Preface
-------

Introduction
~~~~~~~~~~~~
{osp-full} ({osp-short}) is a pipeline which processes clinical notes
and identifies types of clinical named entities -- drugs,
diseases/disorders, signs/symptoms, anatomical sites and
procedures. Each named entity has attributes for the text span, the
ontology mapping code, context (family history of, current, unrelated
to patient), and negated/not negated.

include::conventions.adoc[]

How to use this guide
~~~~~~~~~~~~~~~~~~~~~
If you want to:

* Get {osp-short} running quickly, and quickly apply it to clinical documents 
   -> 'Follow <<binary_install>>, skipping <<compile_from_source>>'

* Run {osp-short}, make use of optional parts, and perhaps develop components
   -> 'Skip <<binary_install>> and follow <<compile_from_source>>, skipping <<compile_from_cli>>'

* Run {osp-short} on a server without a GUI
   -> 'Skip <<binary_install>> and follow <<compile_from_source>>, skipping <<compile_in_eclipse>>'  

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EDITING NOTE:
DO NOT INSERT ANY TEXT BEFORE THE 'PREFACE' LINE, EVEN INCLUDE MACROS
WILL MAKE THE DOCBOOK BUILD FAIL, BECAUSE A2X WILL GENERATE TWO
PREFACE CHAPTERS IN DOCBOOK XML. Blank lines seem OK.
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