[R] Analyzing Publications from Pubmed via XML

Farrel Buchinsky fjbuch at gmail.com
Fri Dec 14 21:16:59 CET 2007

On Dec 13, 2007 11:35 PM, Robert Gentleman <rgentlem at fhcrc.org> wrote:
> or just try looking in the annotate package from Bioconductor

Yip. annotate seems to be the most streamlined way to do this.
1) How does one turn the list that is created into a dataframe whose
column names are along the lines of date, title, journal, authors etc
2) I have already created a standing search in pubmed using MyNCBI.
There are many ways I can feed those results to the pubmed() function.
The most brute force way of doing it is by running the search and
outputing the data as a UI List and getting that into the pubmed
brackets. A way that involved more finesse would allow me to create a
rss feed based on my search and then give the rss feed url to the
pubmed function. Or perhaps once could just plop the query inside the
pubmed functions
pubmed(somefunction("Laryngeal Neoplasms"[MeSH] AND "Papilloma"[MeSH])
OR ((("recurrence"[TIAB] NOT Medline[SB]) OR "recurrence"[MeSH Terms]
OR recurrent[Text Word]) AND respiratory[All Fields] AND
(("papilloma"[TIAB] NOT Medline[SB]) OR "papilloma"[MeSH Terms] OR
papillomatosis[Text Word])))

Does "somefunction" exist?

If there are any further questions do you think I should migrate this
conversation to the bioconductor mailing list?

Farrel Buchinsky

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