BIBLIOS

Document type
Book chapters


Title
Semantic Similarity in Cheminformatics

Participants in the publication
João D. Ferreira (Author)
Dep. Informática
LASIGE
Francisco M. Couto (Author)
Dep. Informática
LASIGE

Summary
Similarity in chemistry has been applied to a variety of problems: to predict biochemical properties of molecules, to disambiguate chemical compound references in natural language, to understand the evolution of metabolic pathways, to predict drug-drug interactions, to predict therapeutic substitution of antibiotics, to estimate whether a compound is harmful, etc. While measures of similarity have been created that make use of the structural properties of the molecules, some ontologies (the Chemical Entities of Biological Interest (ChEBI) being one of the most relevant) capture chemistry knowledge in machine-readable formats and can be used to improve our notions of molecular similarity. Ontologies in the biomedical domain have been extensively used to compare entities of biological interest, a technique known as ontology-based semantic similarity. This has been applied to various biologically relevant entities, such as genes, proteins, diseases, and anatomical structures, as well as in the chemical domain. This chapter introduces the fundamental concepts of ontology-based semantic similarity, its application in cheminformatics, its relevance in previous studies, and future potential. It also discusses the existing challenges in this area, tracing a parallel with other domains, particularly genomics, where this technique has been used more often and for longer.


Where published
Cheminformatics and its Applications [Working Title]

Publication Identifiers

Publisher
IntechOpen


Document Identifiers
DOI - https://doi.org/10.5772/intechopen.89032
URL - http://dx.doi.org/10.5772/intechopen.89032
URL - https://www.intechopen.com/online-first/semantic-similarity-in-cheminformatics

Notes
The book is set to be published by April 2020, but the chapter is already reviewed and available.