How can I download all supported species information table of STRINGdb V11
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Evan-GIBH • 0
@user-24198
Last seen 14 months ago

Hello, Is it possible to download all STRINGdb V11 supported species information as a CSV/TSV table? I noticed that there is a function (get_STRING_species) in the older version that can do that work, and it only can download the species for version 10. So how can I download the species information for version 11? Thanks to anyone who can support help!

STRINGdb STRING • 228 views
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@vincent-j-carey-jr-4
Last seen 15 days ago
United States
> library(readr)
1/7 packages newly attached/loaded, see sessionInfo() for details.
> z = read_tsv("https://stringdb-static.org/download/species.v11.0.txt")

── Column specification ────────────────────────────────────────────────────────────────────────────────────────
cols(
  `## taxon_id` = col_double(),
  STRING_type = col_character(),
  STRING_name_compact = col_character(),
  official_name_NCBI = col_character()
)

> z[1:5,]
# A tibble: 5 x 4
  `## taxon_id` STRING_type STRING_name_compact       official_name_NCBI        
          <dbl> <chr>       <chr>                     <chr>                     
1           287 core        Pseudomonas aeruginosa    Pseudomonas aeruginosa    
2           292 core        Burkholderia cepacia      Burkholderia cepacia      
3           301 core        Pseudomonas oleovorans    Pseudomonas oleovorans    
4           340 core        Xanthomonas campestris c… Xanthomonas campestris pv…
5           359 core        Agrobacterium rhizogenes  Agrobacterium rhizogenes  

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