Evolution of biomedical ontologies and mappings: Overview of recent approaches

Computational and Structural Biotechnology Journal

Volumn 14, Issue , 2016, Pages 333-340

  Groß, Anika ^a   Pruski, Cédric ^b   Rahm, Erhard ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b LUXEMBOURG INSTITUTE OF SCIENCE AND TECHNOLOGY   (Luxembourg)

Author keywords

Biomedical annotation; Biomedical ontology; Mapping adaptation; Mapping evolution; Ontology evolution; Ontology based mapping

Indexed keywords

ONTOLOGY;

AUTOMATED APPROACH; BIOMEDICAL ANNOTATION; BIOMEDICAL ONTOLOGIES; MAPPING ADAPTATION; MAPPING EVOLUTION; ONTOLOGY EVOLUTION; ONTOLOGY MAPPING; ONTOLOGY'S; ONTOLOGY-BASED; ONTOLOGY-BASED MAPPING;

MAPPING;

BIOMEDICINE; EVOLUTIONARY ADAPTATION; MEDICAL INFORMATION; MEDICAL ONTOLOGY; ONTOLOGY DEVELOPMENT; ONTOLOGY EVOLUTION; PRIORITY JOURNAL; SHORT SURVEY;

EID: 84985945370     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.1016/j.csbj.2016.08.002     Document Type: Short Survey

References (62)

1. [1] Bodenreider, O., Stevens, R., Bio-ontologies: current trends and future directions. Brief Bioinform 7:3 (2006), 256–274.
2. [2] Lambrix, P., Tan, H., Jakoniene, V., Strömbäck, L., Biological ontologies. Semantic web, 2007, 85–99.
3. [3] Noy, N.F., Shah, N., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Montegut, M., Rubin, D.L., Youn, C., Musen, M.A., BioPortal: a web repository for biomedical ontologies and data resources. Proceedings of the poster and demonstration session at the 7th international semantic web conference (ISWC), vol. 401, 2008.
4. [4] The gene ontology consortium, the gene ontology project in 2008. Nucleic Acids Res, 36, 2008, D440–D444.
5. [5] Tilford, C., Siemers, N., Gene set enrichment analysis. Methods Mol Biol 563 (2009), 99–121.
6. [6] De Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., Steinbeck, C., Chemical entities of biological interest: an update. Nucleic Acids Res 38:Suppl. 1 (2010), D249–D254.
7. [7] Donnelly, K., SNOMED-CT: the advanced terminology and coding system for eHealth. Stud Health Technol Inform–Med Care Compunetics 3:121 (2006), 279–290.
8. [8] Gruber, T.R., A translation approach to portable ontology specifications. Knowl Acquis 5:2 (1993), 199–221.
9. [9] Lassila, O., McGuinness, D., The role of frame-based representation on the semantic web. Linköping Electron Articles Comput Inform Sci, 6(5), 2001, 2001.
10. [10] Miles, A., Bechhofer, S., SKOS simple knowledge organization system reference. W3C recommendation, Vol. 18, 2009, W3C.
11. [11] Raunich, S., Rahm, E., Target-driven merging of taxonomies with ATOM. Inform Syst 42 (2014), 1–14.
12. [12] Stumme, G., Maedche, A., FCA-MERGE: bottom-up merging of ontologies. Proceedings of the seventeenth international joint conference on artificial intelligence (IJCAI), 2001, 225–234.
13. [13] Bodenreider, O., The unified medical language system (umls): integrating biomedical terminology. Nucleic Acids Res 32:Suppl. 1 (2004), D267–D270.
14. [14] Rahm, E., Towards large-scale schema and ontology matching. Schema matching and mapping, 2011, Springer, 3–27 [Ch. 1].
15. [15] Shvaiko, P., Euzenat, J., Ontology matching: state of the art and future challenges. IEEE Trans Knowl Data Eng 25:1 (2013), 158–176.
16. [16] Neves, M.L., Leser, U., A survey on annotation tools for the biomedical literature. Brief Bioinform 15:2 (2014), 327–340.
17. [17] Radivojac, P., Clark, W.T., Oron, T.R., Schnoes, A.M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. A large-scale evaluation of computational protein function prediction. Nat Methods 10:3 (2013), 221–227.
18. [18] Vrousgou, O., Burdett, T., Parkinson, H.E., Jupp, S., Biomedical ontology evolution in the EMBL-EBI ontology lookup service. Proceedings of the workshops of the EDBT/ICDT 2016 joint conference, EDBT/ICDT workshops 2016, 2016.
19. [19] Tudorache, T., Noy, N.F., Tu, S., Musen, M.A., Supporting collaborative ontology development in Protégé. The semantic web-ISWC 2008, 2008, Springer, 17–32.
20. [20] Day-Richter, J., Harris, M.A., Haendel, M., Lewis, S., et al. OBO-Edit – an ontology editor for biologists. Bioinformatics 23:16 (2007), 2198–2200.
21. [21] Sioutos, N., Coronado, S.d., Haber, M.W., Hartel, F.W., Shaiu, W.-L., Wright, L.W., NCI thesaurus: a semantic model integrating cancer-related clinical and molecular information. J Biomed Inform 40:1 (2007), 30–43.
22. [22] Hartung, M., Terwilliger, J., Rahm, E., Recent advances in schema and ontology evolution. Schema matching and mapping, 2011, Springer, 149–190 [Ch. 6].
23. [23] Kondylakis, H., Plexousakis, D., Ontology evolution without tears. Web semantics: science, services and agents on the world wide web, Vol. 19, 2013, 42–58.
24. [24] Zablith, F., Antoniou, G., d'Aquin, M., Flouris, G., Kondylakis, H., Motta, E., Plexousakis, D., Sabou, M., Ontology evolution: a process-centric survey. Knowl Eng Rev 30:01 (2015), 45–75.
25. [25] Da Silveira, M., Dos Reis, J.C., Pruski, C., Management of dynamic biomedical terminologies: current status and future challenges. Yearb Med Inform 10:1 (2015), 125–133.
26. [26] Arnold, P., Rahm, E., Enriching ontology mappings with semantic relations. Data Knowl Eng 93 (2014), 1–18.
27. [27] Hartung, M., Groß, A., Rahm, E., COnto-Diff: generation of complex evolution mappings for life science ontologies. J Biomed Inform 46:1 (2013), 15–32.
28. [28] Groß, A., Dos Reis, J.C., Hartung, M., Pruski, C., Rahm, E., Semi-automatic adaptation of mappings between life science ontologies. Proceedings of the 9th international conference on data integration in the life sciences (DILS), 2013, Springer, 90–104.
29. [29] Noy, N.F., Musen, M.A., PromptDiff: a fixed-point algorithm for comparing ontology versions. Proceedings of the eighteenth national conference on artificial intelligence (AAAI), 2002, 744–750.
30. [30] Yingjie, S., Bin, Z., Yanyan, M., An approach to detect conflicts for collaborative evolution of medicine ontology. Int J Control Autom 8:3 (2015), 387–404.
31. [31] Dos Reis, J.C., Dinh, D., Da Silveira, M., Pruski, C., Reynaud-Delatre, C., Recognizing lexical and semantic change patterns in evolving life science ontologies to inform mapping adaptation. Artif Intell Med 63:3 (2015), 153–170.
32. [32] Seppälä, S., Smith, B., Ceusters, W., Applying the realism-based ontology-versioning method for tracking changes in the basic formal ontology. FOIS, 2014, 227–240.
33. [33] Ceusters, W., Applying evolutionary terminology auditing to the gene ontology. J Biomed Inform 42:3 (2009), 518–529.
34. [34] Ceusters, W., Applying evolutionary terminology auditing to snomed ct. AMIA annual symposium proceedings, vol. 2010, 2010, American Medical Informatics Association, 96.
35. [35] Hartung, M., Groß, A., Rahm, E., CODEX: exploration of semantic changes between ontology versions. Bioinformatics 28:6 (2012), 895–896.
36. [36] Horridge, M., Tudorache, T., Nyulas, C., Vendetti, J., Noy, N.F., Musen, M.A., Webprotégé: a collaborative web-based platform for editing biomedical ontologies. Bioinformatics 30:16 (2014), 2384–2385.
37. [37] Ochs, C., Perl, Y., Geller, J., Haendel, M., Brush, M., Arabandi, S., Tu, S., Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a diff abstraction network. J Biomed Inform 56 (2015), 127–144.
38. [38] Christen, V., Hartung, M., Groß, A., Region Evolution eXplorer - a tool for discovering evolution trends in ontology regions. J Biomed Semant, 6, 2015, 26.
39. [39] Hartung, M., Kirsten, T., Groß, A., Rahm, E., OnEX: exploring changes in life science ontologies. BMC Bioinformatics, 10(1), 2009, 1.
40. [40] Burch, M., Lohmann, S., Visualizing the evolution of ontologies: a dynamic graph perspective. Proceedings of the international workshop on visualizations and user interfaces for ontologies and linked data (VOILA15) CEUR workshop proceedings, vol. 1456, 2015, 69–76.
41. [41] Walk, S., Pöschko, J., Strohmaier, M., Andrews, K., Tudorache, T., Noy, N.F., Nyulas, C., Musen, M.A., Pragmatix: an interactive tool for visualizing the creation process behind collaboratively engineered ontologies. Int J Semant Web Inform Syst, 9(1), 2013, 45.
42. [42] Wang, H., Tudorache, T., Dou, D., Noy, N.F., Musen, M.A., Analysis and prediction of user editing patterns in ontology development projects. J Data Semant 4:2 (2015), 117–132.
43. [43] Pesquita, C., Couto, F.M., Predicting the extension of biomedical ontologies. PLoS Comput Biol, 8(9), 2012, e1002630.
44. [44] Tsatsaronis, G., Varlamis, I., Kanhabua, N., Nørvåg, K., Temporal classifiers for predicting the expansion of medical subject headings. Computational linguistics and intelligent text processing, 2013, Springer, 98–113.
45. [45] Hartung, M., Kirsten, T., Rahm, E., Analyzing the evolution of life science ontologies and mappings. Proceedings of the 5th international workshop on data integration in the life sciences (DILS), 2008, Springer, 11–27.
46. [46] Groß, A., Hartung, M., Thor, A., Rahm, E., How do computed ontology mappings evolve? - a case study for life science ontologies. Proceedings of the 2nd joint workshop on knowledge evolution and ontology dynamics (EvoDyn) CEUR workshop proceedings, vol. 890, 2012.
47. [47] Ribón, I.T., Vidal, M., Palma, G., AnnEvol: an evolutionary framework to description ontology-based annotations. Proceedings of the 11th international conference on data integration in the life sciences (DILS), 2015, 87–103.
48. [48] Dos Reis, J.C., Pruski, C., Reynaud-Delatre, C., State-of-the-art on mapping maintenance and challenges towards a fully automatic approach. Expert Syst Appl 42:3 (2015), 1465–1478.
49. [49] Martins, H., Silva, N., A user-driven and a semantic-based ontology mapping evolution approach. Proceedings of the 11th international conference on enterprise information systems (ICEIS), 2009, 214–221.
50. [50] Khattak, A., Pervez, Z., Latif, K., Lee, S., Time efficient reconciliation of mappings in dynamic web ontologies. Knowl-Based Syst 35 (2012), 369–374.
51. [51] Khattak, A., Pervez, Z., Khan, W., Khan, A., Latif, K., Lee, S., Mapping evolution of dynamic web ontologies. Inform Sci 303 (2015), 101–119.
52. [52] Khattak, A.M., Latif, K., Khan, S., Ahmed, N., Managing change history in web ontologies. Fourth international conference on semantics, knowledge and grid (SKG), 2008, IEEE, 347–350.
53. [53] Hu, W., Qu, Y., Falcon-AO: a practical ontology matching system. Web semantics: science, services and agents on the world wide web, Vol. 6 (3), 2008, 237–239.
54. [54] Hamdi, F., Zargayouna, H., Safar, B., Reynaud, C., TaxoMap in the OAEI 2008 alignment contest. Proceedings of the 3rd international workshop on ontology matching (OM), 2008, CEUR-WS.org, 206–213.
55. [55] Dos Reis, J.C., Dinh, D., Pruski, C., Da Silveira, M., Reynaud-Delatre, C., Mapping adaptation actions for the automatic reconciliation of dynamic ontologies. Proceedings of the 22Nd ACM international conference on information & knowledge management, CIKM '13, 2013, ACM, 599–608.
56. [56] Dos Reis, J.C., Pruski, C., Da Silveira, M., Reynaud-Delatre, C., Understanding semantic mapping evolution by observing changes in biomedical ontologies. J Biomed Inform 47 (2014), 71–82.
57. [57] Giunchiglia, F., Shvaiko, P., Yatskevich, M., S-Match: an algorithm and an implementation of semantic matching. The semantic web: research and applications, first European semantic web symposium (ESWS), 2004, 61–75.
58. [58] Ivanova, V., Lambrix, P., User involvement for large-scale ontology alignment. Visualizations and user interfaces for knowledge engineering and linked data analytics (VISUAL) EKAW CEUR workshop proceedings, vol. 1299, 2014, 34–47.
59. [59] Mungall, C.J., Torniai, C., Gkoutos, G.V., Lewis, S.E., Haendel, M.A., et al. Uberon, an integrative multi-species anatomy ontology. Genome Biol, 13(1), 2012, R5.
60. [60] Grosjean, J., Merabti, T., Dahamna, B., Kergourlay, I., Thirion, B., Soualmia, L.F., Darmoni, S.J., Health multi-terminology portal: a semantic added-value for patient safety. Stud Health Technol Inform 166:66 (2011), 129–138.
61. [61] Jonquet, C., Emonet, V., Musen, M.A., Roadmap for a multilingual BioPortal. MSW4'15: 4th workshop on the multilingual semantic web CEUR workshop proceedings, vol. 1532, 2015.
62. [62] Fu, B., Brennan, R., OSullivan, D., Cross-lingual ontology mapping–an investigation of the impact of machine translation. Asian semantic web conference, 2009, Springer, 1–15.