1. Partial Integration of GO with the Ingenuity Ontology
Molly James
Ontology Modeling, Ingenuity System
Mountain View, CA

2. Ingenuity Ontology Private ontology Very large ontology
Stores information extracted from scientific literature
Very large ontology
575,000 classes
10 million instances
370 slots
Uses frame-based knowledge representation system

3. biological_temporal_thing gross_anatomical_part
High Level Classes
generic_thing
biological_temporal_thing
property
molecular_function
organism
information
cell
domain
molecular_complex
small_molecule
gross_anatomical_part
cell_component
macromolecule

4. Ontology Construction via Downloads
generic_thing
biological_temporal_thing
property
molecular_function
organism
information
cell
domain
molecular_complex
small_molecule
gross_anatomical_part
cell_component
macromolecule
Subclasses are created based on information in LocusLink.

5. Using GO to Supplement the Ontology
generic_thing
Future: Add GO processes to our process branch.
biological_temporal_thing
property
molecular_function
organism
information
Add GO functions to fill out this branch.
cell
domain
Add GO annotation information.
molecular_complex
small_molecule
gross_anatomical_part
macromolecule
cell_component

6. 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.

7. gene_product_function
molecular_function
gene_product_function
%transporter ; GO:
%carrier ; GO: ; synonym:carrier type transporter
%electrochemical potential-driven transporter ; GO:
%porter ; GO: synonym:active transporter
%amino acid-polyamine transporter ; GO: ; % amino acid transporter ; GO: % polyamine transporter ; GO:
transporter
carrier
electrochemical_potential_dash_driven_transporter
polyamine_transporter
porter
amino_acid_transporter
amino_acid_dash_polyamine_transporter

8. database_id: "GO:0005215" molecular_function gene_product_function
%transporter ; GO:
%carrier ; GO: ; synonym:carrier type transporter
%electrochemical potential-driven transporter ; GO:
%porter ; GO: synonym:active transporter
%amino acid-polyamine transporter ; GO: ; % amino acid transporter ; GO: % polyamine transporter ; GO:
transporter
database_id: "GO: "
carrier
electrochemical_potential_dash_driven_transporter
polyamine_transporter
porter
amino_acid_transporter
amino_acid_dash_polyamine_transporter

9. Adding Functional Annotation Information
information_based_thing
macromolecule
gene_product_function
molecular_function_family_assertion_information
dna_helicase
recql5_hs_concept
database_id: "GO: ", "GO: "
curation_id: "LL:9400"
molecular_function_family_assertion_information_14336
molecular_function_family_defined_by
molecular_function_family_member
assertion_supported_by
assertion_identifier:"GO: "
assertion_reference_metadata
assertion_downloaded_from_database: "LocusLink"
assertion_downloaded_from_database_version: "Oct 20, 2003
source_responsible_for_assertion: "Gene Ontology EBI"

10. Use of Functions in Ingenuity Pathway Analysis

11. Shapes indicate function
Kinase
Nuclear Receptor
Transcription Factor
Enzyme

12. GO Annotations are imported and displayed on NodeView pages.

13. Processes are used to annotate groups of genes

14. Aligning GO Processes with Ingenuity Processes
%keratinocyte differentiation; GO:
cell
biological_temporal_thing
keratinocyte
differentiation
keratinocyte_01
differentiation_01
object