Improving the interoperability of biomedical ontologies with compound alignments

Journal of Biomedical Semantics

Volumn 9, Issue 1, 2018, Pages

  Oliveira, Daniela ^a,b   Pesquita, Catia ^b  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b UNIVERSITY OF LISBON   (Portugal)

Author keywords

Algorithms; Biomedical ontologies; Ontology alignment

Indexed keywords

ALGORITHM; BIOLOGICAL ONTOLOGY; CONTROLLED VOCABULARY;

ALGORITHMS; BIOLOGICAL ONTOLOGIES; VOCABULARY, CONTROLLED;

EID: 85040355501     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/s13326-017-0171-8     Document Type: Article

References (36)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25(1):25-9.
2. Euzenat J, Shvaiko P, et al. Ontology Matching vol. 18. Berlin: Springer; 2007.
3. Pesquita C, Faria D, Stroe C, Santos E, Cruz IF, Couto FM. What's in a 'nym'? Synonyms in Biomedical Ontology Matching. In: The Semantic Web - ISWC Lecture Notes in Computer Science. Berlin: Springer;2013.
4. Cheatham M, Dragisic Z, Euzenat J, Faria D, Ferrara A, Flouris G, Fundulaki I, Granada R, Ivanova V, Jiménez-Ruiz E, et al. Results of the Ontology Alignment Evaluation Initiative 2015. 10th ISWC workshop on ontology matching (OM), Oct 2015, Bethlehem, United States No commercial editor. 2016. p. 60-115.
5. Pesquita C, Cheatham M, Faria D, Barros J, Santos E, Couto FM. Building reference alignments for compound matching of multiple ontologies using obo cross-products. In: Ontology Matching Workshop at ISWC 2014. Aachen: CEUR-WS.org;2014.
6. Ritze D, Meilicke C, Šváb-Zamazal O, Stuckenschmidt H. A pattern-based ontology matching approach for detecting complex correspondences. In: Proceedings of the 4th International Conference on Ontology Matching, OM'09, vol. 551. Aachen: CEUR-WS.org;2009. p. 25-36.
7. Ritze D, Völker J, Meilicke C, Šváb-Zamazal O. Linguistic analysis for complex ontology matching. In: Proceedings of the 5th International Conference on Ontology Matching, vol. 689. Aachen: CEUR-WS.org.
8. Doan A, Madhavan J, Dhamankar R, Domingos P, Halevy A. Learning to match ontologies on the semantic web. VLDB J Int J Very Large Data Bases. 2003; 12(4):303-19.
9. Dhamankar R, Lee Y, Doan A, Halevy A, Domingos P. imap: Discovering complex semantic matches between database schemas. In: Proceedings of the 2004 ACM SIGMOD International Conference on Management of Data, SIGMOD '04. New York: ACM;2004. p. 383-94.
10. Dhombres F, Bodenreider O. Interoperability between phenotypes in research and healthcare terminologies-Investigating partial mappings between HPO and SNOMED CT. J Biomed Semantics. 2016; 7(1):3.
11. Oliveira D, Pesquita C. Compound matching of biomedical ontologies. In: International Conference on Biomedical Ontology (ICBO). Aachen: CEUR-WS.org;2015.
12. Couto FM, Silva MJ, Coutinho PM. Finding genomic ontology terms in text using evidence content. BMC Bioinformatics. 2005; 6(Suppl 1):21.
13. Faria D, Pesquita C, Santos E, Palmonari M, Cruz IF, Couto FM. The agreementmakerlight ontology matching system. In: On the Move to Meaningful Internet Systems: OTM 2013 Conferences. Berlin: Springer;2013. p. 527-541.
14. Faria D, Pesquita C, Balasubramani BS, Martins C, Cardoso J, Curado H, Couto FM, Cruz IF. Oaei 2016 results of aml. In: International Workshop on Ontology Matching@ ISWC. Aachen: CEUR-WS.org;2016. p. 138-45.
15. Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. Cross-product extensions of the Gene Ontology. J Biomed Inf. 2011; 44(1):80-6.
16. Faria D, Pesquita C, Santos E, Cruz IF, Couto FM. Automatic background knowledge selection for matching biomedical ontologies. PLoS ONE. 2014; 9(11):e111226.
17. Mungall CJ. Obol: Integrating Language and Meaning in Bio-Ontologies. Comp Funct Genomics. 2004; 5(6-7):509-20.
18. Hoehndorf R, Harris MA, Herre H, Rustici G, Gkoutos GV. Semantic integration of physiology phenotypes with an application to the cellular phenotype ontology. Bioinformatics. 2012; 28(13):1783-9.
19. Jiménez-Ruiz E, Grau BC, Horrocks I, Berlanga R. Logic-based assessment of the compatibility of UMLS ontology sources. J Biomed Semantics. 2011; 2(S1):2.
20. Faria D, Jiménez-Ruiz E, Pesquita C, Santos E, Couto FM. Towards annotating potential incoherences in BioPortal mappings. In: International Semantic Web Conference. Cham: Springer;2014. p. 17-32.
21. Santos E, Faria D, Pesquita C, Couto FM. Ontology alignment repair through modularization and confidence-based heuristics. PloS ONE. 2015; 10(12):0144807.
22. Jiménez E, Meilicke C, Grau BC, Horrocks I, et al. Evaluating mapping repair systems with large biomedical ontologies. In: 26th International Workshop on Description Logics. Aachen: CEUR-WS.org;2013.
23. Pesquita C, Faria D, Santos E, Couto FM. To repair or not to repair: Reconciling correctness and coherence in ontology reference alignments. In: Proceedings of the 8th International Conference on Ontology Matching - Volume 1111, OM'13. Aachen: CEUR-WS.org;2013. p. 13-24.
24. Shrestha R, Arnaud E, Mauleon R, Senger M, Davenport GF, Hancock D, Morrison N, Bruskiewich R, McLaren G. Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature. AoB Plants. 2010; 2010:plq008.
25. Arnaud E, Cooper L, Shrestha R, Menda N, Nelson RT, Matteis L, Skofic M, Bastow R, Jaiswal P, Mueller LA, et al. Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes. In: Proceedings of the 4th International Conference on Knowledge Engineering and Ontology Development. Barcelona: 2012. p. 220-5.
26. Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant Cell Physiol. 2013; 54(2):1.
27. Berlanga R, Jiménez-Ruiz E, Nebot V. Exploring and linking biomedical resources through multidimensional semantic spaces. BMC Bioinformatics. 2012; 13(1):1.
28. Egaña M, Rector A, Stevens R, Antezana E. Applying ontology design patterns in bio-ontologies. In: International Conference on Knowledge Engineering and Knowledge Management. Berlin: Springer;2008. p. 7-16.
29. Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome Biol. 2005; 6(2):21.
30. Rosse C, Mejino JL. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inf. 2003; 36(6):478-500.
31. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2013; 42(D1):D966-74.
32. Smith CL, Goldsmith C-AW, Eppig JT. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 2004; 6(1):7.
33. Gkoutos GV, Schofield PN, Hoehndorf R. The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes. Int Rev Neurobiol. 2012; 103:69-87.
34. Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol. 2010; 11(1):2.
35. Haendel MA, BalhoffJP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. 2014; 5(1):21.
36. Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW. Worm Phenotype Ontology: integrating phenotype data within and beyond the C, elegans community. BMC Bioinformatics. 2011; 12:32.