Obo and common logic

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Obo and common logic

  1. 1. OBO Format and Common Logic<br />
  2. 2. History<br />2000/2001<br />OBO format 1.0 created<br />simple<br />graph-oriented<br />cvs-able<br />2004-2006<br />OBO format 1.2 and related efforts<br />http://www.geneontology.org/GO.format.obo-1_2.shtml<br />backwards and forwards incompatible with 1.0<br />Extended to allow simple genus-differentia logical definitions<br />Mappings to OWL<br />2009<br />OBO format 1.3 and CL<br />Backwards and forwards compatible with 1.2<br />Minor extensions<br />relation intersections, unions, compositions<br />http://www.geneontology.org/GO.format.obo-1_3.shtml<br />Formal semantics specified in terms of CL<br />
  3. 3. ISO Common Logic<br />Standard for first-order logic (FOL)<br />Family of syntaxes<br />CLIF<br />CL-XML<br />A CL text is a collection of sentences (axioms)<br />Sentences can be<br />atomic; e.g. part_of(nucleus,cell)<br />boolean; not has_part(mammalian_erythrocyte,nucleus) <br />quantified; e.g. all nnucleus(n)  exist c,tpart_of(n,c) ^ cell(c)<br />Why do we need this when we have OWL/OWL2?<br />RO uses n-ary relations<br />Difficulties defining relations in OWL<br />Type level relations<br />FOL has been around for over a century<br />
  4. 4. OBOF &lt;-&gt; CL<br />OBOF tags mapped to CL predicates<br />id: ?r<br />is_transitive: true transitive(?r)<br />CL predicates defined in a set of axioms called obolog<br />transitive(rel) ∧ rel(X, Y ) ∧ rel(Y , Z ) -> rel(X, Z )<br />transitive(rel) ∧ rel(x, y, t) ∧ rel(y, z , t) -> rel(x, z , t) <br />
  5. 5. Every .obo file is a CL text<br />This mapping is invisible and not directly to the majority of users<br />.obo becomes a simple surface syntax for CL<br />Most OBO files use a subset including only atomic sentences<br />Exceptions: relation definitions<br />
  6. 6. Examples<br />http://www.fruitfly.org/~cjm/ro/ro.html<br />http://www.fruitfly.org/~cjm/ro/ro-gaz.html<br />http://www.fruitfly.org/~cjm/ro/ro-development.html<br />SO genome interval relations<br />x starts yiffα(x) = α(y) ∧ ω(x) &lt; ω(y) <br />
  7. 7. Mapping to OWL<br />OBOF mapping to OWL now specified in terms of CL<br />3 different mappings<br />OWL-Full, with type-level relations<br />Two DL mappings depending on treatment of time<br />
  8. 8. Reasoning<br />Relation reasoning<br />Theorem provers over CL<br />Ontology reasoning<br />DL reasoners over OWL translation<br />Ontology + data reasoning<br />Datalog subset<br />

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