Ontology:Chemical Compound and Chemical Functional Group Ontology - Revision history

MichaelUschold at 21:20, 5 March 2010

2010-03-05T21:20:28Z

EnricoDaga at 11:07, 4 March 2010

2010-03-04T11:07:28Z

MichaelUschold at 06:51, 19 February 2010

2010-02-19T06:51:48Z

MichelDumontier at 23:33, 17 February 2010

2010-02-17T23:33:03Z

MichelDumontier at 23:31, 17 February 2010

2010-02-17T23:31:24Z

MichelDumontier at 23:01, 17 February 2010

2010-02-17T23:01:54Z

MichelDumontier: New page: {{Ontology |Name=Chemical Compound and Chemical Functional Group Ontology |OntologyOrganization=Carleton University :: Dumontier Lab |OntologyAuthor=Michel Dumontier |Description=The ontol...

2010-02-17T23:01:23Z

New page: {{Ontology |Name=Chemical Compound and Chemical Functional Group Ontology |OntologyOrganization=Carleton University :: Dumontier Lab |OntologyAuthor=Michel Dumontier |Description=The ontol...

New page

{{Ontology
|Name=Chemical Compound and Chemical Functional Group Ontology
|OntologyOrganization=Carleton University :: Dumontier Lab
|OntologyAuthor=Michel Dumontier
|Description=The ontology contains classes of chemical compounds and chemical functional groups. Chemical compounds are fully defined in terms of functional groups.
|SubmittedBy=MichelDumontier
|OntologyPurpose=An ontology to classify chemical compounds based on the presence of chemical functional groups.
|OWLImplementation=http://ontology.dumontierlab.com/organic-compound-complex
|LongDescription=Functional groups describe the semantics of chemical reactivity in terms of atoms and their connectivity, which exhibit characteristic chemical behavior when present in a compound. This OWL-DL ontology can be used for the classification of chemical compounds based on the presence of chemical functional groups. We highlight the capabilities and limitations OWL 1.0 and the proposed OWL 1.1 in terms of our domain requirements. We also illustrate how cyclic structures may be identified from SWRL rules and suggest extensions for reasoners to achieve this objective. This work represents a preliminary step towards describing, reasoning and querying about structure and function of molecules.
|Justification=stub
|Domain=Pharmaceutical
|Scenario=structure classification
|KnownIssues=computationally expensive
|OntologyLicensing=creative-commons - by attribution
|WebReference=http://dumontierlab.com/index.php?page=ontologies
|OtherReference=http://dumontierlab.com/pdf/2007_OWLED_CFG.pdf
}}

← Older revision		Revision as of 11:07, 4 March 2010
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	\|OtherReference=http://dumontierlab.com/pdf/2007_OWLED_CFG.pdf		\|OtherReference=http://dumontierlab.com/pdf/2007_OWLED_CFG.pdf
	}}		}}
		+
		+	{{My references}}

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 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.
-|OWLImplementation=http://ontology.dumontierlab.com/organic-compound-complex
+|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.

@@ Line 1: / Line 1: @@
 {{Ontology
 |Name=Chemical Compound and Functional Groups
-|OntologyOrganization=Carleton University :: Dumontier Lab
+|OntologyOrganization=Carleton University - Dumontier Lab
 |OntologyAuthor=Michel Dumontier
 |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.
@@ Line 8: / Line 8: @@
 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.
 |OWLImplementation=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.
- 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).
 |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
 |Scenario=structure classification

@@ Line 17: / Line 17: @@
 |KnownIssues=computationally expensive
 |OntologyLicensing=creative-commons - by attribution
 }}
 {{My references}}

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 |LongDescription=Functional groups describe the semantics of chemical reactivity in terms of atoms and their connectivity, which exhibit characteristic chemical behavior when present in a compound. This OWL-DL ontology can be used for the classification of chemical compounds based on the presence of chemical functional groups. We highlight the capabilities and limitations OWL 1.0 and the proposed OWL 1.1 in terms of our domain requirements. We also illustrate how cyclic structures may be identified from SWRL rules and suggest extensions for reasoners to achieve this objective. This work represents a preliminary step towards describing, reasoning and querying about structure and function of molecules.
 |Justification=stub
-|Domain=Pharmaceutical
+|OntologyDomain=Chemistry, Pharmaceutical
 |Scenario=structure classification
 |KnownIssues=computationally expensive