1. Project 2 Ontology alignment

2. SIGNAL-ONTOLOGY (SigO) Immune Response i- Allergic Response i- Antigen Processing and Presentation i- B Cell Activation i- B Cell Development i- Complement Signaling synonym complement activation i- Cytokine Response i- Immune Suppression i- Inflammation i- Intestinal Immunity i- Leukotriene Response i- Leukotriene Metabolism i- Natural Killer Cell Response i- T Cell Activation i- T Cell Development i- T Cell Selection in Thymus GENE ONTOLOGY (GO) immune response i- acute-phase response i- anaphylaxis i- antigen presentation i- antigen processing i- cellular defense response i- cytokine metabolism i- cytokine biosynthesis synonym cytokine production … p- regulation of cytokine biosynthesis … i- B-cell activation i- B-cell differentiation i- B-cell proliferation i- cellular defense response … i- T-cell activation i- activation of natural killer cell activity …

3. Ontology Alignment equivalent concepts equivalent relations is-a relation SIGNAL-ONTOLOGY (SigO) Immune Response i- Allergic Response i- Antigen Processing and Presentation i- B Cell Activation i- B Cell Development i- Complement Signaling synonym complement activation i- Cytokine Response i- Immune Suppression i- Inflammation i- Intestinal Immunity i- Leukotriene Response i- Leukotriene Metabolism i- Natural Killer Cell Response i- T Cell Activation i- T Cell Development i- T Cell Selection in Thymus GENE ONTOLOGY (GO) immune response i- acute-phase response i- anaphylaxis i- antigen presentation i- antigen processing i- cellular defense response i- cytokine metabolism i- cytokine biosynthesis synonym cytokine production … p- regulation of cytokine biosynthesis … i- B-cell activation i- B-cell differentiation i- B-cell proliferation i- cellular defense response … i- T-cell activation i- activation of natural killer cell activity … Defining the relations between the terms in different ontologies

4. An Alignment Framework

5. Strategies based on linguistic matching Structure-based strategies Constraint-based approaches Instance-based strategies Use of auxiliary information Matcher Strategies

6. Aim Gain understanding about the ontology alignment process Gain understanding about about advantages and disadvantages of different strategies for ontology alignment: matching strategies and single threshold filtering Gain understanding about evaluation of strategies using precision, recall, f-measure Learn about the Ontology Alignment Evaluation Initiative (OAEI) Learn to use the tools and data sets of the OAEI

7. Tasks 1. Tutorial - learn how to use the tools provided by the OAEI (matching, single threshold filtering, evaluation) 2. Run existing algorithms on the benchmark test and discuss results 3. Implement own matcher, evaluate and discuss results 4. (study other test cases and discuss what kind of matchers would be appropiate)

8. Task 2 – using task 1 data Method Precision Recall F-score Threshold SMOA 0.69 0.96 0.80 0.5 SMOA 0.73 0.96 0.83 0.6 SMOA 0.79 0.96 0.87 0.7 SMOA 0.80 0.94 0.87 0.8 SMOA 0.88 0.73 0.80 0.9 Levenshtein 0.80 0.94 0.87 0.5 Levenshtein 0.86 0.77 0.81 0.6 Levenshtein 0.92 0.46 0.61 0.7 Levenshtein 0.94 0.35 0.52 0.8 Levenshtein 0.99 0.35 0.52 0.9

9. Task 3 Implementation of own matchers. - Definition of similarity computation - Testing using thresholds

10. Task 3

13. Task 3 – performance on task1 data Method Precision Recall F-score Threshold equal 1.00 0.23 0.37 1 SMOA 0.69 0.96 0.80 0.5 Levenshtein 0.68 0.98 0.80 0.33 Levenshtein 0.53 1.00 0.69 0 BOWOverlap 0.87 0.85 0.86 0.3 WordOverlap 1.00 0.60 0.75 0.3 BOTOverlap 0.76 0.85 0.80 0.3 TrigramOverlap 0.80 0.92 0.85 0.1 FinalScore 0.87 0.94 0.90 0.2 NEW 0.48 0.92 0.63 0 NEW 0.74 0.88 0.80 0.88

14. Task 2 - benchmark Benchmark 1xx (4): same ontology, no overlap, language generalization, language restriction 2xx (ca 40): base ontology with modified base ontology (e.g. change names, remove relations, spelling mistakes, use of sysnonyms, change of natural language) 3xx (4): real cases

15. Task 2 – benchmark data Best system OAEI 2007: p: 0.95; r: 0.9 Range: p: 0.98 (with r: 0.64) - 0.76 (with r: 0.7) r: 0.90 (with p: 0.95) - 0.21 (with p: 0.92) According to category: 1xx: several systems p:1, r:1 2xx: p: 0.95, r: 0.9; p: 0.97, r: 0.89 3xx: p: 0.94, r: 0.68

16. Task 2 - benchmark Approximate string matching (WordNet) Multilingual WordNet Structure Instances

17. Task 2/3