rpsychologist / PubMed

DEPRECATED: PubMed datamining in R

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Discarded search terms

rpsychologist opened this issue · comments

Posted on my site by Andrew Su:
"Great script, thanks for writing it! One caveat I noticed when I was running/modifying it. I was searching for a count of “Dangeardiella macrospora”. The API call (no years) shows that there are 109 hits:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&rettype=count&term=%22Dangeardiella%20macrospora%22

but, searching at PubMed shows that the search result should actually be zero (since “Dangeardiella” is not found in PubMed, they conveniently just discard that search term):

http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Dangeardiella+macrospora%22

To ask that PubMed not discard terms, you need to append “[All fields]“. For example:

http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Dangeardiella+macrospora%22%5BAll+fields%5D
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&rettype=count&term=%22Dangeardiella%20macrospora%22All%20fields

Hope that’s helpful!"