IMPACT ANALYSIS IN DESCRIPTION LOGIC ONTOLOGIES A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Engineering and Physical Sciences 2014 By Jo~aoRafael Landeiro de Sousa Gon¸calves School of Computer Science Contents Abstract 10 Declaration 11 Copyright 12 Acknowledgements 13 1 Introduction 14 1.1 Desiderata for Impact Analysis................... 15 1.2 State of the Art............................ 17 1.3 Goals and Contributions....................... 18 1.4 Published Work............................ 20 2 Preliminaries 21 2.1 Description Logics.......................... 21 2.1.1 Syntax and Semantics.................... 22 2.1.2 Standard Reasoning Services................. 23 2.1.3 Non-Standard Reasoning Services.............. 25 2.1.4 Structural Notions...................... 26 2.2 OWL: The Web Ontology Language................. 28 2.3 Experimental Setup.......................... 30 2.3.1 Infrastructure......................... 30 2.3.2 Ontology Corpora....................... 31 3 Impact Analysis 33 3.1 Impact in OWL............................ 33 3.2 NCIt Case Study........................... 34 3.2.1 Methods and Materials.................... 35 3.2.2 Results............................. 36 3.2.2.1 Parsing Times................... 36 3.2.2.2 Asserted Axioms.................. 36 3.2.2.3 Inferred Axioms.................. 38 3.2.2.4 Reasoner Performance............... 41 3.3 Conclusions.............................. 42 4 Related Work 44 4.1 Diffing Techniques.......................... 44 4.1.1 Syntactic........................... 45 4.1.2 Semantic............................ 46 4.2 Reasoner Performance........................ 48 4.3 Discussion............................... 50 5 Axiom-Centric Impact Analysis 51 5.1 Motivation............................... 51 5.2 Overview................................ 53 5.3 Specification.............................. 55 5.3.1 Axiom Categorisation.................... 55 5.3.1.1 Ineffectual Change Categorisation......... 56 5.3.1.2 Effectual Change Categorisation......... 60 5.3.2 Example Walkthrough.................... 63 5.4 Implementation............................ 66 5.4.1 Algorithms.......................... 66 5.4.2 Preliminary Evaluation.................... 67 5.5 Empirical Evaluation......................... 71 5.5.1 Case Study.......................... 72 5.5.1.1 Coarse-Grained Change Analysis......... 72 5.5.1.2 Ineffectual Changes................. 73 5.5.1.3 Effectual Changes................. 75 5.5.1.4 Discussion...................... 77 5.5.2 NCIt Axiom Diff Walkthrough................ 78 5.6 Conclusions.............................. 83 6 Term-Centric Impact Analysis 85 6.1 Motivation............................... 85 6.2 Specification.............................. 87 6.2.1 Characterising Concept Impact............... 88 6.2.2 Diff Functions......................... 90 6.2.2.1 CEX-Based Functions............... 92 6.2.3 Example Walkthrough.................... 94 6.3 Implementation............................ 96 6.3.1 Algorithms.......................... 97 6.3.2 Preliminary Evaluation.................... 99 6.4 Empirical Evaluation......................... 100 6.4.1 Case Study.......................... 100 6.4.1.1 Diff Function Comparison............. 101 6.4.1.2 Splitting Direct and Indirect Changes...... 103 6.4.1.3 Change Log Analysis................ 103 6.4.2 NCIt Concept Diff Walkthrough............... 106 6.5 Conclusions.............................. 108 7 Term and Axiom Change Alignment 111 7.1 Motivation............................... 111 7.2 Specification.............................. 112 7.2.1 Aligning Changes....................... 112 7.2.2 Example Walkthrough.................... 113 7.3 Implementation............................ 115 7.3.1 Algorithms.......................... 115 7.3.2 ecco: A Diff Tool for OWL 2 Ontologies.......... 116 7.4 Tool Walkthrough........................... 119 7.5 Conclusions.............................. 122 8 Performance Heterogeneity and Homogeneity 125 8.1 Motivation............................... 125 8.2 Specification.............................. 127 8.3 Implementation............................ 128 8.4 Empirical Evaluation......................... 130 8.4.1 Materials and Methods.................... 130 8.4.2 Results............................. 131 8.5 Conclusions.............................. 136 9 Performance Hot Spots 140 9.1 Motivation............................... 140 9.2 Specification.............................. 142 9.2.1 Finding Hot Spots...................... 142 9.2.2 Reasoning with Hot Spots.................. 143 9.2.2.1 Approximation Techniques............. 143 9.2.2.2 Compilation Techniques.............. 144 9.3 Implementation............................ 145 9.4 Empirical Evaluation......................... 146 9.4.1 Finding Hot Spots...................... 147 9.4.1.1 Hot Spot Analysis................. 148 9.4.1.2 Comparison with Pellint.............. 150 9.4.2 Hot Spot Based Reasoning.................. 152 9.4.2.1 Approximations................... 152 9.4.2.2 Compilations.................... 153 9.5 Conclusions.............................. 154 10 Conclusions 157 10.1 Contributions and Significance.................... 157 10.2 Research Impact and Future Directions............... 160 Bibliography 163 Word Count: 39,304 List of Tables 2.1 Concept constructors for the ALC DL................ 22 5.1 Compound change categories..................... 54 5.2 Effectual change categories...................... 55 5.3 Example ontologies O1 and O2.................... 63 5.4 Categorisation of removals in diff(O1; O2).............. 64 5.5 Categorisation of additions in diff(O1; O2).............. 65 5.6 Operation times per comparison throughout the NCIt (in seconds). 70 5.7 Coarse-grained changes throughout the NCIt............ 73 5.8 Ineffectual removals of diff(Oi, Oi+1), for 1 ≤ i ≤ 112........ 74 5.9 Ineffectual additions of diff(Oi, Oi+1), for 1 ≤ i ≤ 112....... 75 5.10 Effectual removals of diff(Oi, Oi+1), for 1 ≤ i ≤ 112......... 76 5.11 Effectual additions of diff(Oi, Oi+1), for 1 ≤ i ≤ 112........ 76 5.12 Effectual additions in diff(O32, O33)................. 78 5.13 Ineffectual additions in diff(O32, O33)................ 78 5.14 Effectual removals in diff(O32, O33).................. 79 5.15 Ineffectual removals in diff(O32, O33)................. 79 5.16 Mapping of term names in the NCIt to abbreviations........ 80 6.1 Example ontologies O1 and O2.................... 88 6.2 Affected concepts (specialised, generalised and total) between O1 and O2 according to the mentioned diff notions........... 92 6.3 Breakdown of concept impact in At-AT(O1; O2)Σ.......... 94 6.4 Breakdown of concept impact in Sub-AT(O1; O2)Σ......... 95 6.5 Breakdown of concept impact in Gr-AT(O1; O2)Σ.......... 96 6.6 Number of concepts processed per minute by each diff function Φ. 100 6.7 Number of affected atomic concepts found by each diff function for Σ := Σu, and their respective coverage w.r.t. Gr-AT(Oi; Oi+1)Σ.. 102 L 6.8 Number of directly affected concepts (1) in AT(O1; O2)Σ (denoted R \L"), (2) in AT(O1; O2)Σ (denoted \R"), (3) in the union of those two sets (denoted \Total"), and (4) that do not appear in the NCIt change logs (denoted \Missed"), found by AtDiff(O1; O2)Σ and SubDiff(O1; O2)Σ for Σ := Σu.................. 105 6.9 Number of affected atomic concepts, AT(Oi; Oi+1)Σ, found by each diff function (in addition to Un-AT := fCex1-AT [ Cex2-AT [ Sub-ATg) for Σ := Σu within the NCIt change logs......... 106 6.10 Affected concepts (specialised, generalised and total) between O1 and O2 according to the mentioned diff notions........... 107 6.11 Number of changes in At-AT(O1; O2)Σ according to impact.... 107 6.12 Number of changes in Sub-AT(O1; O2)Σ according to impact.... 108 7.1 Example ontologies O1 and O2.................... 113 7.2 Affected concepts in At-AT(O1; O2)Σ with corresponding witness axioms and justifications........................ 114 7.3 Additional affected concept in Sub-AT(O1; O2)Σ with correspond- ing witness axiom and justification.................. 114 8.1 Basic metrics and classification times (in seconds) of selected Bio- Portal ontologies. Ontologies marked with ∗ are in the OWL 2 EL profile.................................. 131 9.1 Comparison of hot spots found via SAT-guided (white rows) and random (grey rows) concept selection approach. CPU times in seconds................................. 148 9.2 Expressivity of each original ontology (O), its various hot spots (Mi, for 1 ≤ i ≤ 3) and corresponding remainders (O n Mi).... 149 9.3 Number of GCIs contained in each ontology, its hot spots, and their corresponding remainders. The \average reduction" represents the percentage of GCIs removed from O into O n Mi, for 1 ≤ i ≤ 3.. 150 9.4 Ontology/reasoner combinations for which Pellint found lints... 151 9.5 Reasoning times and degree of completeness of the devised approx- imations, and tr-Ap(O). The degree of completeness is denoted \compl."................................ 153 9.6 Compilation results for the devised compilation techniques (time in seconds, where unit is not shown)................. 154 List of Figures 3.1 Axiom growth of the NCIt, where annotation axioms dominate (x-axis: NCIt version, y-axis: number of axioms).......... 37 3.2 Breakdown of logical axioms occurring in the NCIt (x-axis: NCIt version, y-axis: number of axioms). Note that in Figure 3.2a role axioms are grouped together, and then broken down in Figure 3.2b. 38 3.3 Entailment growth of NCIt: asserted and inferred entailment counts