When is db=all not db=all? When you use Entrez ELink.

Just a brief technical note. I figured that for a given compound in PubChem, it would be interesting to know whether that compound had been used in a high-throughput experiment, which you might find in GEO. Very easy using the E-utilities, as implemented in the R package rentrez: library(rentrez) links <- entrez_link(dbfrom = "pccompound", db = "gds", id = "62857") length(links$pccompound_gds) # [1] 741 Browsing the rentrez documentation, I note that db can take the value “all”. Sounds useful! links <- entrez_link(dbfrom = "pccompound", db = "all", id = "62857") length(links$pccompound_gds) # [1] 0 That’s odd. In fact, this query does not even link pccompound to gds: length(names(links)) # [1] 39 which(names(links) == "pccompound_gds") # integer(0) It’s not a rentrez issue, since the same result occurs using the E-utilities URL. The good people at ropensci have opened an issue, contacting NCBI for clarification. We’ll keep you posted. Filed under: bioinformatics, programming, research diary Tagged: api, elink, entrez, ncbi, rentrez
Source: What You're Doing Is Rather Desperate - Category: Bioinformaticians Authors: Tags: bioinformatics programming research diary api elink entrez ncbi rentrez Source Type: blogs