HESML V1R5 Java software library of ontology-based semantic similarity measures and information content models

HESML V1R5 is a linearly scalable and efficient Java software library of ontology-based semantic similarity measures and Information Content (IC) models for ontolgies like WordNet, SNOMED-CT, MeSH, GO and any other ontologies based on the OBO file format. HESML V1R5 implements most ontology-based semantic similarity measures and Information Content (IC) models reported in the literature, as well as the evaluation of three pre-trained word embedding models.

It also provides a XML-based input file format in order to specify the execution of reproducible word/concept similarity experiments based on WordNet, SNOMED-CT, MeSH, or GO without software coding. HESML V1R5 introduces the following novelties: (1) the parsing and in-memory representation of the SNOMED-CT, MeSH and any other ontologies based on the OBO file format such as the Gene Ontology (GO); (2) a new collection of efficient path-based similarity measures based on the reformulation of previous path-based measures which are based on the new Ancestors-based Shortest-Path Length (AncSPL) algorithm; and (3) a collection of groupwise similarity measures.