Download GO Talk - The Gene Ontology

Partial Integration of GO with the
Ingenuity Ontology
Molly James
Ontology Modeling, Ingenuity System
Mountain View, CA
Proprietary and Confidential
1
Ingenuity Ontology
• Private ontology
• Stores information extracted from scientific literature
• Very large ontology
• 575,000 classes
• 10 million instances
• 370 slots
• Uses frame-based knowledge representation system
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2
High Level Classes
generic_thing
biological_temporal_thing
property
molecular_function
information
organism
cell
molecular_complex
domain
small_molecule
gross_anatomical_part
cell_component
macromolecule
Proprietary and Confidential
3
Ontology Construction via Downloads
generic_thing
biological_temporal_thing
property
molecular_function
information
organism
cell
molecular_complex
domain
small_molecule
gross_anatomical_part
cell_component
macromolecule
Subclasses are created
based on information in
LocusLink.
Proprietary and Confidential
4
Using GO to Supplement the Ontology
generic_thing
Future: Add GO
processes to our
process branch.
biological_temporal_thing
property
molecular_function
information
Add GO
annotation
information.
organism
cell
molecular_complex
domain
Add GO
functions to fill
out this branch.
small_molecule
gross_anatomical_part
macromolecule
cell_component
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Adding GO functions.
• Took only "is-a" relationships from GO.
• Excluded functions not applicable to human, mouse, or
rat.
• Excluded functions not part of our function model.
• E.g. anticoagulant is a drug in our ontology.
• Converted GO names into our naming format.
• Fix duplicates that were imported.
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molecular_function
gene_product_function
%transporter ; GO:0005215
%carrier ; GO:0005386 ;
synonym:carrier type transporter
transporter
%electrochemical potentialdriven transporter ; GO:0015290
carrier
%porter ; GO:0015291
synonym:active transporter
electrochemical_potential_dash_driven_transporter
polyamine_transporter
porter
%amino acid-polyamine
transporter ; GO:0005279 ; %
amino acid transporter ;
GO:0015171 % polyamine
transporter ; GO:0015203
amino_acid_transporter
amino_acid_dash_polyamine_transporter
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molecular_function
gene_product_function
%transporter ; GO:0005215
transporter
database_id: "GO:0005215"
%carrier ; GO:0005386 ;
synonym:carrier type transporter
%electrochemical potentialdriven transporter ; GO:0015290
carrier
%porter ; GO:0015291
synonym:active transporter
electrochemical_potential_dash_driven_transporter
polyamine_transporter
porter
%amino acid-polyamine
transporter ; GO:0005279 ; %
amino acid transporter ;
GO:0015171 % polyamine
transporter ; GO:0015203
amino_acid_transporter
amino_acid_dash_polyamine_transporter
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8
Adding Functional Annotation Information
information_based_thing
macromolecule
gene_product_function
molecular_function_family_assertion_information
dna_helicase
recql5_hs_concept
database_id:
"GO:0003678",
"GO:0003679"
molecular_function_family_assertion_information_14336
curation_id:
"LL:9400"
molecular_function_family_defined_by
molecular_function_family_member
assertion_supported_by
assertion_identifier:"GO:0003678"
assertion_reference_metadata
assertion_downloaded_from_database:
"LocusLink"
assertion_downloaded_from_database
_version: "Oct 20, 2003
source_responsible_for_assertion:
"Gene Ontology Annotation @ EBI"
Proprietary and Confidential
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Use of Functions in Ingenuity Pathway Analysis
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Shapes indicate function
Kinase
Nuclear
Receptor
Transcription
Factor
Enzyme
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GO Annotations are imported and
displayed on NodeView pages.
Proprietary and Confidential
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Processes are used to annotate
groups of genes
Proprietary and Confidential
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Aligning GO Processes with Ingenuity Processes
%keratinocyte differentiation; GO:0030216
cell
biological_temporal_thing
keratinocyte
differentiation
keratinocyte_01
differentiation_01
object
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www.ingenuity.com
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