The data provided by PubMed is reduced to a small set. This set is then suitable for further rendering.
The identifiers used to find Abstracts
The base name of the annotation package to use.
We rely on the annotation in the package associated with the
basename to provide PubMed identifiers for the genes described by
the gene identifiers.
With these in hand we then use the
pmfetch utility to download the
PubMed abstracts in XML form. These are then translated (transformed) to a
shorter version containing a small subset of the data provided by PubMed.
This function has the side effect of creating an environment in
.GlobalEnv that contains the mapping for the requested data.
This is done for efficiency – so we don't continually read in the data
when there are many different queries to be performed.
A list of lists containing objects of class
There will be one element of the list for each identifier.
Each of these elements is a list containing one abstract (of
pubMedAbst for each PubMed identifier associated with
the gene identifier.
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