Structured chemical class definitions and automated matching for chemical ontology evolution

Structured chemical class definitions and automated matching for chemical ontology evolution

Ontologies encode the knowledge of human experts in order to allow computers to automate common tasks in a domain. They are hierarchically organised and backed by computational logic which allows automated inferences of the implicit consequences of explicitly stated knowledge. ChEBI is a database and ontology of chemical entities of biological interest [1]. Within the ontology, chemical entitie...

Automated compound classification using a chemical ontology

UNLABELLED BACKGROUND Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of bio...

Inferring logical definitions using compound ontology matching

OBO logical definitions are a means to support the creation of integrated reference ontologies. In ontologies they exist for, logical definitions currently cover a small portion of classes, which limits the potential for integration. We present a novel preliminary strategy to derive logical definition candidates based on an ontology compound matching algorithm. Preliminary results show that thi...

Heuristics for chemical compound matching.

We have developed an efficient algorithm for comparing two chemical compounds, where the chemical structure is treated as a 2D graph consisting of atoms as vertices and covalent bonds as edges. Based on the concept of functional groups in chemistry, 68 atom types (vertex types) are defined for carbon, nitrogen, oxygen, and other atomic species with different environments, which has enabled dete...

Chemical Evolution