Valentina Ivanova
Department of Computer and Information Science, and Swedish e-Science Researche Centre, Linköping University, Linköping, Sweden
Jonas Laurila Bergman
Division of Information Technology, National Food Agency, Uppsala, Sweden
Ulf Hammerling
Department of Risk Benefit Assessment, National Food Agency, Uppsala, Sweden
Patrick Lambrix
Department of Computer and Information Science, and Swedish e-Science Researche Centre, Linköping University, Linköping, Sweden
Download articlePublished in: Proceedings of the First International Workshop on Debugging Ontologies and Ontology Mappings - WoDOOM12; Galway; Ireland; October 8; 2012
Linköping Electronic Conference Proceedings 79:3, p. 25-36
Published: 2012-11-28
ISBN:
ISSN: 1650-3686 (print), 1650-3740 (online)
As part of an initiative to facilitate adequate identification and display of substance-associated health effects a toxicological ontology - ToxOntology - was created. Further; an alignent with MeSH was accomplished to obtain an indirect index to the scientific literature.
To arrive at satisfactory results in the semantically-enabled applications; highquality ontologies and alignments are both necessary. A key step towards high quality in this area is debugging the ontologies and their alignments. In this paper we present an experience report on the debugging of ToxOntology and MeSH as well as an alignment.
1. DJ Dix; KA Houck; MT Martin; AM Richard; RW Setzer; and RJ Kavlock. The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol. Sci.; 95:5–12; 2007.
2. A Edberg; D Soeria-Atmadja; J Bergman Laurila; F Johansson; MG Gustafsson; and U Hammerling. Assessing relative bioactivity of chemical substances using quantitative molecular network topology analysis. J. Chem. Inf. Model.; 52:1238–1249; 2012.
3. J Euzenat and P Shvaiko. Ontology Matching. Springer; 2007.
4. B Hardy; N Douglas; C Helma; M Rautenberg; N Jeliazkova; V Jeliazkov; I Nikolova; R Benigni; O Tcheremenskaia; S Kramer; T Girschick; F Buchwald; J Wicker; A Karwath; M Gutlein; A Maunz; HS Sarimveis; G Melagraki; A Afantitis; P Sopasakis; D Gallagher; V Poroikov; D Filimonov; A Zakharov; A Lagunin; T Gloriozova; S Novikov; N Skvortsova; D Druzhilovsky; S Chawla; I Ghosh; S Ray; H Patel; and S Escher. Collaborative development of predictive toxicology applications. J. Cheminform.; 2:7; 2010.
5. Medical Subject Headings. http://www.nlm.nih.gov/mesh/.
6. N Jeliazkova and V Jeliazkova. AMBIT RESTful web services: an implementation of the OpenTox application programming interface. J. Cheminform.; 3:18; 2011.
7. E Jimenez-Ruiz; B Cuenca Grau; I Horrocks; and R Berlanga. Ontology integration using mappings: Towards getting the right logical consequences. In Proceedings of the 6th European Semantic Web Conference; volume 5554 of LNCS; pages 173–187. Springer; 2009.
8. RS Judson; RJ Kavlock; RWSetzer; EA Cohen Hubal; MT Martin; TB Knudsen; KA Houck; RS Thomas; BAWetmore; and DJ Dix. Estimating toxicity related biological pathway altering doses for high-throughput chemical risk assessment. Chem. Res. Toxicol.; 24:451–462; 2011.
9. RS Judson; AM Richard; DJ Dix; K Houck; F Elloumi; M Martin; T Cathey; TR Transue; R Spencer; and M Wolf. ACToR - aggregated computational toxicology resource. Toxicol. Appl. Pharmacol.; 233(1):7–13; 2008.
10. RS Judson; AM Richard; DJ Dix; K Houck; M Martin; R Kavlock; V Dellarco; T Henry; T Holderman; P Sayre; S Tan; T Carpenter; and E Smith. The toxicity data landscape for environmental chemicals. Environ. Health Perspect.; 117:685–695; 2009.
11. P Lambrix and V Ivanova. A unified approach for debugging is-a structure and mappings in networked taxonomies. submitted; 2012.
12. P Lambrix and Q Liu. Using partial reference alignments to align ontologies. In Proceedings of the 6th European SemanticWeb Conference; volume 5554 of LNCS; pages 188–202; 2009.
13. P Lambrix; Q Liu; and H Tan. Repairing the missing is-a structure of ontologies. In Proceedings of the 4th Asian Semantic Web Conference; volume 5926 of LNCS; pages 76–90; 2009.
14. P Lambrix and H Tan. SAMBO - a system for aligning and merging biomedical ontologies. Journal of Web Semantics; 4(3):196–206; 2006.
15. P Lambrix and H Tan. A tool for evaluating ontology alignment strategies. Journal on Data Semantics; VIII:182–202; 2007.
16. W Lilienblum; W Dekant; H Foth; T Gebel; JG Hengstler; R Kahl; PJ Kramer; H Schweinfurth; and KMWollin. Alternative methods to safety studies in experimental animals: role in the risk assessment of chemicals under the new European Chemicals Legislation (REACH). Arch. Toxicol.; 82:211–236; 2008.
17. F Maddah; D Soeria-Atmadja; P Malm; MG Gustafsson; and U Hammerling. Interrogating health-related public databases from a food toxicology perspective: Computational analysis of scoring data. Food Chem Toxicol.; 49:2830–2840; 2011.
18. CJ Mattingly; MC Rosenstein; AP Davis; GT Colby; JN Forrest Jr; and JL Boyer. The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. Toxicol. Sci.; 92:587–595; 2006.
19. PubMed. http://www.ncbi.nlm.nih.gov/pubmed/.
20. AM Richard; LS Gold; and MC Nicklaus. Chemical structure indexing of toxicity data on the internet: moving toward a flat world. Curr. Opin. Drug Discov. Devel.; 9:314–325; 2006.
21. AM Richard; C Yang; and RS Judson. Toxicity data informatics: supporting a new paradigm for toxicity prediction. Toxicol. Mech. Methods; 18:103–118; 2008.
22. SJ Shukla; R Huang; CP Austin; and M Xia. The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform. Drug Discov. Today; 15:997–1007; 2010.
23. Unified Medical Language System. http://www.nlm.nih.gov/research/umls/.
24. H Tan; V Jakoniene; P Lambrix; J Aberg; and N Shahmehri. Alignment of biomedical ontologies using life science literature. In Proceedings of the InternationalWorkshop on Knowledge Discovery in Life Science Literature; volume 3886 of LNBI; pages 1–17; 2006.
25. O Tcheremenskaia; R Benigni; I Nikolova; N Jeliazkova; SE Escher ans M Batke; T Baier; V Poroikov; A Lagunin; M Rautenberg; and B Hardy. OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia. J. Biomed. Semantics; 3 Suppl 1:S7; 2012.
26. GM Woodall and RB Goldberg. Summary of the workshop on the power of aggregated toxicity data. Toxicol. Appl. Pharmacol.; 233:71–75; 2008.
27. WordNet. http://wordnet.princeton.edu/.