Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network

Journal of Biomedical Informatics

Volumn 56, Issue , 2015, Pages 127-144

  Ochs, Christopher ^a   Perl, Yehoshua ^a   Geller, James ^a   Haendel, Melissa ^b   Brush, Matthew ^b   Arabandi, Sivaram ^c   Tu, Samson ^d  

^a University Heights   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^c Ontopro LLC   (United States)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Abstraction networks; Ontology diff; Ontology quality assurance; Ontology version change; Summarizing ontology change; Summarizing ontology evolution; Visualizing ontology evolution

Indexed keywords

ABSTRACTING; QUALITY ASSURANCE; SLEEP RESEARCH; TAXONOMIES;

BIOMEDICAL ONTOLOGIES; BIOMEDICAL RESEARCH; CONTENT AND STRUCTURE; CRITICAL COMPONENT; KNOWLEDGE STRUCTURES; ONTOLOGY CHANGES; ONTOLOGY EVOLUTION; ONTOLOGY QUALITIES;

COMPLEX NETWORKS;

ARTICLE; CLINICAL RESEARCH; COHORT ANALYSIS; DATA ANALYSIS; DIFF ABSTRACTION NETWORK; MEDICAL ONTOLOGY; MEDICAL RESEARCH; METHODOLOGY; PRIORITY JOURNAL; QUALITY CONTROL; SEMANTICS; TAXONOMY; ALGORITHM; BIOLOGICAL ONTOLOGY; CONTROLLED VOCABULARY; DRUG DESIGN; INFORMATION PROCESSING; SLEEP; SOFTWARE; TECHNOLOGY;

ALGORITHMS; BIOLOGICAL ONTOLOGIES; BIOMEDICAL RESEARCH; DATA COLLECTION; DRUG DESIGN; QUALITY CONTROL; SLEEP; SOFTWARE; TECHNOLOGY; VOCABULARY, CONTROLLED;

EID: 84938574995     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2015.05.018     Document Type: Article

References (55)

1. Rubin D.L., Shah N.H., Noy N.F. Biomedical ontologies: a functional perspective. Brief. Bioinform. 2008, 9(1):75-90.
2. Bodenreider O. Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb. Med. Inform. 2008, 67-79.
3. Fensel D. Ontology-based knowledge management. Computer 2002, 35(11):56-59.
4. Maedche A., Motik B., Stojanovic L., et al. Ontologies for enterprise knowledge management. Intell. Syst., IEEE 2003, 18(2):26-33.
5. Cao F., Sun X., Wang X., et al. Ontology-based knowledge management for personalized adverse drug events detection. Stud. Health Technol. Inform. 2011, 169:699-703.
6. Kiryakov A. Ontologies for knowledge management. Semantic Web Technologies: Trends and Research in Ontology-Based Systems 2006, 115-138. John Wiley & Sons, Inc., Hoboken, NJ, USA.
7. Y.A. Lussier, Ontologies for natural language processing, in: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 2005; pp. 56.
8. D. Estival, C. Nowak, A. Zschorn, Towards ontology-based natural language processing, in: Proceeedings of the Workshop on NLP and XML (NLPXML-2004), 2004, pp. 59-66.
9. Ovchinnikova E. Integration of World Knowledge for Natural Language Understanding 2012, Springer.
10. The Gene Ontology Consortium Gene ontology annotations and resources. Nucleic Acids Res. 2013, 41:D530-D5.
11. Bodenreider O., Stevens R. Bio-ontologies: current trends and future directions. Brief. Bioinform. 2006, 7(3):256-274.
12. Grenon P., Smith B., Goldberg L. Biodynamic ontology: applying BFO in the biomedical domain. Ontologies in Medicine 2004, 20-38. IOS Press. D.M. Pisanelli (Ed.).
13. Noy N.F., Musen M.A. The PROMPT suite: interactive tools for ontology merging and mapping. Int. J. Hum Comput Stud. 2003, 59(6):983-1024.
14. N.F. Noy, M. Crubézy, R.W. Fergerson, et al., Protege-2000: an open-source ontology-development and knowledge-acquisition environment, in: AMIA Annu. Symp. Proc., 2003, pp. 953.
15. Sim I., Carini S., Tu S., et al. The human studies database project: federating human studies design data using the ontology of clinical research. AMIA Summits Transl. Sci. Proc. 2010, 51-55.
16. Hunt J.W., McIlroy M.D. An Algorithm for Differential File Comparison 1976, Bell Laboratories.
17. N.F. Noy, M. Musen, Promptdiff: a fixed-point algorithm for comparing ontology versions, AAAI/IAAI 2002, 2002, pp. 744-750.
18. P. Kremen, M. Smid, Z. Kouba, OWLDiff: a practical tool for comparison and merge of OWL ontologies. In: 22nd International Workshop on Database and Expert Systems Applications, 2011, pp. 229-233.
19. E. Jiménez-Ruiz, B.C. Grau, I. Horrocks, et al., Building ontologies collaboratively using contentCVS, in: Description Logics, 2009, pp. 447.
20. N.F. Noy, S. Kunnatur, M. Klein, et al., Tracking changes during ontology evolution, in: The Semantic Web-ISWC, 2004, pp. 259-273.
21. S. Arabandi, C. Ogbuji, S. Redline, et al., Developing a sleep domain ontology, in: AMIA Clinical Research Informatics Summit, 2010.
22. C. Torniai, M.H. Brush, N. Vasilevsky, et al., Developing an application ontology for biomedical resource annotation and retrieval: challenges and lessons learned, in: ICBO 2011, 2011, pp. 101-108.
23. C. Ochs, A. Agrawal, Y. Perl, et al., Deriving an abstraction network to support quality assurance in OCRe, in: AMIA Annu. Symp. Proc., 2012, pp. 681-689.
24. C. Ochs, Z. He, Y. Perl, et al., Choosing the granularity of abstraction networks for orientation and quality assurance of the sleep domain ontology, in: Proceedings of the 4th international conference on biomedical ontology, 2013, pp. 84-89.
25. C. Torniai, S. Essaid, B. Lowe, et al., Finding common ground: integrating the eagle-i and VIVO ontologies, in: ICBO 2013, 2013, pp. 46-49.
26. S. Mitchell, S. Chen, M. Ahmed, et al., The VIVO ontology: enabling networking of scientists, in: ACM WebScience Conference, 2011, pp. 14-17.
27. B. Motik, P.F. Patel-Schneider, B. Parsia, OWL 2 web ontology language structural specification and functional style syntax, in: W3C - World Wide Web Consortium, 2009.
28. Smith B., Ashburner M., Rosse C., et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 2007, 25(11):1251-1255.
29. R.S. Gonçalves, B. Parsia, U. Sattler, Ecco: a hybrid diff tool for OWL 2 ontologies, in: OWLED, 2012.
30. T. Redmond, N. Noy, Computing the changes between ontologies, in: Joint Workshop on Knowledge Evolution and Ontology Dynamics, 2011, pp. 1-14.
31. M. Halper, H. Gu, Y. Perl, et al., Abstraction networks for terminologies: supporting management of "Big Knowledge", in: Artificial intelligence in medicine, 2015 (Epub ahead of print), . http://dx.doi.org/10.1016/j.artmed.2015.03.005.
32. Z. He, C. Ochs, A. Agrawal, et al., A family-based framework for supporting quality assurance of biomedical ontologies in BioPortal, in: Proc AMIA Annu. Symp., 2013, pp. 581-590.
33. Whetzel P.L., Noy N.F., Sham N.H., et al. BioPortal: enhanced functionality via new web services from the national center for biomedical ontology to access and use ontologies in software applications. Nucleic Acids Res. (NAR) 2011, 39(Web Server issue):W541-W545.
34. Z. He, C. Ochs, L. Soldatova, et al., Auditing redundant import in reuse of a top level ontology for the drug discovery investigations ontology, in: VDOS, 2013.
35. Da Q., King R., Hopkins A., et al. An ontology for description of drug discovery investigations. J. Integr. Bioinform. 2010, 7(3):126-139.
36. Zeginis D., Hasnain A., Loutas N., et al. A collaborative methodology for developing a semantic model for interlinking cancer chemoprevention linked-data sources. Semantic Web 2014, 5(2):127-142.
37. Min H., Perl Y., Chen Y., et al. Auditing as part of the terminology design life cycle. J. Am. Med. Inform. Assoc. 2006, 13(6):676-690.
38. C. Ochs, Y. Perl, M. Halper, et al., Gene ontology summarization to support visualization and quality assurance, in: BICoB 2015, 2015.
39. Ashburner M., Ball C.A., Blake J.A., et al. Gene ontology: tool for the unification of biology. Nat. Genet. 2000, 25(1):25-29.
40. Fragoso G., de Coronado S., Haber M., et al. Overview and utilization of the NCI thesaurus. Comp. Funct. Genom. 2004, 5(8):648-654.
41. A. Goldfain, Ontology for General Medical Science (OGMS) (10.02.15). http://code.google.com/p/ogms/.
42. Beisswanger E., Schulz S., Stenzhorn H., et al. BioTop: an upper domain ontology for the life sciences. A description of its current structure, contents and interfaces to OBO ontologies. Appl. Ontol. 2008, 3(4):205-212.
43. R. Shearer, B. Motik, I. Horrocks, HermiT: a highly-efficient OWL reasoner, OWLED, 2008.
44. D.B. Krafft, N.A. Cappadona, B. Caruso, et al., Vivo: enabling national networking of scientists, in: Proceedings of the Web Science Conference, 2010, pp. 1310-1313.
45. Noy N.F., Klein M. Ontology evolution: not the same as schema evolution. Knowl. Inf. Syst. 2004, 6(4):428-440.
46. Horridge M., Bechhofer S. The OWL API: a Java API for working with OWL 2 ontologies. OWLED 2009, 529:11-21.
47. M. Ahmed, S. Chen, Y. Ding, et al., Aligning research resource and researcher representation: the eagle-i and VIVO use case, in: ICBO 2013, 2013, pp. 260-262.
48. N. Vasilevsky, T. Johnson, K. Corday, et al., Research resources: curating the new eagle-i discovery system, in: Database 2012, 2012, pp. bar067.
49. Connect-isf: the ontology developed in the context of CTSAConnect to represent agents, resources and grants. (24.09.14). https://code.google.com/p/connect-isf/.
50. Obo-relations: the OBO relations ontology (18.09.14). https://code.google.com/p/obo-relations/.
51. Smith C.L., Goldsmith C.-A.W., Eppig J.T. The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 2004, 6(1):R7.
52. Malone J., Brown A., Lister A.L., et al. The software ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. J. Biomed. Semant. 2014, 5(1).
53. Mungall C.J., Torniai C., Gkoutos G.V., et al. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012, 13(1):R5.
54. Ochs C., Geller J., Perl Y., et al. A tribal abstraction network for SNOMED CT hierarchies without attribute relationships. J. Am. Med. Inform. Assoc. 2014, doi: http://dx.doi.org/amiajnl-2014-003173.
55. J. Geller, C. Ochs, Y. Perl, et al., New abstraction networks and a new visualization tool in support of auditing the SNOMED CT content, in: AMIA Annu. Symp. Proc., 2012, pp. 237-246.