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Partial Integration of GO with the Ingenuity Ontology

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gaye
15 diapositives · 403 Views · Jan 17, 2013

Partial Integration of GO with the Ingenuity Ontology. Molly James Ontology Modeling, Ingenuity System Mountain View, CA. Ingenuity Ontology. Private ontology Stores information extracted from scientific literature Very large ontology 575,000 classes 10 million instances 370 slots

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

  2. 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

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

  4. Ontology Construction via Downloads generic_thing biological_temporal_thing property molecular_function organism information cell domain molecular_complex small_molecule gross_anatomical_part macromolecule cell_component 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. molecular_function gene_product_function • %transporter ; GO:0005215 • %carrier ; GO:0005386 ; synonym:carrier type transporter • %electrochemical potential-driven transporter ; GO:0015290 • %porter ; GO:0015291 synonym:active transporter • %amino acid-polyamine transporter ; GO:0005279 ; % amino acid transporter ; GO:0015171 % polyamine transporter ; GO:0015203 transporter carrier electrochemical_potential_dash_driven_transporter polyamine_transporter amino_acid_transporter porter amino_acid_dash_polyamine_transporter

  8. molecular_function gene_product_function • %transporter ; GO:0005215 • %carrier ; GO:0005386 ; synonym:carrier type transporter • %electrochemical potential-driven transporter ; GO:0015290 • %porter ; GO:0015291 synonym:active transporter • %amino acid-polyamine transporter ; GO:0005279 ; % amino acid transporter ; GO:0015171 % polyamine transporter ; GO:0015203 transporter database_id: "GO:0005215" carrier electrochemical_potential_dash_driven_transporter polyamine_transporter amino_acid_transporter porter amino_acid_dash_polyamine_transporter

  9. assertion_reference_metadata molecular_function_family_assertion_information_14336 assertion_downloaded_from_database: "LocusLink" assertion_downloaded_from_database_version: "Oct 20, 2003 source_responsible_for_assertion: "Gene Ontology Annotation @ EBI" 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" curation_id: "LL:9400" molecular_function_family_defined_by molecular_function_family_member assertion_supported_by assertion_identifier:"GO:0003678"

  10. Use of Functions in Ingenuity Pathway Analysis

  11. Shapes indicate function Kinase NuclearReceptor Transcription Factor Enzyme

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

  13. Processes are used to annotate groups of genes

  14. differentiation_01 keratinocyte_01 Aligning GO Processes with Ingenuity Processes %keratinocyte differentiation; GO:0030216 cell biological_temporal_thing keratinocyte differentiation object

  15. www.ingenuity.com