Overview of chemical ontologies

TL;DR

This paper reviews the current state of chemical ontologies, highlighting their definitions, structures, and the challenges faced in their development and acceptance within the scientific community.

Contribution

It provides an overview of existing chemical ontologies, discusses their limitations, and categorizes major developments in chemical analytical methods, name reactions, and scientific units.

Findings

Chemical ontologies are still in early development stages.

No chemical ontology has achieved widespread acceptance.

Current ontologies are often fragmentary or incomplete.

Abstract

Ontologies order and interconnect knowledge of a certain field in a formal and semantic way so that they are machine-parsable. They try to define allwhere acceptable definition of concepts and objects, classify them, provide properties as well as interconnect them with relations (e.g. "A is a special case of B"). More precisely, Tom Gruber defines Ontologies as a "specification of a conceptualization; [...] a description (like a formal specification of a program) of the concepts and relationships that can exist for an agent or a community of agents." [1] An Ontology is made of Individuals which are organized in Classes. Both can have Attributes and Relations among themselves. Some complex Ontologies define Restrictions, Rules and Events which change attributes or relations. To be computer accessible they are written in certain ontology languages, like the OBO language or the more used Common Algebraic Specification Language. With the rising of a digitalized, interconnected and globalized world, where common standards have to be found, ontologies are of great interest. [2] Yet, the development of chemical ontologies is in the beginning. Indeed, some interesting basic approaches towards chemical ontologies can be found, but nevertheless they suffer from two main flaws. Firstly, we found that they are mostly only fragmentary completed or are still in an architecture state. Secondly, apparently no chemical ontology is widespread accepted. Therefore, we herein try to describe the major ontology-developments in the chemical related fields Ontologies about chemical analytical methods, Ontologies about name reactions and Ontologies about scientific units.