Entrez link discription

Question

[tsutsui.data.analysis]

Dear all,

I'm working around NCBI API using rentrez to get pubmed id which linked to certain gene. Below one is my code example.

library(rentrez)
x <- entrez_link(dbfrom="gene", id=c("7157"), db="pubmed") # TP53 for example
x$link
elink result with information from 8 databases:
[1] gene_pubmed                gene_pubmed_all
[3] gene_pubmed_highlycited    gene_pubmed_reviews
[5] gene_pubmed_rif            gene_pubmed_citedinomim
[7] gene_pubmed_latest         gene_pubmed_pmc_nucleotide

Here I've gotten 8 databases which linked to TP53 gene. Some of those, gene_pubmed_all for example, can't be found in Entrez link description (https://www.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html#gene).

I want to get all publication which links to my genes. To do that, should I use ids from gene_pubmed instead of gene_pubmed_all? Does someone known where can I find more description about gene_pubmed links?

Thanks

Answer 1

[GenoMax]

Using EntrezDirect (results truncated):

$ esearch -db gene -query 7157 | elink -target pubmed | efetch -format docsum | xtract -pattern DocumentSummary -element Id 

36049099
36045334
36037124
35996546
35921289

OR

$ esearch -db gene -query 7157 | elink -target pubmed | efetch | grep -e "DOI:" -e "PMID:" 
DOI: 10.21614/chirurgia.2744 
PMID: 36049099  [Indexed for MEDLINE]
DOI: 10.1186/s12885-022-10039-y 
PMID: 36045334  [Indexed for MEDLINE]

[tsutsui.data.analysis]

Thanks,
This must be a simpler solution than rentrez.