# R Interface to UniProt Web Services

## Documentation for package ‘UniProt.ws’ version 2.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I K L M N O P R S T U V W X Z misc

## -- A --

AARHUS/GHENT-2DPAGE | Descriptions of available values for 'columns' and 'keytypes'.
AGD | Descriptions of available values for 'columns' and 'keytypes'.
ALLERGOME | Descriptions of available values for 'columns' and 'keytypes'.
ARACHNOSERVER | Descriptions of available values for 'columns' and 'keytypes'.
availableUniprotSpecies | UniProt.ws objects and their related methods and functions

## -- B --

BIOCYC | Descriptions of available values for 'columns' and 'keytypes'.

## -- C --

CGD | Descriptions of available values for 'columns' and 'keytypes'.
CITATION | Descriptions of available values for 'columns' and 'keytypes'.
class:UniProt.ws | UniProt.ws objects and their related methods and functions
CLEANEX | Descriptions of available values for 'columns' and 'keytypes'.
CLUSTERS | Descriptions of available values for 'columns' and 'keytypes'.
cols | UniProt.ws objects and their related methods and functions
columns | UniProt.ws objects and their related methods and functions
columns-method | UniProt.ws objects and their related methods and functions
COMMENTS | Descriptions of available values for 'columns' and 'keytypes'.
CONOSERVER | Descriptions of available values for 'columns' and 'keytypes'.
CYGD | Descriptions of available values for 'columns' and 'keytypes'.

## -- D --

DATABASE(PDB) | Descriptions of available values for 'columns' and 'keytypes'.
DATABASE(PFAM) | Descriptions of available values for 'columns' and 'keytypes'.
DICTYBASE | Descriptions of available values for 'columns' and 'keytypes'.
DIP | Descriptions of available values for 'columns' and 'keytypes'.
DISPROT | Descriptions of available values for 'columns' and 'keytypes'.
DMDM | Descriptions of available values for 'columns' and 'keytypes'.
DNASU | Descriptions of available values for 'columns' and 'keytypes'.
DOMAIN | Descriptions of available values for 'columns' and 'keytypes'.
DOMAINS | Descriptions of available values for 'columns' and 'keytypes'.
DRUGBANK | Descriptions of available values for 'columns' and 'keytypes'.

## -- E --

EC | Descriptions of available values for 'columns' and 'keytypes'.
ECHOBASE | Descriptions of available values for 'columns' and 'keytypes'.
ECO2DBASE | Descriptions of available values for 'columns' and 'keytypes'.
ECOGENE | Descriptions of available values for 'columns' and 'keytypes'.
EGGNOG | Descriptions of available values for 'columns' and 'keytypes'.
EMBL/GENBANK/DDBJ | Descriptions of available values for 'columns' and 'keytypes'.
EMBL/GENBANK/DDBJ_CDS | Descriptions of available values for 'columns' and 'keytypes'.
ENSEMBL | Descriptions of available values for 'columns' and 'keytypes'.
ENSEMBL_GENOMES | Descriptions of available values for 'columns' and 'keytypes'.
ENSEMBL_GENOMES PROTEIN | Descriptions of available values for 'columns' and 'keytypes'.
ENSEMBL_GENOMES TRANSCRIPT | Descriptions of available values for 'columns' and 'keytypes'.
ENSEMBL_PROTEIN | Descriptions of available values for 'columns' and 'keytypes'.
ENSEMBL_TRANSCRIPT | Descriptions of available values for 'columns' and 'keytypes'.
ENTREZ_GENE | Descriptions of available values for 'columns' and 'keytypes'.
EUHCVDB | Descriptions of available values for 'columns' and 'keytypes'.
EUPATHDB | Descriptions of available values for 'columns' and 'keytypes'.
EXISTENCE | Descriptions of available values for 'columns' and 'keytypes'.

## -- F --

FAMILIES | Descriptions of available values for 'columns' and 'keytypes'.
FEATURES | Descriptions of available values for 'columns' and 'keytypes'.
FLYBASE | Descriptions of available values for 'columns' and 'keytypes'.

## -- G --

GENECARDS | Descriptions of available values for 'columns' and 'keytypes'.
GENEFARM | Descriptions of available values for 'columns' and 'keytypes'.
GENES | Descriptions of available values for 'columns' and 'keytypes'.
GENETREE | Descriptions of available values for 'columns' and 'keytypes'.
GENOLIST | Descriptions of available values for 'columns' and 'keytypes'.
GENOMERNAI | Descriptions of available values for 'columns' and 'keytypes'.
GERMONLINE | Descriptions of available values for 'columns' and 'keytypes'.
GI_NUMBER* | Descriptions of available values for 'columns' and 'keytypes'.
GO | Descriptions of available values for 'columns' and 'keytypes'.
GO-ID | Descriptions of available values for 'columns' and 'keytypes'.

## -- H --

H-INVDB | Descriptions of available values for 'columns' and 'keytypes'.
HGNC | Descriptions of available values for 'columns' and 'keytypes'.
HOGENOM | Descriptions of available values for 'columns' and 'keytypes'.
HOVERGEN | Descriptions of available values for 'columns' and 'keytypes'.
HPA | Descriptions of available values for 'columns' and 'keytypes'.
HSSP | Descriptions of available values for 'columns' and 'keytypes'.

## -- I --

ID | Descriptions of available values for 'columns' and 'keytypes'.
INTERACTOR | Descriptions of available values for 'columns' and 'keytypes'.
INTERPRO | Descriptions of available values for 'columns' and 'keytypes'.
IPI | Descriptions of available values for 'columns' and 'keytypes'.

## -- K --

KEGG | Descriptions of available values for 'columns' and 'keytypes'.
keys | UniProt.ws objects and their related methods and functions
keys-method | UniProt.ws objects and their related methods and functions
keytypes | UniProt.ws objects and their related methods and functions
keytypes-method | UniProt.ws objects and their related methods and functions
KEYWORD-ID | Descriptions of available values for 'columns' and 'keytypes'.
KEYWORDS | Descriptions of available values for 'columns' and 'keytypes'.
KO | Descriptions of available values for 'columns' and 'keytypes'.

## -- L --

LAST-MODIFIED | Descriptions of available values for 'columns' and 'keytypes'.
LEGIOLIST | Descriptions of available values for 'columns' and 'keytypes'.
LENGTH | Descriptions of available values for 'columns' and 'keytypes'.
LEPROMA | Descriptions of available values for 'columns' and 'keytypes'.
lookupUniprotSpeciesFromTaxId | UniProt.ws objects and their related methods and functions

## -- M --

MAIZEGDB | Descriptions of available values for 'columns' and 'keytypes'.
MEROPS | Descriptions of available values for 'columns' and 'keytypes'.
MGI | Descriptions of available values for 'columns' and 'keytypes'.
MIM | Descriptions of available values for 'columns' and 'keytypes'.
MINT | Descriptions of available values for 'columns' and 'keytypes'.

## -- N --

NEXTBIO | Descriptions of available values for 'columns' and 'keytypes'.
NEXTPROT | Descriptions of available values for 'columns' and 'keytypes'.

## -- O --

OMA | Descriptions of available values for 'columns' and 'keytypes'.
ORGANISM | Descriptions of available values for 'columns' and 'keytypes'.
ORGANISM-ID | Descriptions of available values for 'columns' and 'keytypes'.
ORPHANET | Descriptions of available values for 'columns' and 'keytypes'.
ORTHODB | Descriptions of available values for 'columns' and 'keytypes'.

## -- P --

PATHWAY | Descriptions of available values for 'columns' and 'keytypes'.
PATRIC | Descriptions of available values for 'columns' and 'keytypes'.
PDB | Descriptions of available values for 'columns' and 'keytypes'.
PEROXIBASE | Descriptions of available values for 'columns' and 'keytypes'.
PHARMGKB | Descriptions of available values for 'columns' and 'keytypes'.
PHOSSITE | Descriptions of available values for 'columns' and 'keytypes'.
PIR | Descriptions of available values for 'columns' and 'keytypes'.
POMBASE | Descriptions of available values for 'columns' and 'keytypes'.
PPTASEDB | Descriptions of available values for 'columns' and 'keytypes'.
PROTCLUSTDB | Descriptions of available values for 'columns' and 'keytypes'.
PROTEIN NAMES | Descriptions of available values for 'columns' and 'keytypes'.
PSEUDOCAP | Descriptions of available values for 'columns' and 'keytypes'.

## -- R --

REACTOME | Descriptions of available values for 'columns' and 'keytypes'.
REBASE | Descriptions of available values for 'columns' and 'keytypes'.
REFSEQ_NUCLEOTIDE | Descriptions of available values for 'columns' and 'keytypes'.
REFSEQ_PROTEIN | Descriptions of available values for 'columns' and 'keytypes'.
REVIEWED | Descriptions of available values for 'columns' and 'keytypes'.
RGD | Descriptions of available values for 'columns' and 'keytypes'.

## -- S --

SCORE | Descriptions of available values for 'columns' and 'keytypes'.
select | UniProt.ws objects and their related methods and functions
select-method | UniProt.ws objects and their related methods and functions
SEQUENCE | Descriptions of available values for 'columns' and 'keytypes'.
SGD | Descriptions of available values for 'columns' and 'keytypes'.
show-method | UniProt.ws objects and their related methods and functions
species | UniProt.ws objects and their related methods and functions
species-method | UniProt.ws objects and their related methods and functions

## -- T --

TAIR | Descriptions of available values for 'columns' and 'keytypes'.
taxId | UniProt.ws objects and their related methods and functions
taxId-method | UniProt.ws objects and their related methods and functions
taxId<- | UniProt.ws objects and their related methods and functions
taxId<--method | UniProt.ws objects and their related methods and functions
taxname2domain | Utility functions
taxname2species | Utility functions
taxname2taxid | Utility functions
TAXONOMY-LINEAGE | Descriptions of available values for 'columns' and 'keytypes'.
TCDB | Descriptions of available values for 'columns' and 'keytypes'.
TIGR | Descriptions of available values for 'columns' and 'keytypes'.
TOOLS | Descriptions of available values for 'columns' and 'keytypes'.
TUBERCULIST | Descriptions of available values for 'columns' and 'keytypes'.

## -- U --

UCSC | Descriptions of available values for 'columns' and 'keytypes'.
UNIPARC | Descriptions of available values for 'columns' and 'keytypes'.
UNIPATHWAY | Descriptions of available values for 'columns' and 'keytypes'.
UniProt.ws | UniProt.ws objects and their related methods and functions
UniProt.ws-class | UniProt.ws objects and their related methods and functions
UNIPROTKB | Descriptions of available values for 'columns' and 'keytypes'.
UNIREF100 | Descriptions of available values for 'columns' and 'keytypes'.
UNIREF50 | Descriptions of available values for 'columns' and 'keytypes'.
UNIREF90 | Descriptions of available values for 'columns' and 'keytypes'.
updatespecfile | Utility functions
utilities | Utility functions

## -- V --

VECTORBASE | Descriptions of available values for 'columns' and 'keytypes'.
VERSION | Descriptions of available values for 'columns' and 'keytypes'.

## -- W --

WORLD-2DPAGE | Descriptions of available values for 'columns' and 'keytypes'.
WORMBASE | Descriptions of available values for 'columns' and 'keytypes'.
WORMBASE_PROTEIN | Descriptions of available values for 'columns' and 'keytypes'.
WORMBASE_TRANSCRIPT | Descriptions of available values for 'columns' and 'keytypes'.

## -- X --

XENBASE | Descriptions of available values for 'columns' and 'keytypes'.

## -- Z --

ZFIN | Descriptions of available values for 'columns' and 'keytypes'.

## -- misc --

3D | Descriptions of available values for 'columns' and 'keytypes'.