Ontology:Chemical Compound and Chemical Functional Group Ontology
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{{Ontology | {{Ontology | ||
| - | |Name=Chemical Compound and | + | |Name=Chemical Compound and Functional Groups |
| - | |OntologyOrganization=Carleton University | + | |OntologyOrganization=Carleton University - Dumontier Lab |
|OntologyAuthor=Michel Dumontier | |OntologyAuthor=Michel Dumontier | ||
| - | |Description= | + | |Description=A set of OWL ontologies for the classification of compounds based on the presence of functional groups, which are described in terms of atoms and their connectivity. |
|SubmittedBy=MichelDumontier | |SubmittedBy=MichelDumontier | ||
| - | |OntologyPurpose= | + | |OntologyPurpose=Chemical classification is critically important in chemistry and in drug discovery. The purpose of the ontology is to classify compounds. It demonstrates how we can use an OWL reasoner over a chemical knowledge base to classify compounds based on the description of their chemical structure. |
| - | | | + | |
| - | |LongDescription=Functional groups | + | For instance, the ontology can be used to classify ethanol as an alcohol because ethanol contains a set of carbon, oxygen and hydrogen atoms that are connected in such a way that on reasoning, it is discovered to contain a hydroxyl group (R-O-H) which is a necessary and sufficient condition to be a kind of alcohol. |
| - | | | + | |OntologyURI=http://ontology.dumontierlab.com/organic-compound-complex |
| + | |LongDescription=Functional groups are described by patterns of atomic connectivity which exhibit characteristic chemical reactivity in compounds that contain them. Being able to identify such compounds is important to both synthetic and medicinal chemistry and for drug discovery. | ||
| + | This collection of OWL ontologies makes possible the classification of compounds based on the presence of acyclic functional groups using an OWL reasoner. The presence of functional group is inferred from the chemical structure, defined in terms of atoms and the bonds they share. | ||
| + | |Justification=Each compound and chemical functional group can be fully described (e.g. in terms of necessary and sufficient conditions) using lower granular terms (e.g. a compound is defined in terms of its functional groups, functional groups are defined in terms of atoms). | ||
| + | |CompetencyQuestion=Q. What kind of compound is Ethanol? Ethanol is an Alcohol. | ||
|OntologyDomain=Chemistry, Pharmaceutical | |OntologyDomain=Chemistry, Pharmaceutical | ||
|Scenario=structure classification | |Scenario=structure classification | ||
|KnownIssues=computationally expensive | |KnownIssues=computationally expensive | ||
|OntologyLicensing=creative-commons - by attribution | |OntologyLicensing=creative-commons - by attribution | ||
| - | |||
| - | |||
}} | }} | ||
| + | |||
| + | {{My references}} | ||
Current revision
Return to Catalogue of Exemplary Ontologies
Ontology Overview
| Name: | Chemical Compound and Functional Groups |
|---|---|
| Description: | A set of OWL ontologies for the classification of compounds based on the presence of functional groups, which are described in terms of atoms and their connectivity. |
| Purpose: | Chemical classification is critically important in chemistry and in drug discovery. The purpose of the ontology is to classify compounds. It demonstrates how we can use an OWL reasoner over a chemical knowledge base to classify compounds based on the description of their chemical structure.
For instance, the ontology can be used to classify ethanol as an alcohol because ethanol contains a set of carbon, oxygen and hydrogen atoms that are connected in such a way that on reasoning, it is discovered to contain a hydroxyl group (R-O-H) which is a necessary and sufficient condition to be a kind of alcohol. |
| Organization(s): | Carleton University - Dumontier Lab |
| Author(s): | Michel Dumontier |
| Justification | Each compound and chemical functional group can be fully described (e.g. in terms of necessary and sufficient conditions) using lower granular terms (e.g. a compound is defined in terms of its functional groups, functional groups are defined in terms of atoms). |
| Recommended by: | |
| Submitted by: | MichelDumontier |
| Competency Questions: | Q. What kind of compound is Ethanol? Ethanol is an Alcohol. |
| Domains: | Chemistry, Pharmaceutical |
| Scenario: | structure classification |
| Known issues: | computationally expensive |
| OntologyURI: |
http://ontology.dumontierlab.com/organic-compound-complex (1551) |
| Licensing: | creative-commons - by attribution |
| Web references: | |
| Other references: |
Long Description
Functional groups are described by patterns of atomic connectivity which exhibit characteristic chemical reactivity in compounds that contain them. Being able to identify such compounds is important to both synthetic and medicinal chemistry and for drug discovery. This collection of OWL ontologies makes possible the classification of compounds based on the presence of acyclic functional groups using an OWL reasoner. The presence of functional group is inferred from the chemical structure, defined in terms of atoms and the bonds they share.
Additional Information
References
- Paper: "Describing chemical functional groups in OWL-DL for the classification of chemical compounds."
by Natalia Villanueva-Rosales1, Michel Dumontier Documentation | reference page
- Related ontologies in personalized medicine Ontologies | reference page
