Add table of contents, some cleanup.
Added section on Term Status; small improvements.
Adding TermMapper class

Include tweaks to some example data and updated CommandLineInterface.
Also minor fixes for build.xml.
Added missing JavaDoc
Improved introduction

- added section on goals
- more explanation of data-after
- updated links
Tweaked metadata for more compact code listings in PDF
Replaced footnote with parenthetical note
Many improvements to Using and Reusing section

- changed base IRI from 'application.owl' to 'obo-tutorial.owl'
- changed 'study' prefix to 'tutorial'
- using relative imports in application.owl
- added GO 'biological process' to application.owl
- added several subClassOf assertions to fix application hierarchy
- extracted new Uberon module
Adjusted Ontofox annotations, imports from MPATH

- removed 'pathological entity'
- added 'pathological anatomical entity'
- replace most includeAllAxiomsRecursively with
  includeAllAnnotationProperties, which is what I intended
Added TripleConverter class

The TripleConverter loads a CSV file and creates a Turtle file, with one
subject-predicate-object triple for each row-column-cell.

- updated ivy.xml to import Apache Jena
- added prefixes.ttl with default prefixes
- added data-raw.ttl example output
- added TripleConverter.java code
Added Modeller class

The Modeller loads "raw" triples and the application ontology into
named graphs in Jena, then runs SPARQL Update from a given SPARQL
file. It saves the new named graph to Turtle.

- added Modeller.java code
- added model.rq example SPARQL code
- added data-after.ttl example results
Added Merger class

The Merger loads one or more ontologies and merges them into a single
ontology. It will load imports that are in the same directory as the
source ontology files, or from the Internet, but it does not read
the catalog.xml file.

- added Merger.java code
- added obo-tutorial.owl, merging the application ontology with
  data-after.ttl
Added TripleConverter, Modeller, and Merger to CommandLineInterface
Added log4j configuration to stop Jena from complaining
Major additions to Processing Data section

- added background on tables and triples
- added section on converting tables to RDF
  with example for TripleConverter code
- added screenshot for Protege Individuals
- added section on SPARQL querying
- added screenshort for SPARQL in Protege
- added section on modelling
  with example for Modeller code,
  and example for Merger code
- added links for DL Query
- added links for reasoners
- added warnings about current reasoning
Added requirements, build instructions, and examples
Major additions to Updating, Testing, and Releasing Ontologies

- added sections on filing term requests and bug reports
- added term submission guidelines
- added section on TermGenie
- links to some incomplete sections