Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language
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The document describes the Ontology Pre-Processor Language (OPPL), which is a "macro" language for manipulating the content of OWL ontologies. OPPL allows authors to perform tasks like adding, removing, and selecting ontology components with instructions that are easier to use than typical programming APIs. Examples are provided of how OPPL has been used for axiomatically enriching bio-ontologies and integrating knowledge across multiple cell cycle ontologies generated by a pipeline.
Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language
- 1. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Ontology Pre-Processor Language (OPPL) http://oppl.sourceforge.net/ Mikel Ega単a (mikel.eganaaranguren@cs.man.ac.uk) Robert Stevens (robert.stevens@manchester.ac.uk) Bio-Health Informatics Group (BHIG), University of Manchester Erick Antezana (erant@psb.ugent.be) Department of Plant Systems Biology, VIB, Gent, Belgium Department of Molecular Genetics, Ghent University, Gent, Belgium OWLED 2008 DC Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 2. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Introduction to OPPL Macro language for manipulating content of OWL ontologies Motivation: authors needs when creating/maintaining bio-ontologies (Use cases) Nearly API-level functionality with minimum programming/OWL knowledge Manchester OWL Syntax + SELECT, ADD, REMOVE Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 3. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Introduction to OPPL Macro language for manipulating content of OWL ontologies Motivation: authors needs when creating/maintaining bio-ontologies (Use cases) Nearly API-level functionality with minimum programming/OWL knowledge Manchester OWL Syntax + SELECT, ADD, REMOVE Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 4. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Introduction to OPPL Macro language for manipulating content of OWL ontologies Motivation: authors needs when creating/maintaining bio-ontologies (Use cases) Nearly API-level functionality with minimum programming/OWL knowledge Manchester OWL Syntax + SELECT, ADD, REMOVE Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 5. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Introduction to OPPL Macro language for manipulating content of OWL ontologies Motivation: authors needs when creating/maintaining bio-ontologies (Use cases) Nearly API-level functionality with minimum programming/OWL knowledge Manchester OWL Syntax + SELECT, ADD, REMOVE Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 6. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction SELECT Class: admin;ADD label "of鍖ce admin"; OPPL statement OPPL statement OPPL instruction Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 7. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction examples ADD Class: undergraduate; REMOVE Class: undergraduate; SELECT equivalentTo participates_in only (intellectual_dinner and party); ADD label "professor"; REMOVE subClassOf lives_on only (not campus); Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 8. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction examples ADD Class: undergraduate; REMOVE Class: undergraduate; SELECT equivalentTo participates_in only (intellectual_dinner and party); ADD label "professor"; REMOVE subClassOf lives_on only (not campus); Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 9. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction examples ADD Class: undergraduate; REMOVE Class: undergraduate; SELECT equivalentTo participates_in only (intellectual_dinner and party); ADD label "professor"; REMOVE subClassOf lives_on only (not campus); Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 10. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction examples SELECT subClassOf MoleOfSalt; ADD subClassOf hasDensity value 0.0; SELECT inverse participates_in; ADD range student; ADD Class: professor; ADD label "staff"; ADD equivalentTo participates_in only (intellectual_dinner and party); Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 11. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction examples SELECT subClassOf MoleOfSalt; ADD subClassOf hasDensity value 0.0; SELECT inverse participates_in; ADD range student; ADD Class: professor; ADD label "staff"; ADD equivalentTo participates_in only (intellectual_dinner and party); Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 12. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction examples SELECT subClassOf MoleOfSalt; ADD subClassOf hasDensity value 0.0; SELECT inverse participates_in; ADD range student; ADD Class: professor; ADD label "staff"; ADD equivalentTo participates_in only (intellectual_dinner and party); Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 13. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction examples disjointWith, differentFrom, sameAs, type, descendantOf, ancestorOf, subPropertyOf, ... http://oppl.sourceforge.net/test.oppl Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 14. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL instruction examples disjointWith, differentFrom, sameAs, type, descendantOf, ancestorOf, subPropertyOf, ... http://oppl.sourceforge.net/test.oppl Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 15. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL extra instructions SELECT_PRIMITIVE descendantOf student; SELECT_DEFINED descendantOf student; SELECT descendantOf person; ADD disjointWithSiblings; SELECT assertedSubClassOf participates_in some sport; Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 16. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL extra instructions SELECT_PRIMITIVE descendantOf student; SELECT_DEFINED descendantOf student; SELECT descendantOf person; ADD disjointWithSiblings; SELECT assertedSubClassOf participates_in some sport; Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 17. Introduction to OPPL OPPL instruction OPPL Syntax OPPL instruction examples Using OPPL OPPL extra instructions Future of OPPL OPPL extra instructions SELECT_PRIMITIVE descendantOf student; SELECT_DEFINED descendantOf student; SELECT descendantOf person; ADD disjointWithSiblings; SELECT assertedSubClassOf participates_in some sport; Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 18. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL OPPL software http://oppl.sourceforge.net/ OPPLInstructionManager Java library for processing OPPL instructions (LGPL) OWL API, Pellet, FaCT++, DIG OPPL reference implementation: OPPL instructions in 鍖at 鍖le java -jar oppl.jar pellet ins.oppl ont.owl new_ont.owl Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 19. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL OPPL software http://oppl.sourceforge.net/ OPPLInstructionManager Java library for processing OPPL instructions (LGPL) OWL API, Pellet, FaCT++, DIG OPPL reference implementation: OPPL instructions in 鍖at 鍖le java -jar oppl.jar pellet ins.oppl ont.owl new_ont.owl Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 20. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL OPPL software http://oppl.sourceforge.net/ OPPLInstructionManager Java library for processing OPPL instructions (LGPL) OWL API, Pellet, FaCT++, DIG OPPL reference implementation: OPPL instructions in 鍖at 鍖le java -jar oppl.jar pellet ins.oppl ont.owl new_ont.owl Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 21. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 1: Bio-ontology axiomatic enrichment Gene Ontology Next Generation http://www.gong.manchester.ac.uk/ alanine:sodium symporter activity Axiomatic enrichment based in rdfs:label EquivalentTo: symporter activity and transports only (alanine or sodium) Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 22. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 1: Bio-ontology axiomatic enrichment Gene Ontology Next Generation http://www.gong.manchester.ac.uk/ alanine:sodium symporter activity Axiomatic enrichment based in rdfs:label EquivalentTo: symporter activity and transports only (alanine or sodium) Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 23. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 1: Bio-ontology axiomatic enrichment rdfs:label: alanine:sodium symporter activity rdfs:label: glycine:potassium symporter activity rdfs:label: valine:sodium symporter activity ... SELECT label "(.+):(.+) (symporter activity)"; ADD equivalentTo symporter_activity and transports only (<1> or <2>); Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 24. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 2: Cell Cycle Ontology http://www.cellcycleontology.org/ Gather knowledge about the cell cycle in 5 ontologies Ontologies created anew each pipeline execution Impossible to add new axioms by hand to 5 ontologies: - Axioms overwritten each time the pipeline is executed - Many axioms in different places - Ontologies too big Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 25. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 2: Cell Cycle Ontology http://www.cellcycleontology.org/ Gather knowledge about the cell cycle in 5 ontologies Ontologies created anew each pipeline execution Impossible to add new axioms by hand to 5 ontologies: - Axioms overwritten each time the pipeline is executed - Many axioms in different places - Ontologies too big Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 26. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 2: Cell Cycle Ontology Add axioms automatically each time the pipeline is executed Explicit development Querying capabilities Flexible development Ontology Design Patterns http://odps.sourceforge.net Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 27. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 2: Cell Cycle Ontology Add axioms automatically each time the pipeline is executed Explicit development Querying capabilities Flexible development Ontology Design Patterns http://odps.sourceforge.net Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 28. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 2: Cell Cycle Ontology Add axioms automatically each time the pipeline is executed Explicit development Querying capabilities Flexible development Ontology Design Patterns http://odps.sourceforge.net Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 29. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 2: Cell Cycle Ontology Add axioms automatically each time the pipeline is executed Explicit development Querying capabilities Flexible development Ontology Design Patterns http://odps.sourceforge.net Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 30. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 2: Cell Cycle Ontology Add axioms automatically each time the pipeline is executed Explicit development Querying capabilities Flexible development Ontology Design Patterns http://odps.sourceforge.net Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 31. Introduction to OPPL OPPL software OPPL Syntax Use case 1: Bio-ontology axiomatic enrichment Using OPPL Use case 2: Cell Cycle Ontology Future of OPPL Use case 2: Cell Cycle Ontology # Create object property inmediately_precedes ADD ObjectProperty: inmediately_precedes;ADD functional; ADD subPropertyOf precedes;ADD inverse inmediately_preceded_by;ADD domain CCO_U0000002;ADD range CCO_U0000002; # Meiotic cell cycle: G1 -> S -> G2 -> M SELECT Class: CCO_P0000327;ADD subClassOf inmediately_preceded_by some CCO_P0000325;ADD subClassOf inmediately_precedes some CCO_P0000326; # Query 1: Proteins acting in the mitotic S phase (At) ADD Class: query_1;ADD subClassOf query;REMOVE subClassOf Thing; ADD comment "Proteins acting in the mitotic S phase"; SELECT subClassOf participates_in some (CCO_P0000014 or (part_of some CCO_P0000014));ADD subClassOf query_1; Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 32. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Future of OPPL Syntax closer to OWL? ADD Class: professor ADD professor subClassOf Thing Loops, conditional control, subroutines, ... Variables? SELECT subClassOf part_of some ?x; ADD equivalentTo part_of only ?x; SET professor label "new label"; Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 33. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Future of OPPL Syntax closer to OWL? ADD Class: professor ADD professor subClassOf Thing Loops, conditional control, subroutines, ... Variables? SELECT subClassOf part_of some ?x; ADD equivalentTo part_of only ?x; SET professor label "new label"; Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 34. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Future of OPPL Syntax closer to OWL? ADD Class: professor ADD professor subClassOf Thing Loops, conditional control, subroutines, ... Variables? SELECT subClassOf part_of some ?x; ADD equivalentTo part_of only ?x; SET professor label "new label"; Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 35. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Future of OPPL Syntax closer to OWL? ADD Class: professor ADD professor subClassOf Thing Loops, conditional control, subroutines, ... Variables? SELECT subClassOf part_of some ?x; ADD equivalentTo part_of only ?x; SET professor label "new label"; Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 36. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Future of OPPL Formal grammar Prot辿g辿 plugin (autocomplete, syntax validation, logs, ...) Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 37. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Future of OPPL Formal grammar Prot辿g辿 plugin (autocomplete, syntax validation, logs, ...) Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
- 38. Introduction to OPPL OPPL Syntax Using OPPL Future of OPPL Acknowledgements Mikel Ega単a: University of Manchester and EPSRC Erick Antezana: European Science Foundation (ESF) for the activity entitled Frontiers of Functional Genomics http://oppl.sourceforge.net/ Mikel Ega単a, Robert Stevens, Erick Antezana Ontology Pre-Processor Language