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Updated: Aug 16, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
Published on: June 6, 2025
CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules
Howard J Feldman1, Michel Dumontier, Susan Ling
1The Blueprint Initiative of the Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, ON, Canada.
Abstract:
A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities.
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Introduction to Functional Groups
Functional groups are group of atoms with specific chemical properties that occur within organic molecules and sometimes denoted as “R”. Functional groups are found along the carbon backbone of macromolecules can form chains or rings of carbon atoms. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of common functional groups
The table below summarizes some of the major functional groups in organic chemistry. (The...
Functional Groups
Functional Groups
Functional Groups
Overview of Advanced Functional Groups
Functional groups are groups of atoms with specific chemical properties that occur within organic molecules and are sometimes denoted as “R”. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of Advanced Functional Groups
The table below summarizes some of the major functional groups in organic chemistry.
Overview of Functional Groups