 (MetaSel (Just "rc") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [(Token, Text)]) :: S1 (MetaSel (Just "rx") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [(BibliographicDB, Text)]))) :: ((S1 (MetaSel (Just "rg") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text]) :: S1 (MetaSel (Just "ra") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text])) :: (S1 (MetaSel (Just "rt") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe Text)) :*: S1 (MetaSel (Just "rl") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))))

type Topic = Text #

The comment blocks are arranged according to what we designate as topics.

data CC #

Free text comments on the entry, and are used to convey any useful information.

Constructors

CC
Fields topic :: Topic comment :: Text

Instances

Eq CC #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: CC -> CC -> Bool # (/=) :: CC -> CC -> Bool #
Ord CC #
Instance details Defined in Bio.Uniprot.Type Methods compare :: CC -> CC -> Ordering # (<) :: CC -> CC -> Bool # (<=) :: CC -> CC -> Bool # (>) :: CC -> CC -> Bool # (>=) :: CC -> CC -> Bool # max :: CC -> CC -> CC # min :: CC -> CC -> CC #
Show CC #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> CC -> ShowS # show :: CC -> String # showList :: [CC] -> ShowS #
Generic CC #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep CC :: Type -> Type # Methods from :: CC -> Rep CC x # to :: Rep CC x -> CC #
type Rep CC #
Instance details Defined in Bio.Uniprot.Type type Rep CC = D1 (MetaData "CC" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "CC" PrefixI True) (S1 (MetaSel (Just "topic") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Topic) :*: S1 (MetaSel (Just "comment") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text)))

data DR #

Database cross-Reference - pointers to information in external data resources that is related to UniProtKB entries.

Constructors

DR
Fields resourceAbbr :: Text The abbreviated name of the referenced resource (e.g. PDB). resourceId :: Text An unambiguous pointer to a record in the referenced resource. optionalInfo :: [Text] Used to provide optional information.

Instances

Eq DR #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: DR -> DR -> Bool # (/=) :: DR -> DR -> Bool #
Ord DR #
Instance details Defined in Bio.Uniprot.Type Methods compare :: DR -> DR -> Ordering # (<) :: DR -> DR -> Bool # (<=) :: DR -> DR -> Bool # (>) :: DR -> DR -> Bool # (>=) :: DR -> DR -> Bool # max :: DR -> DR -> DR # min :: DR -> DR -> DR #
Show DR #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> DR -> ShowS # show :: DR -> String # showList :: [DR] -> ShowS #
Generic DR #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep DR :: Type -> Type # Methods from :: DR -> Rep DR x # to :: Rep DR x -> DR #
type Rep DR #
Instance details Defined in Bio.Uniprot.Type type Rep DR = D1 (MetaData "DR" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "DR" PrefixI True) (S1 (MetaSel (Just "resourceAbbr") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: (S1 (MetaSel (Just "resourceId") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: S1 (MetaSel (Just "optionalInfo") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text]))))

data PE #

Protein existence - indication on the evidences that we currently have for the existence of a protein. Because most protein sequences are derived from translation of nucleotide sequences and are mere predictions, the PE line indicates what the evidences are of the existence of a protein.

Constructors

EvidenceAtProteinLevel
EvidenceAtTranscriptLevel
InferredFromHomology
Predicted
Uncertain

Instances

Eq PE #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: PE -> PE -> Bool # (/=) :: PE -> PE -> Bool #
Ord PE #
Instance details Defined in Bio.Uniprot.Type Methods compare :: PE -> PE -> Ordering # (<) :: PE -> PE -> Bool # (<=) :: PE -> PE -> Bool # (>) :: PE -> PE -> Bool # (>=) :: PE -> PE -> Bool # max :: PE -> PE -> PE # min :: PE -> PE -> PE #
Show PE #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> PE -> ShowS # show :: PE -> String # showList :: [PE] -> ShowS #
Generic PE #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep PE :: Type -> Type # Methods from :: PE -> Rep PE x # to :: Rep PE x -> PE #
type Rep PE #
Instance details Defined in Bio.Uniprot.Type type Rep PE = D1 (MetaData "PE" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) ((C1 (MetaCons "EvidenceAtProteinLevel" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "EvidenceAtTranscriptLevel" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "InferredFromHomology" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "Predicted" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "Uncertain" PrefixI False) (U1 :: Type -> Type))))

newtype KW #

KeyWord - information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.

Constructors

KW
Fields keywords :: [Text]

Instances

Eq KW #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: KW -> KW -> Bool # (/=) :: KW -> KW -> Bool #
Ord KW #
Instance details Defined in Bio.Uniprot.Type Methods compare :: KW -> KW -> Ordering # (<) :: KW -> KW -> Bool # (<=) :: KW -> KW -> Bool # (>) :: KW -> KW -> Bool # (>=) :: KW -> KW -> Bool # max :: KW -> KW -> KW # min :: KW -> KW -> KW #
Show KW #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> KW -> ShowS # show :: KW -> String # showList :: [KW] -> ShowS #
Generic KW #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep KW :: Type -> Type # Methods from :: KW -> Rep KW x # to :: Rep KW x -> KW #
type Rep KW #
Instance details Defined in Bio.Uniprot.Type type Rep KW = D1 (MetaData "KW" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" True) (C1 (MetaCons "KW" PrefixI True) (S1 (MetaSel (Just "keywords") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text])))

data Endpoint #

Constructors

ExactEP Int
NTerminalEP Int
CTerminalEP Int
UncertainEP Int
UnknownEP

Instances

Eq Endpoint #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Endpoint -> Endpoint -> Bool # (/=) :: Endpoint -> Endpoint -> Bool #
Ord Endpoint #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Endpoint -> Endpoint -> Ordering # (<) :: Endpoint -> Endpoint -> Bool # (<=) :: Endpoint -> Endpoint -> Bool # (>) :: Endpoint -> Endpoint -> Bool # (>=) :: Endpoint -> Endpoint -> Bool # max :: Endpoint -> Endpoint -> Endpoint # min :: Endpoint -> Endpoint -> Endpoint #
Show Endpoint #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Endpoint -> ShowS # show :: Endpoint -> String # showList :: [Endpoint] -> ShowS #
Generic Endpoint #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Endpoint :: Type -> Type # Methods from :: Endpoint -> Rep Endpoint x # to :: Rep Endpoint x -> Endpoint #
type Rep Endpoint #
Instance details Defined in Bio.Uniprot.Type type Rep Endpoint = D1 (MetaData "Endpoint" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) ((C1 (MetaCons "ExactEP" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)) :+: C1 (MetaCons "NTerminalEP" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int))) :+: (C1 (MetaCons "CTerminalEP" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)) :+: (C1 (MetaCons "UncertainEP" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)) :+: C1 (MetaCons "UnknownEP" PrefixI False) (U1 :: Type -> Type))))

data FT #

Feature Table - means for the annotation of the sequence data.

Constructors

FT
Fields keyName :: Text Key name. fromEP :: Endpoint `From` endpoint. toEP :: Endpoint `To` endpoint. description :: [Text] Description.

Instances

Eq FT #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: FT -> FT -> Bool # (/=) :: FT -> FT -> Bool #
Ord FT #
Instance details Defined in Bio.Uniprot.Type Methods compare :: FT -> FT -> Ordering # (<) :: FT -> FT -> Bool # (<=) :: FT -> FT -> Bool # (>) :: FT -> FT -> Bool # (>=) :: FT -> FT -> Bool # max :: FT -> FT -> FT # min :: FT -> FT -> FT #
Show FT #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> FT -> ShowS # show :: FT -> String # showList :: [FT] -> ShowS #
Generic FT #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep FT :: Type -> Type # Methods from :: FT -> Rep FT x # to :: Rep FT x -> FT #
type Rep FT #
Instance details Defined in Bio.Uniprot.Type type Rep FT = D1 (MetaData "FT" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "FT" PrefixI True) ((S1 (MetaSel (Just "keyName") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :: S1 (MetaSel (Just "fromEP") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Endpoint)) :: (S1 (MetaSel (Just "toEP") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Endpoint) :*: S1 (MetaSel (Just "description") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Text]))))

data SQ #

SeQuence header - sequence data and a quick summary of its content.

Constructors

SQ
Fields length :: Int Length of the sequence in amino acids. molWeight :: Int Molecular weight rounded to the nearest mass unit (Dalton). crc64 :: Text Sequence 64-bit CRC (Cyclic Redundancy Check) value. sequence :: Text Sequence of the protein

Instances

Eq SQ #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: SQ -> SQ -> Bool # (/=) :: SQ -> SQ -> Bool #
Ord SQ #
Instance details Defined in Bio.Uniprot.Type Methods compare :: SQ -> SQ -> Ordering # (<) :: SQ -> SQ -> Bool # (<=) :: SQ -> SQ -> Bool # (>) :: SQ -> SQ -> Bool # (>=) :: SQ -> SQ -> Bool # max :: SQ -> SQ -> SQ # min :: SQ -> SQ -> SQ #
Show SQ #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> SQ -> ShowS # show :: SQ -> String # showList :: [SQ] -> ShowS #
Generic SQ #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep SQ :: Type -> Type # Methods from :: SQ -> Rep SQ x # to :: Rep SQ x -> SQ #
type Rep SQ #
Instance details Defined in Bio.Uniprot.Type type Rep SQ = D1 (MetaData "SQ" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "SQ" PrefixI True) ((S1 (MetaSel (Just "length") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int) :: S1 (MetaSel (Just "molWeight") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)) :: (S1 (MetaSel (Just "crc64") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text) :*: S1 (MetaSel (Just "sequence") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Text))))

data Record #

Full UniProt record in UniProt-KB format.

Constructors

Record
Fields id :: ID ac :: AC dt :: DT de :: DE gn :: [GN] os :: OS og :: [OG] oc :: OC ox :: OX oh :: [OH] refs :: [Reference] cc :: [CC] dr :: [DR] pe :: PE kw :: Maybe KW ft :: [FT] sq :: SQ

Instances

Eq Record #
Instance details Defined in Bio.Uniprot.Type Methods (==) :: Record -> Record -> Bool # (/=) :: Record -> Record -> Bool #
Ord Record #
Instance details Defined in Bio.Uniprot.Type Methods compare :: Record -> Record -> Ordering # (<) :: Record -> Record -> Bool # (<=) :: Record -> Record -> Bool # (>) :: Record -> Record -> Bool # (>=) :: Record -> Record -> Bool # max :: Record -> Record -> Record # min :: Record -> Record -> Record #
Show Record #
Instance details Defined in Bio.Uniprot.Type Methods showsPrec :: Int -> Record -> ShowS # show :: Record -> String # showList :: [Record] -> ShowS #
Generic Record #
Instance details Defined in Bio.Uniprot.Type Associated Types type Rep Record :: Type -> Type # Methods from :: Record -> Rep Record x # to :: Rep Record x -> Record #
type Rep Record #
Instance details Defined in Bio.Uniprot.Type type Rep Record = D1 (MetaData "Record" "Bio.Uniprot.Type" "uniprot-kb-0.1.2.0-2jQNi2MIlXDFWstOwhMKEH" False) (C1 (MetaCons "Record" PrefixI True) ((((S1 (MetaSel (Just "id") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ID) :: S1 (MetaSel (Just "ac") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 AC)) :: (S1 (MetaSel (Just "dt") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 DT) :: S1 (MetaSel (Just "de") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 DE))) :: ((S1 (MetaSel (Just "gn") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [GN]) :: S1 (MetaSel (Just "os") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 OS)) :: (S1 (MetaSel (Just "og") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [OG]) :: S1 (MetaSel (Just "oc") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 OC)))) :: (((S1 (MetaSel (Just "ox") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 OX) :: S1 (MetaSel (Just "oh") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [OH])) :: (S1 (MetaSel (Just "refs") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [Reference]) :: S1 (MetaSel (Just "cc") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [CC]))) :: ((S1 (MetaSel (Just "dr") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [DR]) :: S1 (MetaSel (Just "pe") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 PE)) :: (S1 (MetaSel (Just "kw") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Maybe KW)) :: (S1 (MetaSel (Just "ft") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 [FT]) :: S1 (MetaSel (Just "sq") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 SQ)))))))