Applying Ontology Design Patterns in bio-ontologies
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This document discusses applying ontology design patterns in bio-ontologies using the Ontology Preprocessor Language (OPPL). OPPL allows complex modeling to be stored, shared, and consistently applied to ontologies. It can be used to efficiently apply ontology design patterns, like closure patterns, to encapsulate semantics. Version 2 of OPPL was developed to be more axiom-centric and supports features like variables to represent patterns. The document concludes that OPPL enables easy manipulation of ontologies and consistent application of design patterns to aid in modeling.
Applying Ontology Design Patterns in bio-ontologies
- 1. 粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油 Patternsinbio足ontologies MikelEga単a(eganaarm@cs.man.ac.uk),AlanRector,RobertStevens BioHealthInformaticsGroup,SchoolofComputerScience,UniversityofManchester,UK ErickAntezana DepartmentofPlantSystemsBiology,VIB,Gent,Belgium DepartmentofMolecularGenetics,GentUniversity,Belgium EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 2. 或鰻意或晦或赫額油永檎掘永檎或遺掘皆皆或檎油晦粥鰻赫雨粥赫掘油(或永永晦) HighlevelscriptinglanguageforOWL. SelectEntities Semantics Add/removeaxioms Actions Annotations Add/removeannota足 tions Add/removeentities Annotationprocessing(bio足ontologies) Asserted/inferredmode(Pellet,FaCT++,anyDIGreasoner). Currentlytwoversions: OPPL1(http://oppl.sf.net/) OPPL2(http://www.cs.man.ac.uk/~iannonel/oppl/) EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 3. 或鰻意或晦或赫額油永檎掘永檎或遺掘皆皆或檎油晦粥鰻赫雨粥赫掘油(或永永晦) ONTOLOGYPREPROCESSORLANGUAGE OPPLsyntax(ManchesterOWLSyntax+OPPLkeywords) SELECT equivalentTo part_of only (mitochondria or chloroplast); ADD subClassOf has_function some energy_production; OPPLsoftware(java) EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 4. 或鰻意或晦或赫額油永檎掘永檎或遺掘皆皆或檎油晦粥鰻赫雨粥赫掘油(或永永晦) ONTOLOGYPREPROCESSORLANGUAGE Storeandsharecomplexmodellingforconsistentapplication: bydifferentontologists atdifferentstages indifferentpartsoftheontology(viaqueries) Documentedandexplicitmodelling:tracemodelling. Trycomplexmodellingeasily,thendecide:prototypes. Ontologycleansing/enrichment. Ontologycleansing/enrichmentinpipelines(e.g.CCO http://www.cellcycleontology.org/). Automatedmodification/queryingofbigontologies. EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 5. 或永永晦油酷或檎油或鰻意或晦或赫額油禽掘皆鴛赫鰻油永粥意意掘檎鰻皆油(或禽永壊) OntologyDesignPatterns(ODPs):encapsulatecomplexsemantics, easiermodelling. e.g.ClosureODP:prop only filler and prop some filler Bio足ontologies:leanaxiomisation Ontology1 ClosureODP! Ontology2 RCB2 subClassOf RCB2 subClassOf has_function only has_function only iron_binding iron_binding and has_function some HowcanIclose iron_binding thefunctionsof RCB2? ClosureODP! EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 6. 或永永晦油酷或檎油或鰻意或晦或赫額油禽掘皆鴛赫鰻油永粥意意掘檎鰻皆油(或禽永壊) OPPLFORONTOLOGYDESIGNPATTERNS OPPL:store(flatfiles)andapplyODPsinOWLontologies. Entity足QualityODP(E足QODP) ODPsformodifiers Entity足Property足QualityODP(E足P足QODP) Entity足Feature足ValueODP(E足F足VODP) TryE足Q,E足P足Q,E足F足V,andthendecide. E足QODPintheGeneOntology(GO):positionofcellparts(e.g. thepositionofapicalcomplexistheapicalsideofthecell). ApplyE足QinGOviaannotationqueryandprocessingwithOPPL: 24/20,000. LocalvsglobalODPs. EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 7. 或永永晦油酷或檎油或鰻意或晦或赫額油禽掘皆鴛赫鰻油永粥意意掘檎鰻皆油(或禽永壊) OPPLFORONTOLOGYDESIGNPATTERNS Entity足QualityODP(E足QODP) EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 8. 或永永晦油酷或檎油或鰻意或晦或赫額油禽掘皆鴛赫鰻油永粥意意掘檎鰻皆油(或禽永壊) OPPLFORONTOLOGYDESIGNPATTERNS E足QODPappliedinGO(OWLversion)viaOPPLscript(flatfile) EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 9. 或鰻意或晦或赫額油永檎掘永檎或遺掘皆皆或檎油晦粥鰻赫雨粥赫掘油2 DevelopedbyLuigiIannone(BioHealthInformaticsGroup, UniversityofManchester). Axiomcentric,notentitycentric:closertoOWLsemantics. Prot辿g辿plugin(autocomplete,...). Variables(e.g.ClosureODP) ?x:CLASS, ?z:CLASS SELECT ?x SubClassOf has_function only ?z BEGIN ADD ?x SubClassOf has_function some ?z END; Decidability:variablesonlytobeboundbynamedentities,notexpressions (Class,ObjectProperty,DataProperty,Individual,Constant). EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 10. CONCLUSION OPPL:easyprogrammaticmanipulationofOWLontologies. ODPs:semanticencapsulation;easemodelling. OPPLforefficientlyandconsistentlyapplyingODPs. ODPssuccesfullyappliedintheCCOwithOPPL: MikelEga単aAranguren,ErickAntezana,MartinKuiper,RobertStevens. OntologyDesignPatternsforbio足ontologies:acasestudyonthe CellCycleOntology.BMCbioinformatics2008,9(Suppl5):S1. http://www.biomedcentral.com/1471足2105/9/S5/S1 http://ontologydesignpatterns.org ODPspublic http://odps.sf.net/ OPPL repos (...) EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies
- 11. ACKNOWLEDGEMENTS OPPL1,OPPL2: ManchesterOWLSyntax. OWLAPI(http://owlapi.sf.net). Funding: MikelEga単a:UniversityofManchesterandEPSRC. ErickAntezana:EuropeanScienceFoundation(ESF), activityFrontiersofFunctionalGenomics. EKAW2008粥沿沿鉛霞庄稼乙油或稼岳看鉛看乙霞油禽艶壊庄乙稼油Patternsinbio足ontologies