first version in local maven repo

• added new habitat, elevation, distribution and phenology markup steps;
• fixed id's in output xml
• fixed model to xml writing (elements attached in multiple locations)
• fixes exceptions in algorithm

maven

• refactored package structure, markup workflow (separated concerns related to markup of different elements), IO and model (merged development branch)
• added MOXy reader/writer using Binder to retain XML Infoset
• created NeXML model and IO
• added and fitted Dongyes unsupervised learning
• organized configuration;
• various bug fixes
• mavenized

IPlant release

• added volume reader to support new common schema in biosemantics/schemas
• created uniqueness of structure and relation id over an input file
• added term categorization required parameter
• added configurability of logging locations
• added unique ID generation and file rearrangement for iPlant wrapper script
• added secret handling for oto light
• added bioportal parameters for ontology submission

0.1.3

• prefix table stores creation time
• added cleanup
• learn/markup/cleanup bash scripts
• resources, src, and workspace directory are configurable per CLI

0.1.2

• Changed encoding of source code to UTF-8
• Made iplant related IO (file read/write, db access) to use UTF-8 encoding
• Fixed unsupervised learning difference between unix/windows

0.1.1: Fixed perl module to accept database host, port, user and password as

• Fixed perl module to accept database host, port, user and password as input parameters