Entering edit mode
3 months ago
Mohamed Samir
▴
30
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]