NEWS

UniProt.ws 2.44.0

'pageSize' and 'n' arguments added to 'queryUniProt' to expose underlying API request defaults. It is recommended to set the pageSize to a large value e.g. 500 for large queries.

Support for directly mapping to 'Ensembl' IDs with 'select'.
Fixed issue with pagination with large queries (over 25 results) in 'queryUniProt' (@jdreyf, #23)

'UniProt.ws' uses the https://rest.uniprot.org/ API interface for queries.
'mapUniprot' is an exported function to directly map identifiers via UniProt and is used by the 'select' method.
'allToKeys' and 'allFromKeys' provide all the available 'to' and 'from' keys for mapping identifiers
'returnFields' provides all the possible inputs to the 'columns' argument in the 'select' and 'mapUniProt' functions (ids in the 'name' column)

(2.27.1) Fix bug when selecting column GENEID. The mapping mapped both GENEID and ENTREZ_GENE to P_ENTREZGENE. When returning columsn used match to identify but would only pick up first match which was ENTREZ_GENE entry.

UniProt.ws creates an object that talks directly to the web services at UniProt. As such, it provides access to a tremendous library of IDs etc. directly from UniProt.
When the package loads there will be acces to a Uniprot.ws object, this object has select, keys, cols and keytypes methods that behave the way these methods normally do for the other annotation packages.
One important difference from other packages is that the user must use the species method to set the species to their organism of choice (by default it is set for humans). This is because the web resource is too big to return values for all these species at the same time. Uniprot currently has support for over 21,000 different species.
Please see the manual pages and associated vignette for more detailed information about how to use this resource.