if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("UniProt.ws")The UniProt.ws
package provides a select interface to the UniProt web service.
suppressPackageStartupMessages({
library(UniProt.ws)
})
up <- UniProt.ws(taxId=9606)If you already know about the select interface, you can immediately learn about the various methods for this object by just looking it’s the help page.
help("UniProt.ws")When you load the
UniProt.ws
package, it creates a UniProt.ws object. If you look at the object you
will see some helpful information about it.
up
#> UniProt.ws interface object:
#> Taxonomy ID: 9606
#> Species name: Homo sapiens (Human)
#> List species with 'availableUniprotSpecies()'By default, you can see that the UniProt.ws object is set to retrieve
records from Homo sapiens. But you can change that of course. In order
to change it, you first need to look up the appropriate taxonomy ID for
the species that you are interested in. Uniprot provides support for
over 20 thousand species, so there are a few to choose from! In order to
make this easier, we have provided the helper function
availableUniprotSpecies which will list all the supported species
along with their taxonomy ids. When you call the
availableUniprotSpecies function, it’s recommended that you make use
of the pattern argument to limit your queries like this:
availableUniprotSpecies(pattern="musculus")
#> kingdom Taxon Node Official (scientific) name
#> ANTMS E 520121 Anthocoris musculus
#> ANTMU E 208057 Anthoscopus musculus
#> APOMU E 238007 Apomys musculus
#> BAIMU E 213557 Baiomys musculus
#> BALMU E 9771 Balaenoptera musculus
#> BLEMU E 197864 Blepharisma musculus
#> MOUSE E 10090 Mus musculus
#> MUSMB E 35531 Mus musculus bactrianus
#> MUSMC E 10091 Mus musculus castaneus
#> MUSMM E 57486 Mus musculus molossinus
#> MUSMS E 186842 Mus musculus x Mus spretus
#> MUSMX E 477816 Mus musculus musculus x Mus musculus castaneus
#> POVM1 V 1891730 Mus musculus polyomavirus 1Once you have learned the taxonomy ID for the species of interest, you
can then change the taxonomy id for the UniProt.ws object using
taxId setter or by calling the constructor for UniProt.ws
mouseUp <- UniProt.ws(10090)
mouseUp
#> UniProt.ws interface object:
#> Taxonomy ID: 10090
#> Species name: Mus musculus (Mouse)
#> List species with 'availableUniprotSpecies()'As you can see the species is different for the mouseUp new object.
Once you are safisfied that you have an uniport.ws that is using the
appropriate organsims, you can make use of the standard set of methods
in a select interface. Specifically: columns, keytypes, keys and
select.
You will probably notice that there are a large number of columns that can be retrieved.
head(keytypes(up))
#> [1] "Allergome" "ArachnoServer" "Araport" "BioCyc"
#> [5] "BioGRID" "BioMuta"And most (but not all) of these fields can also be used as keytypes.
head(columns(up))
#> [1] "absorption" "accession"
#> [3] "annotation_score" "cc_activity_regulation"
#> [5] "cc_allergen" "cc_alternative_products"If necessary you can also look up the keys of a given type. But please be warned that the web service is slow at this particular kind of lookup. So if you really want to do this kind of operation you are probably going to want to save the result to your R session.
egs <- keys(up, "GeneID")Finally, you can loop up whatever combinations of columns, keytypes and
keys that you need when using select.
Note. ‘ENTREZ_GENE’ is now ‘GeneID’
keys <- c("1","2")
columns <- c("xref_pdb", "xref_hgnc", "sequence")
kt <- "GeneID"
res <- select(up, keys, columns, kt)
res
#> From Entry PDB
#> 1 1 P04217 <NA>
#> 2 1 V9HWD8 <NA>
#> 3 2 P01023 1BV8;2P9R;6TAV;7O7L;7O7M;7O7N;7O7O;7O7P;7O7Q;7O7R;7O7S;7VON;7VOO;
#> HGNC
#> 1 HGNC:5;
#> 2 <NA>
#> 3 HGNC:7;
#> Sequence
#> 1 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQLFKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPWLSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNYSCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVDFQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELILSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFELHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAVLRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTFESELSDPVELLVAES
#> 2 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQLFKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPWLSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNYSCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVDFQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELILSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFELHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAVLRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTFESELSDPVELLVAES
#> 3 MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETTEKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAENDVLHCVAFAVPKSSSNEEVMFLTVQVKGPTQEFKKRTTVMVKNEDSLVFVQTDKSIYKPGQTVKFRVVSMDENFHPLNELIPLVYIQDPKGNRIAQWQSFQLEGGLKQFSFPLSSEPFQGSYKVVVQKKSGGRTEHPFTVEEFVLPKFEVQVTVPKIITILEEEMNVSVCGLYTYGKPVPGHVTVSICRKYSDASDCHGEDSQAFCEKFSGQLNSHGCFYQQVKTKVFQLKRKEYEMKLHTEAQIQEEGTVVELTGRQSSEITRTITKLSFVKVDSHFRQGIPFFGQVRLVDGKGVPIPNKVIFIRGNEANYYSNATTDEHGLVQFSINTTNVMGTSLTVRVNYKDRSPCYGYQWVSEEHEEAHHTAYLVFSPSKSFVHLEPMSHELPCGHTQTVQAHYILNGGTLLGLKKLSFYYLIMAKGGIVRTGTHGLLVKQEDMKGHFSISIPVKSDIAPVARLLIYAVLPTGDVIGDSAKYDVENCLANKVDLSFSPSQSLPASHAHLRVTAAPQSVCALRAVDQSVLLMKPDAELSASSVYNLLPEKDLTGFPGPLNDQDNEDCINRHNVYINGITYTPVSSTNEKDMYSFLEDMGLKAFTNSKIRKPKMCPQLQQYEMHGPEGLRVGFYESDVMGRGHARLVHVEEPHTETVRKYFPETWIWDLVVVNSAGVAEVGVTVPDTITEWKAGAFCLSEDAGLGISSTASLRAFQPFFVELTMPYSVIRGEAFTLKATVLNYLPKCIRVSVQLEASPAFLAVPVEKEQAPHCICANGRQTVSWAVTPKSLGNVNFTVSAEALESQELCGTEVPSVPEHGRKDTVIKPLLVEPEGLEKETTFNSLLCPSGGEVSEELSLKLPPNVVEESARASVSVLGDILGSAMQNTQNLLQMPYGCGEQNMVLFAPNIYVLDYLNETQQLTPEIKSKAIGYLNTGYQRQLNYKHYDGSYSTFGERYGRNQGNTWLTAFVLKTFAQARAYIFIDEAHITQALIWLSQRQKDNGCFRSSGSLLNNAIKGGVEDEVTLSAYITIALLEIPLTVTHPVVRNALFCLESAWKTAQEGDHGSHVYTKALLAYAFALAGNQDKRKEVLKSLNEEAVKKDNSVHWERPQKPKAPVGHFYEPQAPSAEVEMTSYVLLAYLTAQPAPTSEDLTSATNIVKWITKQQNAQGGFSSTQDTVVALHALSKYGAATFTRTGKAAQVTIQSSGTFSSKFQVDNNNRLLLQQVSLPELPGEYSMKVTGEGCVYLQTSLKYNILPEKEEFPFALGVQTLPQTCDEPKAHTSFQISLSVSYTGSRSASNMAIVDVKMVSGFIPLKPTVKMLERSNHVSRTEVSSNHVLIYLDKVSNQTLSLFFTVLQDVPVRDLKPAIVKVYDYYETDEFAIAEYNAPCSKDLGNAsessionInfo()
#> R Under development (unstable) (2024-11-01 r87285)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.5 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] UniProt.ws_2.47.4 BiocStyle_2.35.0
#>
#> loaded via a namespace (and not attached):
#> [1] rappdirs_0.3.3 generics_0.1.3 RSQLite_2.3.9
#> [4] hms_1.1.3 digest_0.6.37 magrittr_2.0.3
#> [7] evaluate_1.0.1 fastmap_1.2.0 blob_1.2.4
#> [10] jsonlite_1.8.9 progress_1.2.3 AnnotationDbi_1.69.0
#> [13] GenomeInfoDb_1.43.2 DBI_1.2.3 BiocManager_1.30.25
#> [16] httr_1.4.7 purrr_1.0.2 UCSC.utils_1.3.0
#> [19] Biostrings_2.75.3 codetools_0.2-20 httr2_1.0.7
#> [22] cli_3.6.3 rlang_1.1.4 crayon_1.5.3
#> [25] dbplyr_2.5.0 XVector_0.47.1 Biobase_2.67.0
#> [28] bit64_4.5.2 withr_3.0.2 cachem_1.1.0
#> [31] yaml_2.3.10 BiocBaseUtils_1.9.0 tools_4.5.0
#> [34] memoise_2.0.1 dplyr_1.1.4 filelock_1.0.3
#> [37] GenomeInfoDbData_1.2.13 BiocGenerics_0.53.3 curl_6.0.1
#> [40] rjsoncons_1.3.1 vctrs_0.6.5 R6_2.5.1
#> [43] png_0.1-8 stats4_4.5.0 lifecycle_1.0.4
#> [46] BiocFileCache_2.15.0 KEGGREST_1.47.0 S4Vectors_0.45.2
#> [49] IRanges_2.41.2 bit_4.5.0.1 pkgconfig_2.0.3
#> [52] pillar_1.10.0 glue_1.8.0 tidyselect_1.2.1
#> [55] xfun_0.49 tibble_3.2.1 rstudioapi_0.17.1
#> [58] knitr_1.49 AnVILBase_1.1.0 htmltools_0.5.8.1
#> [61] rmarkdown_2.29 compiler_4.5.0 prettyunits_1.2.0