Bio.Uniprot.Type

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

Defined in Bio.Uniprot.Type

Methods

minBound :: Kingdom

maxBound :: Kingdom

Enum Kingdom

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

Defined in Bio.Uniprot.Type

Methods

(==) :: Kingdom -> Kingdom -> Bool

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

Ord Kingdom

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Kingdom -> ShowS

show :: Kingdom -> String

showList :: [Kingdom] -> ShowS

Generic Kingdom

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

Defined in Bio.Uniprot.Type

type Rep Kingdom = D1 ('MetaData "Kingdom" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: Organism -> Organism -> Bool

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

Ord Organism

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Organism -> ShowS

show :: Organism -> String

showList :: [Organism] -> ShowS

Generic Organism

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

Defined in Bio.Uniprot.Type

type Rep Organism = D1 ('MetaData "Organism" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

minBound :: Status

maxBound :: Status

Enum Status

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

Defined in Bio.Uniprot.Type

Methods

(==) :: Status -> Status -> Bool

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

Ord Status

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Status -> ShowS

show :: Status -> String

showList :: [Status] -> ShowS

Generic Status

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

Defined in Bio.Uniprot.Type

type Rep Status = D1 ('MetaData "Status" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: ID -> ID -> Bool

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

Ord ID

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> ID -> ShowS

show :: ID -> String

showList :: [ID] -> ShowS

Generic ID

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

Defined in Bio.Uniprot.Type

type Rep ID = D1 ('MetaData "ID" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: AC -> AC -> Bool

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

Ord AC

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> AC -> ShowS

show :: AC -> String

showList :: [AC] -> ShowS

Generic AC

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

Defined in Bio.Uniprot.Type

type Rep AC = D1 ('MetaData "AC" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: DT -> DT -> Bool

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

Ord DT

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> DT -> ShowS

show :: DT -> String

showList :: [DT] -> ShowS

Generic DT

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

Defined in Bio.Uniprot.Type

type Rep DT = D1 ('MetaData "DT" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: Name -> Name -> Bool

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

Ord Name

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Name -> ShowS

show :: Name -> String

showList :: [Name] -> ShowS

Generic Name

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

Defined in Bio.Uniprot.Type

type Rep Name = D1 ('MetaData "Name" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: AltName -> AltName -> Bool

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

Ord AltName

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> AltName -> ShowS

show :: AltName -> String

showList :: [AltName] -> ShowS

Generic AltName

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

Defined in Bio.Uniprot.Type

type Rep AltName = D1 ('MetaData "AltName" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

minBound :: Flag

maxBound :: Flag

Enum Flag

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

Defined in Bio.Uniprot.Type

Methods

(==) :: Flag -> Flag -> Bool

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

Ord Flag

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

Defined in Bio.Uniprot.Type

Methods

readsPrec :: Int -> ReadS Flag

readList :: ReadS [Flag]

readPrec :: ReadPrec Flag

readListPrec :: ReadPrec [Flag]

Show Flag

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Flag -> ShowS

show :: Flag -> String

showList :: [Flag] -> ShowS

Generic Flag

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

Defined in Bio.Uniprot.Type

type Rep Flag = D1 ('MetaData "Flag" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: DE -> DE -> Bool

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

Ord DE

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> DE -> ShowS

show :: DE -> String

showList :: [DE] -> ShowS

Generic DE

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

Defined in Bio.Uniprot.Type

type Rep DE = D1 ('MetaData "DE" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: GN -> GN -> Bool

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

Ord GN

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> GN -> ShowS

show :: GN -> String

showList :: [GN] -> ShowS

Generic GN

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

Defined in Bio.Uniprot.Type

type Rep GN = D1 ('MetaData "GN" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: OS -> OS -> Bool

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

Ord OS

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> OS -> ShowS

show :: OS -> String

showList :: [OS] -> ShowS

Generic OS

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

Defined in Bio.Uniprot.Type

type Rep OS = D1 ('MetaData "OS" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

minBound :: Plastid

maxBound :: Plastid

Enum Plastid

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

Defined in Bio.Uniprot.Type

Methods

(==) :: Plastid -> Plastid -> Bool

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

Ord Plastid

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Plastid -> ShowS

show :: Plastid -> String

showList :: [Plastid] -> ShowS

Generic Plastid

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

Defined in Bio.Uniprot.Type

type Rep Plastid = D1 ('MetaData "Plastid" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: OG -> OG -> Bool

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

Ord OG

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> OG -> ShowS

show :: OG -> String

showList :: [OG] -> ShowS

Generic OG

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

Defined in Bio.Uniprot.Type

type Rep OG = D1 ('MetaData "OG" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: OC -> OC -> Bool

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

Ord OC

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> OC -> ShowS

show :: OC -> String

showList :: [OC] -> ShowS

Generic OC

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

Defined in Bio.Uniprot.Type

type Rep OC = D1 ('MetaData "OC" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: OX -> OX -> Bool

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

Ord OX

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> OX -> ShowS

show :: OX -> String

showList :: [OX] -> ShowS

Generic OX

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

Defined in Bio.Uniprot.Type

type Rep OX = D1 ('MetaData "OX" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: OH -> OH -> Bool

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

Ord OH

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> OH -> ShowS

show :: OH -> String

showList :: [OH] -> ShowS

Generic OH

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

Defined in Bio.Uniprot.Type

type Rep OH = D1 ('MetaData "OH" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

minBound :: Token

maxBound :: Token

Enum Token

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

Defined in Bio.Uniprot.Type

Methods

(==) :: Token -> Token -> Bool

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

Ord Token

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Token -> ShowS

show :: Token -> String

showList :: [Token] -> ShowS

Generic Token

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

Defined in Bio.Uniprot.Type

type Rep Token = D1 ('MetaData "Token" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

minBound :: BibliographicDB

maxBound :: BibliographicDB

Enum BibliographicDB

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

Defined in Bio.Uniprot.Type

Methods

(==) :: BibliographicDB -> BibliographicDB -> Bool

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

Ord BibliographicDB

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> BibliographicDB -> ShowS

show :: BibliographicDB -> String

showList :: [BibliographicDB] -> ShowS

Generic BibliographicDB

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

Defined in Bio.Uniprot.Type

type Rep BibliographicDB = D1 ('MetaData "BibliographicDB" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: RN -> RN -> Bool

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

Ord RN

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> RN -> ShowS

show :: RN -> String

showList :: [RN] -> ShowS

Generic RN

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

Defined in Bio.Uniprot.Type

type Rep RN = D1 ('MetaData "RN" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: Reference -> Reference -> Bool

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

Ord Reference

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Reference -> ShowS

show :: Reference -> String

showList :: [Reference] -> ShowS

Generic Reference

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

Defined in Bio.Uniprot.Type

type Rep Reference = D1 ('MetaData "Reference" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: CC -> CC -> Bool

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

Ord CC

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> CC -> ShowS

show :: CC -> String

showList :: [CC] -> ShowS

Generic CC

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

Defined in Bio.Uniprot.Type

type Rep CC = D1 ('MetaData "CC" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: DR -> DR -> Bool

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

Ord DR

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> DR -> ShowS

show :: DR -> String

showList :: [DR] -> ShowS

Generic DR

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

Defined in Bio.Uniprot.Type

type Rep DR = D1 ('MetaData "DR" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: PE -> PE -> Bool

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

Ord PE

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> PE -> ShowS

show :: PE -> String

showList :: [PE] -> ShowS

Generic PE

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

Defined in Bio.Uniprot.Type

type Rep PE = D1 ('MetaData "PE" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: KW -> KW -> Bool

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

Ord KW

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> KW -> ShowS

show :: KW -> String

showList :: [KW] -> ShowS

Generic KW

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

Defined in Bio.Uniprot.Type

type Rep KW = D1 ('MetaData "KW" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: Endpoint -> Endpoint -> Bool

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

Ord Endpoint

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Endpoint -> ShowS

show :: Endpoint -> String

showList :: [Endpoint] -> ShowS

Generic Endpoint

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

Defined in Bio.Uniprot.Type

type Rep Endpoint = D1 ('MetaData "Endpoint" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

Defined in Bio.Uniprot.Type

Methods

(==) :: FT -> FT -> Bool

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

Ord FT

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> FT -> ShowS

show :: FT -> String

showList :: [FT] -> ShowS

Generic FT

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

Defined in Bio.Uniprot.Type

type Rep FT = D1 ('MetaData "FT" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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

• len :: 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.

• sequ :: Text

  Sequence of the protein

Instances

Eq SQ

Defined in Bio.Uniprot.Type

Methods

(==) :: SQ -> SQ -> Bool

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

Ord SQ

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> SQ -> ShowS

show :: SQ -> String

showList :: [SQ] -> ShowS

Generic SQ

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

Defined in Bio.Uniprot.Type

type Rep SQ = D1 ('MetaData "SQ" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" 'False) (C1 ('MetaCons "SQ" 'PrefixI 'True) ((S1 ('MetaSel ('Just "len") '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 "sequ") '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

Defined in Bio.Uniprot.Type

Methods

(==) :: Record -> Record -> Bool

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

Ord Record

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

Defined in Bio.Uniprot.Type

Methods

showsPrec :: Int -> Record -> ShowS

show :: Record -> String

showList :: [Record] -> ShowS

Generic Record

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

Defined in Bio.Uniprot.Type

type Rep Record = D1 ('MetaData "Record" "Bio.Uniprot.Type" "cobot-io-0.1.3.20-HPhNL0gUcHREQ55zp5Rm8s" '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)))))))