1. An OWL model of GO annotation

2. Outline These slides illustrate a translation for modeling GO annotations in OWL – Assumes basic knowledge of OWL We start with existing ‘classic’ annotations, and then proceed to enhancements that are supported by OWL The end result is equivalent to what we have been calling ‘LEGO’

3. Elucidation Molecular view of biological process – A process is a coordinated series of molecular activities See: – LEGO white paper 2009 (Paul Thomas) – GO biological process documentation

4. OWL Basics Expressive modeling language Classes – The “ontology” Classes/class expressions connected via axioms Individuals – Instantiations of classes or class expressions in the ontology “type” assertions – Connection between these individuals “triples” (rdf-speak) Aka “facts” (manchester-speak), aka “object property assertion axioms” (owl formal speak)

5. “classic” GO annotations in OWL: MF Proposed OWL interpretation: A molecular function annotation describes a single instance (individual) of an activity (the type), enabled by some instance of a gene product – Note here gene products modeled as classes Individual: gomfi-0000012345 Types: GO:0004672, # enabled_by some PR:P87654 # OWL GAF Visualization protein kinase activity Gask3b c2: P87654 c5: GO:0004672 c9: F

6. “classic” GO annotations in OWL: CC Classic cellular component annotation – some unspecified activity being executed in some material entity (CC) Individual: gomf-0000012345 Types: occurs_in some GO:0005829, enabled_by some PR:P87654 OWL GAF Visualization c2: P87654 c5: GO:0005829 c9: C cytosol Gask3b

7. “classic” GO annotations in OWL: BP BP Individual: gobp-0000000001 Types: GO:0060070 Individual: gomf-0000012345 Facts: part_of gobp-0000000001 Types: enabled_by some PR:P87654 OWL GAF Visualization c2: P87654 c5: GO:0060070 c9: P canonical Wnt signaling P Gask3b

8. Combining Simultaneous MF, BP, CC – Formally stronger than 3 separate individuals Individual: gobp-0000000001 Types: GO:0060070 # Individual: gomf-0000012345 Facts: part_of gobp-0000000001 Types: GO:0004672 occurs_in some GO:0005829 enabled_by some PR:P87654 OWL GAF n/a Visualization protein kinase activity canonical Wnt signaling P Gask3b cytosol

9. Connecting individuals via triples …. Individual: gobp-0000000001 Types: GO:0060070 # Individual: gomf-0000012345 Types: GO:0004672 occurs_in some GO:0005829, enabled_by some PR:P87654 Facts: required_for gomf-0000012346 Individual: gomf-0000012346 Types: GO:0005515, occurs_in some GO:0005829, enabled_by some PR:Q01011 OWL Visualization protein kinase activity canonical Wnt signaling P Gask3b cytosol protein binding Btrc cytosol required_for

10. Class expressions Equivalent to precomposed class defined by an OWL equivalence axiom Individual: gomf-0000012345 Types: enabled_by some PR:P87654, occurs_in some (GO:0005829 and part_of some CL:nnnnnn) OWL GAF Visualization c2: P87654 c5: GO:0005829 c9: C C16: part_of(CL:nnnn) cytosol and part_of some epithelium Gask3b

11. Class expressions: any level of nesting OWL allows arbitrary depth of expressions (e.g. P some C) combined with OR or AND Individual: gomf-0000012345 Types: enabled_by some PR:P87654, occurs_in some (GO:0005829 and part_of some (CL:nnnnnn and part_of some (UBERON:nnnnn) OWL GAF Visualization c2: P87654 c5: GO:0005829 c9: C C16: part_of(CL:nnnn), part_of(UBERON:nnn) NOT STRICTLY EQUIVALENT cytosol and part_of some epithelium and part_of some gut Gask3b

12. Class expressions: anywhere you can have a class OWL allows arbitrary depth of expressions combined with OR or AND Individual: gomf-0000012345 Types: enabled_by some (GO:complex and has_part some PR:A and has_part some PR:B), occurs_in some GO:0005829 OWL GAF Visualization (?) n/a cytosol Complex A B Complex A B

13. Class expression materialization Translation from extensions – Equivalent to class expression Individual: gobp-0000000001 Types: GO:0060070 Individual: gomf-0000012345 Facts: required_for gomf-0000012346 Types: GO:0004672, enabled_by some PR:P87654 # occurs_in some GO:0005829 OWL GAF c2: P87654 c5: GO:0004672 c9: F C16: part_of(GO:0060070 ) Visualization protein kinase activity canonical Wnt signaling P Gask3b cytosol

14. Metadata Attached at level of individual Individual: gobp-0000000001 Types: GO:0000000 # Individual: gomf-0000012345 Types: enabled_by some PR:P87654 # Facts: part_of: gobp-0000000001, describedBy { Types: ECO:nnnnn # IDA Facts: dc:source pmid:7654, with db:1111, aspect ro:occurs_in } OWL Visualization (?) protein kinase activity canonical Wnt signaling P Gask3b cytosol IDA

15. Evidence, evolutionary Visualization (?) protein kinase activity canonical Wnt signaling P GAS3KB cytosol IBD protein kinase activity canonical Wnt signaling P Gask3b cytosol IDA IBD

16. Host-symbiont … Individual: _ Types: occurs_in some (GO:0005886 and part_of some NCBITaxon_9606) enabled_by some PLSMDB:123 Class: PLSMDB:123 SubClassOf: product_of some ( expressed_in some Plasmodium) OWL GPAD Visualization GO:0005886 C8: NCBITaxon_9606 Plasma membrane and part_of some Homo sapiens RIFi1 (plasmodium) RIFi1 (plasmodium) GPI PLSMDB:123 RIFi1 Plasmodium

17. TODO Example of process or function of a symbiont in host Example from POV of host https://docs.google.com/document/d/196nLK iQ2Go4toilCq226w7u0p52odvCkq- bU5qgtzu0/edit https://docs.google.com/document/d/196nLK iQ2Go4toilCq226w7u0p52odvCkq- bU5qgtzu0/edit