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Abstract

The database manager is an API within OmnipathR which is able to load various datasets, keep track of their usage and remove them after an expiry period. Currently it supports a few Gene Ontology and UniProt datasets, but easily can be extended to cover all datasets in the package.

Available datasets

To see a full list of datasets call the omnipath_show_db function:

## # A tibble: 19 × 10
##    name   last_…¹ lifet…² package loader loader_param lates…³ loaded db    key  
##    <chr>  <lgl>     <dbl> <chr>   <chr>  <list>       <lgl>   <lgl>  <lgl> <chr>
##  1 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_b…
##  2 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_f…
##  3 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_a…
##  4 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_a…
##  5 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_s…
##  6 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_c…
##  7 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_d…
##  8 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_c…
##  9 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_m…
## 10 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_p…
## 11 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_m…
## 12 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_p…
## 13 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_p…
## 14 Gene … NA          300 Omnipa… go_on… <named list> NA      FALSE  NA    go_y…
## 15 GO an… NA          300 Omnipa… go_an… <named list> NA      FALSE  NA    goa_…
## 16 UniPr… NA          300 Omnipa… unipr… <named list> NA      FALSE  NA    up_gs
## 17 Ensem… NA        10800 Omnipa… taxon… <NULL>       NA      FALSE  NA    orga…
## 18 All S… NA        10800 Omnipa… all_u… <named list> NA      FALSE  NA    swis…
## 19 All T… NA        10800 Omnipa… all_u… <named list> NA      FALSE  NA    trem…
## # … with abbreviated variable names ¹​last_used, ²​lifetime, ³​latest_param

It returns a tibble where each dataset has a human readable name and a key which can be used to refer to it. We can also check here if the dataset is currently loaded, the time it’s been last used, the loader function and its arguments.

Access a dataset

Datasets can be accessed by the get_db function. Ideally you should call this function every time you use the dataset. The first time it will be loaded, the subsequent times the already loaded dataset will be returned. This way each access is registered and extends the expiry time. Let’s load the human UniProt-GeneSymbol table. Above we see its key is up_gs.

up_gs <- get_db('up_gs')
up_gs
## # A tibble: 20,372 × 2
##    From   To     
##    <chr>  <chr>  
##  1 P63120 ERVK-19
##  2 Q96EC8 YIPF6  
##  3 Q6ZMS4 ZNF852 
##  4 Q8N8L2 ZNF491 
##  5 Q15916 ZBTB6  
##  6 O60384 ZNF861P
##  7 Q3MIS6 ZNF528 
##  8 Q86UK7 ZNF598 
##  9 Q6P280 ZNF529 
## 10 Q969W1 ZDHHC16
## # … with 20,362 more rows

This dataset is a two columns data frame of SwissProt IDs and Gene Symbols. Looking again at the datasets, we find that this dataset is loaded now and the last_used timestamp is set to the time we called get_db:

## # A tibble: 19 × 10
##    name     last_used           lifet…¹ package loader loader_param latest_param
##    <chr>    <dttm>                <dbl> <chr>   <chr>  <list>       <list>      
##  1 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  2 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  3 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  4 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  5 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  6 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  7 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  8 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  9 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 10 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 11 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 12 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 13 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 14 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 15 GO anno… NA                      300 Omnipa… go_an… <named list> <lgl [1]>   
## 16 UniProt… 2022-10-16 16:23:43     300 Omnipa… unipr… <named list> <named list>
## 17 Ensembl… 2022-10-16 16:23:42   10800 Omnipa… taxon… <NULL>       <NULL>      
## 18 All Swi… NA                    10800 Omnipa… all_u… <named list> <lgl [1]>   
## 19 All TrE… NA                    10800 Omnipa… all_u… <named list> <lgl [1]>   
## # … with 3 more variables: loaded <lgl>, db <list>, key <chr>, and abbreviated
## #   variable name ¹​lifetime

The above table contains also a reference to the dataset, and the arguments passed to the loader function:

d <- omnipath_show_db()
d %>% dplyr::pull(db) %>% magrittr::extract2(16)
## # A tibble: 20,372 × 2
##    From   To     
##    <chr>  <chr>  
##  1 P63120 ERVK-19
##  2 Q96EC8 YIPF6  
##  3 Q6ZMS4 ZNF852 
##  4 Q8N8L2 ZNF491 
##  5 Q15916 ZBTB6  
##  6 O60384 ZNF861P
##  7 Q3MIS6 ZNF528 
##  8 Q86UK7 ZNF598 
##  9 Q6P280 ZNF529 
## 10 Q969W1 ZDHHC16
## # … with 20,362 more rows
d %>% dplyr::pull(latest_param) %>% magrittr::extract2(16)
## $to
## [1] "genesymbol"
## 
## $organism
## [1] 9606

If we call get_db again, the timestamp is updated, resetting the expiry counter:

up_gs <- get_db('up_gs')
omnipath_show_db()
## # A tibble: 19 × 10
##    name     last_used           lifet…¹ package loader loader_param latest_param
##    <chr>    <dttm>                <dbl> <chr>   <chr>  <list>       <list>      
##  1 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  2 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  3 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  4 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  5 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  6 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  7 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  8 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
##  9 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 10 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 11 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 12 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 13 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 14 Gene On… NA                      300 Omnipa… go_on… <named list> <lgl [1]>   
## 15 GO anno… NA                      300 Omnipa… go_an… <named list> <lgl [1]>   
## 16 UniProt… 2022-10-16 16:23:53     300 Omnipa… unipr… <named list> <named list>
## 17 Ensembl… 2022-10-16 16:23:42   10800 Omnipa… taxon… <NULL>       <NULL>      
## 18 All Swi… NA                    10800 Omnipa… all_u… <named list> <lgl [1]>   
## 19 All TrE… NA                    10800 Omnipa… all_u… <named list> <lgl [1]>   
## # … with 3 more variables: loaded <lgl>, db <list>, key <chr>, and abbreviated
## #   variable name ¹​lifetime

Where are the loaded datasets?

The loaded datasets live in an environment which belong to the OmnipathR package. Normally users don’t need to access this environment. As we see below, omnipath_show_db presents us all information availble by directly looking at the environment:

OmnipathR:::omnipath.env$db$up_gs
## $name
## [1] "UniProt-GeneSymbol table"
## 
## $last_used
## [1] "2022-10-16 16:23:53 CEST"
## 
## $lifetime
## [1] 300
## 
## $package
## [1] "OmnipathR"
## 
## $loader
## [1] "uniprot_full_id_mapping_table"
## 
## $loader_param
## $loader_param$to
## [1] "genesymbol"
## 
## $loader_param$organism
## [1] 9606
## 
## 
## $latest_param
## $latest_param$to
## [1] "genesymbol"
## 
## $latest_param$organism
## [1] 9606
## 
## 
## $loaded
## [1] TRUE
## 
## $db
## # A tibble: 20,372 × 2
##    From   To     
##    <chr>  <chr>  
##  1 P63120 ERVK-19
##  2 Q96EC8 YIPF6  
##  3 Q6ZMS4 ZNF852 
##  4 Q8N8L2 ZNF491 
##  5 Q15916 ZBTB6  
##  6 O60384 ZNF861P
##  7 Q3MIS6 ZNF528 
##  8 Q86UK7 ZNF598 
##  9 Q6P280 ZNF529 
## 10 Q969W1 ZDHHC16
## # … with 20,362 more rows

How to extend the expiry period?

The default expiry of datasets is given by the option omnipath.db_lifetime. By calling omnipath_save_config this option is saved to the default config file and will be valid in all subsequent sessions. Otherwise it’s valid only in the current session.

options(omnipath.db_lifetime = 600)
omnipath_save_config()

Where are the datasets defined?

The built-in dataset definitions are in a JSON file shipped with the package. Easiest way to see it is by the git web interface.

How to add custom datasets?

Currently no API available for this, but it would be super easy to implement. It would be matter of providing a JSON similar to the above, or calling a function. Please open an issue if you are interested in this feature.

Session information

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Arch Linux
## 
## Matrix products: default
## BLAS:   /usr/lib/libopenblasp-r0.3.21.so
## LAPACK: /usr/lib/liblapack.so.3.10.1
## 
## locale:
##  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
##  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] OmnipathR_3.5.22 BiocStyle_2.25.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9          tidyr_1.2.1         prettyunits_1.1.1  
##  [4] assertthat_0.2.1    rprojroot_2.0.3     digest_0.6.29      
##  [7] utf8_1.2.2          R6_2.5.1            cellranger_1.1.0   
## [10] backports_1.4.1     evaluate_0.17       httr_1.4.4         
## [13] pillar_1.8.1        rlang_1.0.6         progress_1.2.2     
## [16] curl_4.3.3          readxl_1.4.1        jquerylib_0.1.4    
## [19] checkmate_2.1.0     rmarkdown_2.17      pkgdown_2.0.6      
## [22] textshaping_0.3.6   desc_1.4.2          readr_2.1.3        
## [25] stringr_1.4.1       selectr_0.4-2       bit_4.0.4          
## [28] igraph_1.3.5        compiler_4.2.1      xfun_0.33          
## [31] pkgconfig_2.0.3     systemfonts_1.0.4   htmltools_0.5.3    
## [34] tidyselect_1.2.0    tibble_3.1.8        bookdown_0.29      
## [37] fansi_1.0.3         crayon_1.5.2        dplyr_1.0.10       
## [40] tzdb_0.3.0          withr_2.5.0         later_1.3.0        
## [43] rappdirs_0.3.3      jsonlite_1.8.2      lifecycle_1.0.3    
## [46] DBI_1.1.3           magrittr_2.0.3      cli_3.4.1          
## [49] stringi_1.7.8       vroom_1.6.0         cachem_1.0.6       
## [52] fs_1.5.2            xml2_1.3.3          logger_0.2.2       
## [55] bslib_0.4.0         ellipsis_0.3.2      ragg_1.2.3         
## [58] generics_0.1.3      vctrs_0.4.2         tools_4.2.1        
## [61] bit64_4.0.5         glue_1.6.2          purrr_0.3.5        
## [64] hms_1.1.2           fastmap_1.1.0       yaml_2.3.5         
## [67] BiocManager_1.30.18 rvest_1.0.3         memoise_2.0.1      
## [70] knitr_1.40          sass_0.4.2