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

This dataset introduces HESML V1R5 which is the fifth release of the Half-Edge Semantic Measures Library (HESML) detailed in [13]. 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.

HESML library is freely distributed for any non-commercial purpose under a CC By-NC-SA-4.0 license, subject to the citing of the two mains HESML papers as attribution requirement. However, HESML distribution also includes other datasets, databases or data files whose use require the attribution acknowledgement by any user of HEMSL. Thus, we urge to the HESML users to fulfill with licensing terms related to other resources distributed with the library as detailed in its companion release notes.