Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
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5 weeks ago

Dear all, I have been trying to retrieve the metadata of bioprojects that have whole genome seq. experiments/runs for the organism Klebsiella, but I failed. I was able to count them and get their IDs but not any more. I need that as a quick alternative way to search in ncbi (bioprojects) search bars and get into each one-by-one. Any help please

Here is my code that I have tried :

# install.pacakges("devtools")

    devtools::install_github("ropensci/rentrez")
    library(rentrez)

    entrez_dbs()

 [1] "pubmed"          "protein"         "nuccore"        
 [4] "ipg"             "nucleotide"      "structure"      
 [7] "genome"          "annotinfo"       "assembly"       
[10] "bioproject"      "biosample"       "blastdbinfo"    
[13] "books"           "cdd"             "clinvar"        
[16] "gap"             "gapplus"         "grasp"          
[19] "dbvar"           "gene"            "gds"            
[22] "geoprofiles"     "medgen"          "mesh"           
[25] "nlmcatalog"      "omim"            "orgtrack"       
[28] "pmc"             "popset"          "proteinclusters"
[31] "pcassay"         "protfam"         "pccompound"     
[34] "pcsubstance"     "seqannot"        "snp"            
[37] "sra"             "taxonomy"        "biocollections" 
[40] "gtr"            

    entrez_db_searchable('bioproject')

Searchable fields for database 'bioproject'
  ALL    All terms from all searchable fields 
  UID    Unique number assigned to publication 
  FILT   Limits the records 
  ORGN   Organism 
  PRJA   Project Accession 
  TYPE   Project Type 
  STPE   Project Subtype 
  DATE   Registration Date 
  TITL   Title 
  CEN    Submitter Organization(s) 
  ACCN   Space delimited GenBank or RefSeq Replicon Accessions 
  RTYP   Replicon Type 
  RNME   Replicon Name 
  LTP    Locus Tag Prefix 
  WORD   Organism/Project Description 
  KWRD   Keyword 
  PROP   Project/Organism Properties 
  DTPE   Project Data Type 
  GRNT   Grant ID 
  FUND   Funding Agency 
  PMID   Pubmed ID 
  DOID   DOI ID 
  PID    Project ID 
  RELV   Relevance 
  ANME   Assembly Name 
  BPRJ   BioProject ID or accession 
  TPRJ   Top Bioproject ID 
  WGSA   WGS Accessions 
  AACC   Assembly Accession 
  ATNM   Attribute Name 
  ATTR   Attribute 

    Klebsiella <- "Klebsiella [Organism]"
    Klebsiella

[1] "Klebsiella [Organism]"

    Klebsiella_search <- entrez_search(db="bioproject", term=Klebsiella)

    Klebsiella_search

Entrez search result with 5825 hits (object contains 20 IDs and no web_history object)
 Search term (as translated):  "Klebsiella"[Organism] 
R • 173 views
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