HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey

• Published in: BMC bioinformatics Vol. 23; no. 1; pp. 23 - 31
• Main Authors: Lastra-Díaz, Juan J., Lara-Clares, Alicia, Garcia-Serrano, Ana
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 06.01.2022; BioMed Central; BMC
• Subjects: Algorithms; Analysis; Approximation; Benchmarks; Biological Ontologies; Biomedical engineering; Biomedical materials; Computing time; Data libraries; Data mining; Domains; Gene expression; Genetic aspects; Genomics; Graph representations; Graph theory; Graphical representations; HESML; Hypotheses; Information content models; Java; Knowledge representation; Libraries; Mathematical analysis; Medical Subject Headings; Medical Subject Headings-MeSH; MeSH; Methods; Ontology; Ontology-based semantic similarity measures; Polls & surveys; Proteins; Quality management; Real time; Relational data bases; Reproducibility; Reproducibility of Results; Semantic measures library; Semantic networks; Semantics; Shortest-path problems; Similarity; Similarity measures; SNOMED-CT; Software; Software upgrading; Systematized Nomenclature of Medicine; Taxonomy; Time measurement; Word sense disambiguation; Spain; Gene ontology; HESML; Information content models; MeSH; Semantic measures library; Ontology-based semantic similarity measures; WordNet; SNOMED-CT

Ontology-based semantic similarity measures based on SNOMED-CT, MeSH, and Gene Ontology are being extensively used in many applications in biomedical text mining and genomics respectively, which has encouraged the development of semantic measures libraries based on the aforementioned ontologies. How...