  Biomedical research is intensive in processing information in the previously
published papers. This motivated a lot of efforts to provide tools for text
mining and information extraction from PDF documents over the past decade. The
*nix (Unix/Linux) operating systems offer many tools for working with text
files, however, very few such tools are available for processing the contents
of PDF files. This paper reports our effort to develop shell script utilities
for *nix systems with the core functionality focused on viewing and searching
multiple PDF documents combining logical and regular expressions, and enabling
more reliable text extraction from PDF documents with subsequent manipulation
of the resulting blocks of text. Furthermore, a procedure for extracting the
most frequently occurring multi-word phrases was devised and then demonstrated
on several scientific papers in life sciences. Our experiments revealed that
the procedure is surprisingly robust to deficiencies in text extraction and the
actual scoring function used to rank the phrases in terms of their importance
or relevance. The keyword relevance is strongly context dependent, the word
stemming did not provide any recognizable advantage, and the stop-words should
only be removed from the beginning and the end of phrases. In addition, the
developed utilities were used to convert the list of acronyms and the index
from a PDF e-book into a large list of biochemical terms which can be exploited
in other text mining tasks. All shell scripts and data files are available in a
public repository named \pp\ on the Github. The key lesson learned in this work
is that semi-automated methods combining the power of algorithms with the
capabilities of research experience are the most promising for improving the
research efficiency.
