Obo and common logic
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OBO format has evolved over time to allow for more complex logical definitions by extending it to use Common Logic (CL) semantics. CL is a standard for formalizing first-order logic that can represent relations, quantifiers, and other constructs that are difficult to represent in OWL. OBO files are mapped to CL sentences under the hood, making OBO a simple syntax for the more expressive CL. This allows OBO ontologies to formally define relations and take advantage of CL reasoning tools.
Obo and common logic
- 1. OBO Format and Common Logic
- 2. History2000/2001OBO format 1.0 createdsimplegraph-orientedcvs-able2004-2006OBO format 1.2 and related effortshttp://www.geneontology.org/GO.format.obo-1_2.shtmlbackwards and forwards incompatible with 1.0Extended to allow simple genus-differentia logical definitionsMappings to OWL2009OBO format 1.3 and CLBackwards and forwards compatible with 1.2Minor extensionsrelation intersections, unions, compositionshttp://www.geneontology.org/GO.format.obo-1_3.shtmlFormal semantics specified in terms of CL
- 3. ISO Common LogicStandard for first-order logic (FOL)Family of syntaxesCLIFCL-XMLA CL text is a collection of sentences (axioms)Sentences can beatomic; e.g. part_of(nucleus,cell)boolean; not has_part(mammalian_erythrocyte,nucleus) quantified; e.g. all nnucleus(n) exist c,tpart_of(n,c) ^ cell(c)Why do we need this when we have OWL/OWL2?RO uses n-ary relationsDifficulties defining relations in OWLType level relationsFOL has been around for over a century
- 4. OBOF <-> CLOBOF tags mapped to CL predicatesid: ?ris_transitive: true transitive(?r)CL predicates defined in a set of axioms called obologtransitive(rel) ∧ rel(X, Y ) ∧ rel(Y , Z ) -> rel(X, Z )transitive(rel) ∧ rel(x, y, t) ∧ rel(y, z , t) -> rel(x, z , t)
- 5. Every .obo file is a CL textThis mapping is invisible and not directly to the majority of users.obo becomes a simple surface syntax for CLMost OBO files use a subset including only atomic sentencesExceptions: relation definitions
- 6. Exampleshttp://www.fruitfly.org/~cjm/ro/ro.htmlhttp://www.fruitfly.org/~cjm/ro/ro-gaz.htmlhttp://www.fruitfly.org/~cjm/ro/ro-development.htmlSO genome interval relationsx starts yiffα(x) = α(y) ∧ ω(x) < ω(y)
- 7. Mapping to OWLOBOF mapping to OWL now specified in terms of CL3 different mappingsOWL-Full, with type-level relationsTwo DL mappings depending on treatment of time
- 8. ReasoningRelation reasoningTheorem provers over CLOntology reasoningDL reasoners over OWL translationOntology + data reasoningDatalog subset