Changelog¶

v0.3¶

xref tags are now parsed and their content is available in Term. Added appropriate classes for representation.
Added Ontology.getParent().
Removed JaccardIcWeightedSimilarity, JiangSimilarity, LinSimilarity, supporting code and tests.
Refactoring the code for object score I/O into ontolib-io package.
Adding support for score distribution reading and writing to H2 database files.
Ontology.getAncestorTermIds() now also resolves alternative term IDs.
Fixing dependency on slf4j components in ontolib-core and ontolib-io.
Adding getPrimaryTermId() in Ontology.

Making date parser for HPO annotation files more robust. It works now for positive and negative associations.
Small bug fix in HPO OBO parser.
Adding ontolib-cli package that allows score distribution precomputation from the command line.
Removed some dead code.
Added various tests, minor internal refactoring.
Moved OntologyTerms into ontology.algo package.