From bf2d3b0c0a1e3e1c4e2dd54775582775c1650e75 Mon Sep 17 00:00:00 2001 From: Federico Igne Date: Tue, 5 Oct 2021 13:59:49 +0100 Subject: Add script to load debug data to RDFox --- README.md | 150 +++++++++++---------- simulate.rdfox | 21 +++ src/main/scala/uk/ac/ox/cs/rsacomb/Main.scala | 2 +- .../scala/uk/ac/ox/cs/rsacomb/RSAOntology.scala | 9 +- .../scala/uk/ac/ox/cs/rsacomb/util/Logger.scala | 14 +- 5 files changed, 116 insertions(+), 80 deletions(-) create mode 100644 simulate.rdfox diff --git a/README.md b/README.md index e61e889..87b721f 100644 --- a/README.md +++ b/README.md @@ -34,32 +34,11 @@ Combined approach for Conjunctive Query answering in RSA

- -
-Table of Contents -
    -
  1. About
    2. -
  2. Preliminaries
    3. -
  3. - Using the software - -
    4. -
  4. Changes introduced
    5. -
  5. Acknowledgements
    6. -
  6. Credits
    7. -
  7. License
    8. -
-
- ## About -This is a re-implementation of the combined approach for CQ answering over RSA ontologies described in [[1](#references)]. +This is an *improved* re-implementation of the combined approach for CQ answering over RSA ontologies described in [[1](#references)]. -> Please note that the prototype mentioned in [[1](#references)] is not available (and the contributors of this repository have never seen it); +> Please note that the prototype mentioned in [[1](#references)] is not available (and the contributors to this repository have never seen it); > therefore, this "re-implementation" could be completely different from that prototype (potentially using different tools and programming language). ## Preliminaries @@ -68,7 +47,58 @@ In order to use this program you need to have [RDFox](https://www.oxfordsemantic RDFox is proprietary software and as such we are not able to distribute it along with our code. Please refer to [this link](https://www.oxfordsemantic.tech/tryrdfoxforfree) to request a free trial. -This software has been developed and tested with RDFox v.4.1 +This software has been developed and tested with RDFox v5.2.1 + +## Changes introduced + +We tried to implement the system as close as possible to the theoretical description provided in [[1](#references)]. +Regardless, we had to deal with the fact that we are using different tools to carry out reasoning tasks and we are probably using a different language to implement the system. +The following is a (non exhaustive) summary of fixes (🔧), changes (🔄) and improvements (⚡), we introduced along the way: + ++ 🔄 [RDFox](https://www.oxfordsemantic.tech/product) is used instead of DLV as the underlying LP engine. + ++ ⚡ The system accepts unrestricted OWL ontologies as input and takes care of normalising and approximating the ontology to RSA. + At the time of writing, two approximation algorithms are provided, to compute a sound (or complete) set of answer to the input queries, respectively. + ++ ⚡ The different steps of the combined approach (namely, the canonical model computation and the filtering step) are executed in isolation using different *named graphs*. + This allows us to reuse partial products of the computation and can even be used to parellalise filtering and answering steps. + ++ 🔧 In Def.4, the definition of built-in predicate `notIn` is wrong and should reflect the implicit semantics implied by the name, i.e., + + > let [...] `notIn` be a built-in predicate which holds when the first argument is **not** an element of the set given as second argument + + This has been fixed by (1) introducing a built-in predicate `In` (note that instances of `In` can be computed beforehand since they only depend on the input ontology), and (2) implement `notIn` as the negation of `In` using RDFox *NaF* built-in support. + ++ 🔄 Top (`owl:Thing`) axiomatisation is performed introducing rules as follows. + Given `p` predicate (arity *n*) *in the original ontology*, the following rule is introduced: + ``` + owl:Thing[?X1], ..., owl:Thing[?Xn] :- p(?X1, ..., ?Xn) . + ``` + Note that, by definition, arity can be either 1 or 2. + ++ 🔄 Equality axiomatisation is performed introducing the following rules: + ``` + rsacomb:congruent[?X, ?X] :- owl:Thing[?X] . + rsacomb:congruent[?Y, ?X] :- rsacomb:congruent[?X, ?Y] . + rsacomb:congruent[?X, ?Z] :- rsacomb:congruent[?X, ?Y], rsacomb:congruent[?Y, ?Z] . + ``` + defining equivalence as a congruence relation over terms in the ontology. + Substitution rules propagate the equivalence to all existing atoms. + ++ 🔧 In Def. 4, the definition of built-in predicate `NI` is not consistent with its use in Table 3 and related description in Sec. 4.2. + We redefined `NI` as the set of all constants that are *equal* to a constant in the original ontology (according to the internal equality predicate `rsa:congruent`). + Note that, in this scenario, there is no need to introduce `NI` instances as facts in the system; + instead we can add a rule to populate the new predicate: + ``` + rsa:NI[?X] :- rsa:congruent[?X, ?Y], rsa:named[?Y] . + ``` + where `rsa:named` is an internal predicate keeping track of all constants in the original ontology. + ++ ⚡ In Def. 3, regarding the generation of the logic program used for the RSA check, only T5 axioms involving an unsafe role will introduce the internal predicates `PE` and `U`. + ++ ⚡ Both in the canonical model and the filtering program computations, rules without a body are loaded into RDFox as facts. + ++ ⚡ The `cycle` function introduced in Def.4 establishing the direction of the *unraveling* of loops is defined over triples `(A,R,B)`. We are currently limiting the triple only to those appearing in a T5 axiom `A ⊑ ∃R.B`. Note that this greatly limits the size of cycle for a given triple, and as a consequence limits the number of rules used to compute the canonical model. ## Using the software @@ -79,9 +109,9 @@ Download links for specific versions and operating systems can be found [here](h ```{.bash} mkdir -p lib && pushd lib -wget https://rdfox-distribution.s3.eu-west-2.amazonaws.com/release/v4.2.0/RDFox-linux-4.2.0.zip -unzip RDFox-linux-4.2.0.zip -ln -s RDFox-linux-4.2.0.zip/lib/JRDFox.jar +wget https://rdfox-distribution.s3.eu-west-2.amazonaws.com/release/v5.2.1/RDFox-linux-x86_64-5.2.1.zip +unzip RDFox-linux-x86_64-5.2.1.zip +ln -s RDFox-linux-x86_64-5.2.1.zip/lib/JRDFox.jar popd ``` @@ -106,11 +136,7 @@ Run the following from the base directory of the project to produce a standalone sbt assembly ``` -The output of the command will print the location of the produced jar. Execute it with -``` -java -jar [