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Cross- P roduct Status in GO

Cross- P roduct Status in GO. Cross Products. Cross products are logical definitions of GO terms that use ‘simpler’ terms in combination to define a more complex term. Why Cross-Products?. Cross-products can be expressed in OWL Allows for automated checking of ontology logic

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Cross- P roduct Status in GO

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  1. Cross-Product Status in GO

  2. Cross Products Cross products are logical definitions of GO terms that use ‘simpler’ terms in combination to define a more complex term

  3. Why Cross-Products? • Cross-products can be expressed in OWL • Allows for automated checking of ontology logic • Allows for the use TermGenie to automatically place terms in the ontology • Cross-products are necessary to integrate the ontology with annotation extension data. • Cross-products with external ontologies allow us to leverage external expertise (ChEBI).

  4. Cross-Products [Term] id: GO:0000018 name: regulation of DNA recombination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents." [GOC:go_curators, ISBN:0198506732] subset: gosubset_prok is_a: GO:0051052 {is_inferred="true"} ! regulation of DNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006310 ! DNA recombination relationship: regulates GO:0006310 ! DNA recombination

  5. Cross-Products Come in 2 Flavours • Internal Cross Products • Cross products that consist of terms that are in GO (MF, BP, CC). • External Cross Products • Cross products that consist of a term from GO and a term from another ontology

  6. Internal Cross ProductsIn the gene_ontology_write.obo • Regulation • Regulates: 2584 • Positively regulates: 2176 • Negatively regulates: 2200 • Part of: 1465 • Occurs in: 114 • Results in: 122

  7. Regulates [Term] id: GO:0000018 name: regulation of DNA recombination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents." [GOC:go_curators, ISBN:0198506732] subset: gosubset_prok is_a: GO:0051052 {is_inferred="true"} ! regulation of DNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006310 ! DNA recombination relationship: regulates GO:0006310 ! DNA recombination

  8. Part of [Term] id: GO:0000022 name: mitotic spindle elongation namespace: biological_process def: "Lengthening of the distance between poles of the mitotic spindle." [GOC:mah] synonym: "spindle elongation during mitosis" EXACT [] is_a: GO:0051231 {is_inferred="true"} ! spindle elongation intersection_of: GO:0051231 ! spindle elongation intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0007052 ! mitotic spindle organization

  9. Occurs in [Term] id: GO:0000957 name: mitochondrial RNA catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of RNA transcribed from the mitochondrial genome and occurring in the mitochondrion." [GOC:krc, GOC:mah] is_a: GO:0000959 {is_inferred="true"} ! mitochondrial RNA metabolic process is_a: GO:0006401 {is_inferred="true"} ! RNA catabolic process intersection_of: GO:0006401 ! RNA catabolic process intersection_of: occurs_in GO:0005739 ! mitochondrion

  10. Results in [Term] id: GO:0001559 name: regulation of cell growth by detection of nuclear:cytoplasmic ratio namespace: biological_process def: "Any process in which the size of the nucleus with respect to the cytoplasm modulates the frequency, rate or extent of cell growth, the irreversible increase in size of a cell over time." [GOC:dph] synonym: "detection of nuclear:cytoplasmic ratio to regulate cell growth" EXACT [] synonym: "interpretation of nuclear:cytoplasmic ratio to regulate cell growth" EXACT [] synonym: "regulation of cell growth by nuclear:cytoplasmic ratio" EXACT [] synonym: "regulation of cell growth by sensing of nuclear:cytoplasmic ratio" EXACT [] is_a: GO:0016475 {is_inferred="true"} ! detection of nuclear:cytoplasmic ratio is_a: GO:0061387 ! regulation of extent of cell growth intersection_of: GO:0016475 ! detection of nuclear:cytoplasmic ratio intersection_of: results_in GO:0001558 ! regulation of cell growth

  11. Internal Cross ProductsIn gene_ontology_xp_write.obo

  12. Internal Cross Productsin gene_ontology_xp_write.obo [Term] id: GO:0001675 ! acrosome assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0001669 ! acrosomal vesicle [Term] id: GO:0006997 ! nucleus organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005634 ! nucleus [Term] id: GO:0032989 ! cellular component morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of GO:0005575 ! cellular_component

  13. External Cross Productsin gene_ontology_xp_write.obo • Currently implemented with ChEBI • Cross-products with the cell ontology • Cross-products with anatomy

  14. External Cross ProductsIn gene_ontology_xp_write.obo

  15. External Cross Productsin gene_ontology_xp_write.obo [Term] id: GO:0000017 ! alpha-glucoside transport intersection_of: GO:0006810 ! transport intersection_of: transports_or_maintains_localization_of CHEBI:60979 ! alpha-glucoside [Term] id: GO:0000035 ! acyl binding intersection_of: GO:0005488 ! binding intersection_of: has_input CHEBI:22221 ! acyl group [Term] id: GO:0000951 ! methionine catabolic process to 3-methylthiopropanol intersection_of: GO:0009056 ! catabolic process intersection_of: has_input CHEBI:32644 ! methioninate intersection_of: has_output CHEBI:49019 ! 3-methylthiopropanol [Term] id: GO:0001504 ! neurotransmitter uptake intersection_of: GO:0006810 ! transport intersection_of: imports CHEBI:25512 ! Neurotransmitter

  16. Next step: Cell Ontology • The cell ontology is already being used in annotation extensions • It is critical that we also incorporate cell information into GO logical definitions.

  17. Column 16 Data

  18. Future of Cellular terms in GO [Term] id: GO:0002070 name: epithelial cell maturation namespace: biological_process def: "The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface." [GOC:dph] is_a: GO:0048469 ! cell maturation relationship: part_of GO:0002064 ! epithelial cell development intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of CL:0000066 ! epithelial cell

  19. In the Pipeline • Cross-products with the plant ontology: 150 (Tanya) • Cross-products for complexes that are capable of some function: 700 (Harold) • Hand editing non-parsable/incomplete terms.

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