OWL Ontologies

by the Dumontier Lab

The following are the OWL ontologies to represented biological and scientific concepts and relations. Ontologies designated as primitive are "is a" taxonomies with labels and descriptions. Ontologies designated as complex enhance their respective primitive ontologies with the expressiveness afforded by OWL-DL and may include disjunction, negation, union, intersection, class equivalence, existential and universal restrictions and qualified cardinality restrictions.

Note that these ontologies are no longer maintained. We would like to refer you to the Semanticscience Integrated Ontology(SIO).

annotation
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Annotation Properties
atom
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Atom Ontology (primitive)
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Atom Ontology (common)
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Atom (complex) - Atomic Number
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Atom Ontology (disjoint)
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Atom (complex) - Proton
bfo
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Basic Formal Ontology (BFO)
biochemical-reaction
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Biochemical Reaction Ontology
biochemistry
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Biochemistry Ontology (primitive)
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Biochemistry Ontology (complex)
biological-measure
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biomedical measure ontology (primitive)
biomedical-measure
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biomedical measure ontology (primitive)
bro
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OWL 1.0 axioms for the Basic Relationship Ontology (BRO)
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OWL2 axioms for the Basic Relationship Ontology
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Basic Relation Ontology (primitive)
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OWL2 axioms for basic relations
cfg
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Instantiated CFG ontology (examples)
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Chemical Functional Groups
chemistry
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Chemistry Ontology (primitive)
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Chemistry Ontology (complex)
ec
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Enzyme Commission Ontology (primitive)
element
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Element Ontology (primitive)
goslim
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GO SLIM (yeast)
graph
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Inferred graph knowledgebase, after running rules..
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Rules for processing graph knowledgebase.
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Units for example statistical graphs.
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Example line graph: goods sales by quarters, 2006-2007
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Example line graph: Service sales by quarters, 2006-2007
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Sales Ontology (primitive)
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Example line graph: service sales by years, 2000-2005
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Example line graph: goods sales by quarters, 2004-2005
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4 example graph knowledgebase
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Instantiated time intervals for statistical graphs.
igraph
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iGraph ontology
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iGraph examples
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iGraph examples
molecule
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Molecule Ontology (complex)
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Molecule Ontology (Individuals)
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Molecule Ontology (primitive)
nulo
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New Upper Level Ontology (NULO)
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New Upper Level Ontology (NULO) - contraints
organic-compound
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Organic Compound Ontology (primitive)
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Organic Compound Ontology (complex)
organic-functional-group
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Organic Functional Group Ontology (primitive)
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Organic Functional Group Ontology (complex)
periodic-table
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Elements of the Periodic Table Ontology (primitive)
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Elements of the Periodic Table Ontology (complex)
pharmacogenomics
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pharmacogenomics ontology (complex)
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pharmacogenomics ontology (primitive)
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Pharmacogenomics of Depression
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PharmGKB knowledge base
physics
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Physics Ontology (complex)
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Physics Ontology (primitive)
property
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Measured Property Ontology (complex)
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Measured Property Ontology (primitive)
protege-dc
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statistical-graph
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Statistical Graph Ontology (complex)
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Statistical Graph Ontology (primitive)
subatomic-particle
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Subatomic Particle Ontology (complex)
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Subatomic Particle Ontology (primitive)
time
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Instantiated Time Intervals
time-interval
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Time Interval Ontology
unit
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Unit Ontology (complex)
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Unit Ontology (individuals)
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Unit Ontology (primitive)
yowl
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SGD Ontology (primitive)
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SGD Ontology (complex)
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SGD Ontology (primitive)
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UniProt data for yOWL
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UniProt GO to OBO GO mapping
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yOWL HCLS data
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yOWL JBI examples
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yOWL JBI data