normalized text like "plagio-, dicho-, and trichotriaenes." in perl.
fixed a bug in separateNouns in firstNoun in AbstractChunker.
fixed getCharacter() function to match per-marked phrases in pl form.
handled the 'with or without' unexpected parsing by StanfordParser.
made use of ElementRelationGroup to group various entity related
elements (structure, substance, taxon_name => entityElement) -- cleaned
up all direct reference to individual elements in the code.
TextCapture output schema change:
1. structure => biological_entity
2. add attribute type [required] for biological_entity (type
enumeration: structure, substance, taxon_name)
and updated xml bindings, models, and transformers.
Merge branch 'dev'

Conflicts:
	src/main/perl/edu/arizona/biosemantics/semanticmarkup/markupelement/description/ling/learn/lib/perl/unsupervisedClauseMarkupBenchmarked.pl
committed local settings
recovered from a git crash
added ontologies
trying to push
Merge branch 'master' of https://github.com/biosemantics/charaparser.git
merge with master
bug fix in NonOntologyBasedStandardizer