| Safe Haskell | Safe |
|---|---|
| Language | Haskell2010 |
Bio.Uniprot.Type
- data Kingdom
- data Organism = Organism {}
- data Status
- data ID = ID {}
- newtype AC = AC {
- accessionNumbers :: [Text]
- data DT = DT {}
- data Name = Name {}
- data AltName
- data Flag
- data DE = DE {}
- data GN = GN {}
- newtype OS = OS {}
- data Plastid
- data OG
- newtype OC = OC {}
- data OX = OX {}
- data OH = OH {}
- data Token
- = STRAIN
- | PLASMID
- | TRANSPOSON
- | TISSUE
- data BibliographicDB
- data RN = RN {}
- data Reference = Reference {}
- type Topic = Text
- data CC = CC {}
- data DR = DR {
- resourceAbbr :: Text
- resourceId :: Text
- optionalInfo :: [Text]
- data PE
- newtype KW = KW {}
- data Endpoint
- data FT = FT {}
- data SQ = SQ {}
- data Record = Record {}
Documentation
Which taxonomic kingdom an
organism belongs to.
Controlled vocabulary of species
Constructors
| Organism | |
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 |
IDentification
Constructors
| ID | |
Fields
| |
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
| |
DaTe: the date of creation and last modification of the database entry.
Constructors
| DT | |
Fields
| |
Constructors
| Name | |
DEscription - general descriptive information about the sequence stored.
Constructors
| DE | |
Fields
| |
Gene Name - the name(s) of the gene(s) that code for the stored protein sequence.
Constructors
| GN | |
Fields
| |
Organism Species - the organism which was the source of the stored sequence.
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). |
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. |
Organism Classification - the taxonomic classification of the source organism.
Organism taxonomy cross-reference indicates the identifier of a specific organism in a taxonomic database.
Constructors
| OX | |
Fields
| |
Organism Host - indicates the host organism(s) that are susceptible to be infected by a virus. Appears only in viral entries.
Reference comment token.
Constructors
| STRAIN | |
| PLASMID | |
| TRANSPOSON | |
| TISSUE |
data BibliographicDB Source #
Bibliographic database names.
Reference Number - a sequential number to each reference citation in an entry.
Reference lines.
Constructors
| Reference | |
Fields
| |
Free text comments on the entry, and are used to convey any useful information.
Database cross-Reference - pointers to information in external data resources that is related to UniProtKB entries.
Constructors
| DR | |
Fields
| |
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.
KeyWord - information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
Constructors
| ExactEP Int | |
| NTerminalEP Int | |
| CTerminalEP Int | |
| UncertainEP Int | |
| UnknownEP |
Feature Table - means for the annotation of the sequence data.
Constructors
| FT | |
SeQuence header - sequence data and a quick summary of its content.
Constructors
| SQ | |
Full UniProt record in UniProt-KB format.
Constructors
| Record | |