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DOI: 10.15265/IY-2015-002
Management of Dynamic Biomedical Terminologies: Current Status and Future Challenges
Correspondence to:
Publication History
13 August 2015
Publication Date:
10 March 2018 (online)
Summary
Objectives: Controlled terminologies and their dependent artefacts provide a consensual understanding of a domain while reducing ambiguities and enabling reasoning. However, the evolution of a domain’s knowledge directly impacts these terminologies and generates inconsistencies in the underlying biomedical information systems. In this article, we review existing work addressing the dynamic aspect of terminologies as well as their effects on mappings and semantic annotations.
Methods: We investigate approaches related to the identification, characterization and propagation of changes in terminologies, mappings and semantic annotations including techniques to update their content.
Results and conclusion: Based on the explored issues and existing methods, we outline open research challenges requiring investigation in the near future.
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Keywords
Knowledge management - knowledge representation - ontology evolution - biomedical ontologies
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References
- 1 Cimino JJ. Desiderata for controlled medical vocabularies in the twenty-first century. Methods Inf Med 1998; 37: 394-403.
- 2 Medical Subject Headings.. www.nlm.nih.gov/mesh/meshhome.html , Last accessed in 11/11/2014.
- 3 International Classification of Diseases v9.. www.cdc.gov/nchs/icd/icd9cm.htm , Last accessed in 11/11/2014.
- 4 Euzenat J, Shvaiko P. Ontology Matching. Heidelberg (DE): Springer-Verlag; 2007
- 5 Baneyx A, Charlet J. Évaluation, évolution et maintenance d’une ontologie en médecine: état des lieux et expérimentation. [Evaluation, evolution and maintenance of a medical ontology: current status and experimentation] Information-Interaction-Intelligence, Special issue; 2006
- 6 Oliver DE, Shahar Y, Shortliffe EH, Musen MA. Representation of change in controlled medical terminologies. Artif Intell Med 1999; 15: 53-76.
- 7 Dos Reis JC, Pruski C, Silveira MD, Reynaud-Delaître C. Understanding Semantic Mapping Evolution by Observing Changes in Biomedical Ontologies. J Biomed Inform 2014; Feb 47: 71-82.
- 8 Mortensen JM, Minty EP, Januszyk M, Sweeney TE, Rector AL, Noy NF. et al. Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT. J Am Med Inform Assoc 2015; May 22 (03) 640-8.
- 9 International Health Terminology Standards Development Organisation: Systematized Nomenclature of Medicine - Clinical Terms. http://www.ihtsdo.org/snomed-ct , Last accessed in 11/11/2014.
- 10 Noy NF, Shah NH, Whetzel PL. et al. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic acids research 2009; 37: 1-4.
- 11 Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W. et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007; 25: 1251-5.
- 12 Grosjean J, Merabti T, Dahamna B, Kergourlay I, Thirion B, Soualmia LF. et al. Health multi-terminology portal: a semantic added-value for patient safety. Stud Health Technol Inform 2011; 166: 129-38.
- 13 Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C. Understanding Semantic Mappings Evolution by Observing Changes in Biomedical Ontologies. J Biomed Inform 2014; 47: 71-82.
- 14 Gene Ontology Consortium. http://geneontology.org/ , Last accessed in 11/11/2014.
- 15 NCI Thesaurus. http://ncit.nci.nih.gov , Last accessed in 11/11/2014.
- 16 Hartung M, Gross A, Kirsten T, Rahm E. Discovering Evolving Regions in Life Science Ontologies. 7th Int Conference on Data Integration in the Life Sciences (DILS). Springer; 2010. p. 19-34.
- 17 Plessers P, De Troyer O. Ontology Change Detection Using a Version Log. Proceedings of the 4th International Semantic Web Conference. Galway, Ireland: 2005. p. 578-92.
- 18 Noy NF, Musen MA. Promptdiff: a fixed-point algorithm for comparing ontology versions. Eighteenth national conference on Artificial intelligence. Edmonton, Alberta, Canada: American Association for Artificial Intelligence; 2002. p. 744-50.
- 19 Hartung M, Gross A, Rahm E. COnto-Diff: Generation of Complex Evolution Mappings for Life Science Ontologies. J Biomed Inform 2013; 46: 15-32.
- 20 Hartung M, Kirsten T, Gross A, Rahm E. OnEX: Exploring changes in life science ontologies. BMC Bioinformatics 2009; 10: 250.
- 21 Shaban-Nejad A, Haarslev V. Bio-medical Ontologies Maintenance and Change Management. In: Amandeep S, Sidhu and Dillon TS. (eds.). Biomedical Data and Applications. Springer; 2009. p. 143-68.
- 22 Djedidi R, Aufaure M-A. OWL Change Management Patterns. The 5th Workshop on Semantic Web Applications and Perspectives (SWAP2008). Rome, Italy: 2008. p. 1-3.
- 23 Dragisic Z, Lambrix P, Wei-Kleiner F. Completing the is-a structure of biomedical ontologies. Data Integration in the Life Sciences. Lisbon, Portugal: Springer; 2014 p. 66-80.
- 24 Dinh D, Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C. Identifying relevant concept attributes to support mapping maintenance under ontology evolution. Web Semantics: Science, Services and Agents on the World Wide Web 2014; 29: 53-66.
- 25 Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L. The compositional structure of Gene Ontology terms. Pacific Symposium on Biocomputing; 2004 p. 214.
- 26 Abgaz YM, Javed M, Pahl C. Analyzing Impacts of Change Operations in Evolving Ontologies. 2nd Joint Workshop on Knowledge Evolution and Ontology Dynamics EvoDyn; 2012
- 27 Shaban-Nejad A, Haarslev V. Incremental biomedical ontology change management through learning agents. Agent and Multi-Agent Systems: Technologies and Applications. Springer; 2008. p. 526-35.
- 28 Pesquita C, Couto FM. Predicting the extension of biomedical ontologies. PLoS Comput Biol 2012; 8 (09) e1002630.
- 29 Sari AK, Rahayu W, Bhatt M. An approach for sub-ontology evolution in a distributed health care enterprise. Information Systems 2013; 38: 727-44.
- 30 Stojanovic L, Maedche A, Motik B, Stojanovic N. User-driven ontology evolution management. In European Conf Knowledge Eng and Management (EKAW 2002). Springer-Verlag; 2002. p. 285-300.
- 31 Darmoni SJ, Leroy JP, Baudic F, Douyère M, Piot J, Thirion B. CISMeF: a structured health resource guide. Methods Inf Med 2000; 39: 30-5.
- 32 Salvadores M, Alexander PR, Musen MA, Noy NF. Bioportal as a dataset of linked biomedical ontologies and terminologies in RDF. Semantic Web 2013; 4: 277-84.
- 33 Dos Reis JC, Pruski C, Reynaud-Delaître C. State-of-the-art on mapping maintenance and challenges towards a fully automatic approach. Expert Systems with Applications 2015; 42: 1465-78.
- 34 Gal A, Anaby-tavor A, Trombetta A, Montesi D. A framework for modeling and evaluating automatic semantic reconciliation. The VLDB Journal 2005; 14: 50-67.
- 35 Zurawski M, Smaill A, Robertson D. Bounded Ontological Consistency for Scalable Dynamic Knowledge Infrastructures. In: Domingue J, Anutariya C. editors. ASWC. LNCS ed.: Springer; 2008. p. 212-26.
- 36 Mccann R, Alshebli B, Le Q, Nguyen H, Vu L, Doan A. Mapping Maintenance for Data Integration Systems. VLDB ‘05 Proceedings of the 31st International Conference on very large data bases; 2005 p. 1018-29.
- 37 Colazzo D, Sartiani C. Detection of corrupted schema mappings in XML data integration systems. ACM Transactions on Internet Technology 2009; 9: 1-53.
- 38 Abdul-Rahman, Mawlood-Yunis. Fault-tolerant Semantic Mappings Among Heterogeneous and Distributed Local Ontologies. Proceedings of the 2nd international workshop on Ontologies and information systems for the semantic web; 2008 p. 31-8.
- 39 Li A, Miao J, Jia Y. Research on Broken Mappings Detecting Method Based on Fuzzy Aggregation Operators in Deep Web Integration Environment. 2010 International Conference on E-Business and E-Government. IEEE; 2010 p. 125-8.
- 40 Meilicke C, Stuckenschmidt H, Tamilin A. Reasoning Support for Mapping Revision. Journal of Logic and Computation 2008; 19: 807-29.
- 41 Nikitina N, Rudolph S, Glimm B. Reasoning-supported interactive revision of knowledge bases. The twenty-second international joint conference on artificial intelligence, IJCAI’11. AAAI Press; 2011. p. 1027-32.
- 42 Jimenez-Ruiz E, Grau BC. Logmap: Logic-based and scalable ontology matching. The Semantic Web--ISWC 2011. Spinger; 2011. p. 273-88.
- 43 Fagin R, Kolaitis PG, Popa L, Tan W-C. Schema Mapping Evolution Through Composition and Inversion. Data-Centric Systems and Applications. Springer-Verlag; 2011. p. 191-222.
- 44 An Y, Hu X, Song I-Y. Maintaining Mappings between Conceptual Models and Relational Schemas. Journal of Database Management 2010; 21: 36-68.
- 45 Tang F, and Tang R. Minimizing Influence of Ontology Evolution In Ontology-based Data Access System. IEEE International Conference on Progress in Informatics and Computing (PIC); 2010 p. 10-4.
- 46 Maedche A, Motik B, Silva N, Volz R. MAFRA - A MApping FRAmework for Distributed Ontologies in the Semantic Web. Knowledge engineering and knowledge management: ontologies and the semantic web. Springer; 2002. p. 235-50.
- 47 Martins H, Silva N. A User-Driven and a Semantic-Based Ontology Mapping Evolution Approach. 11th International Conference on Enterprise Information Systems. Milan; 2009. p. 6-10.
- 48 Dos Reis JC, Dinh D, Pruski C, Da Silveira M, Reynaud-Delaître C. Mapping Adaptation Actions for the Automatic Reconciliation of Dynamic Ontologies. ACM International Conference on Information and Knowledge Management (CIKM 2013). San Francisco: ACM; 2013. p. 599-608.
- 49 Gross A, Dos Reis JC, Hartung M, Pruski C, Rahm E. Semi-Automatic Adaptation of Mappings between Life Science Ontologies. Data Integration in the Life Sciences (DILS 2013). Montreal, Canada: Springer-Verlag; 2013 p. 90-104.
- 50 Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C. Characterizing Semantic Mappings Adaptation via Biomedical KOS Evolution: A Case Study Investigating SNOMED CT and ICD. AMIA 2013 Annual Symposium. Washington, DC (USA): 2013. p. 333-42.
- 51 Hussain S, Sun H, Sinaci AA, Erturkmen GB, Mead C, Gray AJ. et al. A Framework for Evaluating and Utilizing Medical Terminology Mappings. e-Health - For Continuity of Care - Proceedings of MIE2014, the 25th European Medical Informatics Conference. Istanbul, Turkey: IOS Press; 2014. p. 594-8.
- 52 Dos Reis JC, Da Silveira M, Dinh D, Pruski C, Reynaud-Delaitre C. Requirements for Implementing Mapping Adaptation Systems. WETICE Conference (WETICE), 2014 IEEE 23rd International; 2014 p. 405-10.
- 53 Ananiadou S, Pyysalo S, Tsujii JI, Kell DB. Event extraction for systems biology by text mining the literature. Trends Biotechnol 2010; 28: 381-90.
- 54 Roberts A, Gaizauskas R, Hepple M, Demetriou G, Guo Y, Roberts I. et al. A semantically annotated corpus of clinical texts. Biomed Inform 2009; 42: 950-66.
- 55 Mowery D, Jordan P, Wiebe J, Harkema H, Dowling J, Chapman WW. Semantic Annotation of Clinical Events for Generating a Problem List. AMIA Annu Symp Proc 2013 p. 1032-41.
- 56 Gross A, Hartung M, Kirsten T, Rahm E. Estimating the Quality of Ontology-based Annotations by Considering Evolutionary Changes. 6th Data Integration in the Life Sciences (DILS); 2009 p. 71-87.
- 57 Ensembl genome databases. http://www.ensembl.org/index.html , Last accessed in 11/11/2014.
- 58 UniProtKB / Swiss-Prot Database. http://www.uniprot.org/uniprot/?query=*&fil= , Last accessed in 11/11/2014.
- 59 Gillis J, Pavlidis P. Assessing identity, redundancy and confounds in gene ontology annotations over time. Bioinformatics 2013; 29: 476-82.
- 60 Skunca N, Altenhoff A, Dessimoz C. Quality of computationally inferred gene ontology annotations. PLoS Computl Biol 2012: 8.
- 61 Gross A, Hartung M, Prüfer K, Kelso J, Rahm E. Impact of Ontology Evolution on Functional Analyses. Bioinformatics 2012; 28: 2671-7.
- 62 Park YR, Kim J, Lee HW, Yoon YJ, Kim JH. GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products. BMC Bioinformatics; 2011: 12.
- 63 National Center for Biotechnology Information Taxonomy. http://www.ncbi.nlm.nih.gov/taxonomy , Last accessed in 11/11/2014.
- 64 Köpke J, Eder J. Semantic Invalidation of Annotations Due to Ontology Evolution. OTM Conferences. Hersonissos, Crete, Greece: Springer; 2011. p. 763-80.
- 65 Maynard D, Peters W, d’Aquin M, Sabou M. Change Management for Metadata Evolution. Proceedings of the International Workshop on Ontology Dynamics (IWOD-07); 2007 p. 27-40.
- 66 Volz J, Bizer C, Gaedke M, Kobilarov G. Discovering and maintaining links on the web of data. International Semantic Web Conference (ISWC). Washington, DC. Berlin, Heidelberg: Springer; 2009. p. 650-65.
- 67 Popitsch N, Haslhofer B. DSNotify–A solution for event detection and link maintenance in dynamic datasets. Web Semantics: Science, Services and Agents on the World Wide Web 2011; 9: 266-83.
- 68 Rogozan D. Gestion de l’évolution d’une onto-logie : méthodes et outils pour un référencement sémantique évolutif fondé sur une analyse des changements entre versions d’une ontologie. [Managing ontology evolution: methods and tools for an evolving semantic referring based on an analysis of ontology version changes] PhD Thesis. Rouen: INSA; 2008
- 69 Luong P-H, Dieng-Kuntz R. A Rule-based Approach for Semantic Annotation Evolution. Computational Intelligence 2007; 23: 320-38.
- 70 Luong P-h, Dieng-Kuntz R, Boucher A. Managing semantic annotations evolution in the CosWEM system. Proc 3rd National Symp on Research, Development and Application of Information and Communication Technology,. 2006 p. 215-23.
- 71 Corby O, Dieng-Kuntz R, and Faron-Zucker C. Querying the Semantic Web with the CORESE Search Engine. 16th European Conference on Artificial Intelligence (ECAI’2004). Valencia, Spain: IOS Press; 2004. p. 705-9.
- 72 Tudorache T, Nyulas CI, Noy NF, and Musen MA. Using Semantic Web in ICD-11: Three Years Down the Road. The Semantic Web--ISWC 2013; 2013 p. 195-211.
- 73 Rodrigues JM, Schulz S, Rector A, Spackman K, Üstün B, Chute CG. et al. Do we need a Common Ontology between ICD 11 and SNOMED CT to ensure Seamless Re-Use and Semantic Interoperability?. Stud Health Technol Inform 2013; 192: 343-6.
- 74 Musen MA, Middleton B, Greenes RA. Clinical decision-support systems. Biomedical informatics. Springer; 2014. p. 643-74.
- 75 Burgun A. Desiderata for domain reference ontologies in biomedicine. J Biomed Inform 2006; 39: 307-13.
- 76 Ben Abacha A, Da Silveira M, Pruski C. Medical Ontology Validation through Question Answering. Artificial Intelligence in Medicine. Murcia, Spain: Springer; 2013. p. 196-205.
- 77 Liang S, Stevens R, Scott D, Rector A. Automatic Verbalisation of SNOMED Classes Using OntoVerbal. In: Peleg M, Lavrač N, Combi C. editors. Artificial Intelligence in Medicine. Berlin, Heidelberg: Springer; 2011. p. 338-42.
Correspondence to:
-
References
- 1 Cimino JJ. Desiderata for controlled medical vocabularies in the twenty-first century. Methods Inf Med 1998; 37: 394-403.
- 2 Medical Subject Headings.. www.nlm.nih.gov/mesh/meshhome.html , Last accessed in 11/11/2014.
- 3 International Classification of Diseases v9.. www.cdc.gov/nchs/icd/icd9cm.htm , Last accessed in 11/11/2014.
- 4 Euzenat J, Shvaiko P. Ontology Matching. Heidelberg (DE): Springer-Verlag; 2007
- 5 Baneyx A, Charlet J. Évaluation, évolution et maintenance d’une ontologie en médecine: état des lieux et expérimentation. [Evaluation, evolution and maintenance of a medical ontology: current status and experimentation] Information-Interaction-Intelligence, Special issue; 2006
- 6 Oliver DE, Shahar Y, Shortliffe EH, Musen MA. Representation of change in controlled medical terminologies. Artif Intell Med 1999; 15: 53-76.
- 7 Dos Reis JC, Pruski C, Silveira MD, Reynaud-Delaître C. Understanding Semantic Mapping Evolution by Observing Changes in Biomedical Ontologies. J Biomed Inform 2014; Feb 47: 71-82.
- 8 Mortensen JM, Minty EP, Januszyk M, Sweeney TE, Rector AL, Noy NF. et al. Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT. J Am Med Inform Assoc 2015; May 22 (03) 640-8.
- 9 International Health Terminology Standards Development Organisation: Systematized Nomenclature of Medicine - Clinical Terms. http://www.ihtsdo.org/snomed-ct , Last accessed in 11/11/2014.
- 10 Noy NF, Shah NH, Whetzel PL. et al. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic acids research 2009; 37: 1-4.
- 11 Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W. et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007; 25: 1251-5.
- 12 Grosjean J, Merabti T, Dahamna B, Kergourlay I, Thirion B, Soualmia LF. et al. Health multi-terminology portal: a semantic added-value for patient safety. Stud Health Technol Inform 2011; 166: 129-38.
- 13 Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C. Understanding Semantic Mappings Evolution by Observing Changes in Biomedical Ontologies. J Biomed Inform 2014; 47: 71-82.
- 14 Gene Ontology Consortium. http://geneontology.org/ , Last accessed in 11/11/2014.
- 15 NCI Thesaurus. http://ncit.nci.nih.gov , Last accessed in 11/11/2014.
- 16 Hartung M, Gross A, Kirsten T, Rahm E. Discovering Evolving Regions in Life Science Ontologies. 7th Int Conference on Data Integration in the Life Sciences (DILS). Springer; 2010. p. 19-34.
- 17 Plessers P, De Troyer O. Ontology Change Detection Using a Version Log. Proceedings of the 4th International Semantic Web Conference. Galway, Ireland: 2005. p. 578-92.
- 18 Noy NF, Musen MA. Promptdiff: a fixed-point algorithm for comparing ontology versions. Eighteenth national conference on Artificial intelligence. Edmonton, Alberta, Canada: American Association for Artificial Intelligence; 2002. p. 744-50.
- 19 Hartung M, Gross A, Rahm E. COnto-Diff: Generation of Complex Evolution Mappings for Life Science Ontologies. J Biomed Inform 2013; 46: 15-32.
- 20 Hartung M, Kirsten T, Gross A, Rahm E. OnEX: Exploring changes in life science ontologies. BMC Bioinformatics 2009; 10: 250.
- 21 Shaban-Nejad A, Haarslev V. Bio-medical Ontologies Maintenance and Change Management. In: Amandeep S, Sidhu and Dillon TS. (eds.). Biomedical Data and Applications. Springer; 2009. p. 143-68.
- 22 Djedidi R, Aufaure M-A. OWL Change Management Patterns. The 5th Workshop on Semantic Web Applications and Perspectives (SWAP2008). Rome, Italy: 2008. p. 1-3.
- 23 Dragisic Z, Lambrix P, Wei-Kleiner F. Completing the is-a structure of biomedical ontologies. Data Integration in the Life Sciences. Lisbon, Portugal: Springer; 2014 p. 66-80.
- 24 Dinh D, Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C. Identifying relevant concept attributes to support mapping maintenance under ontology evolution. Web Semantics: Science, Services and Agents on the World Wide Web 2014; 29: 53-66.
- 25 Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L. The compositional structure of Gene Ontology terms. Pacific Symposium on Biocomputing; 2004 p. 214.
- 26 Abgaz YM, Javed M, Pahl C. Analyzing Impacts of Change Operations in Evolving Ontologies. 2nd Joint Workshop on Knowledge Evolution and Ontology Dynamics EvoDyn; 2012
- 27 Shaban-Nejad A, Haarslev V. Incremental biomedical ontology change management through learning agents. Agent and Multi-Agent Systems: Technologies and Applications. Springer; 2008. p. 526-35.
- 28 Pesquita C, Couto FM. Predicting the extension of biomedical ontologies. PLoS Comput Biol 2012; 8 (09) e1002630.
- 29 Sari AK, Rahayu W, Bhatt M. An approach for sub-ontology evolution in a distributed health care enterprise. Information Systems 2013; 38: 727-44.
- 30 Stojanovic L, Maedche A, Motik B, Stojanovic N. User-driven ontology evolution management. In European Conf Knowledge Eng and Management (EKAW 2002). Springer-Verlag; 2002. p. 285-300.
- 31 Darmoni SJ, Leroy JP, Baudic F, Douyère M, Piot J, Thirion B. CISMeF: a structured health resource guide. Methods Inf Med 2000; 39: 30-5.
- 32 Salvadores M, Alexander PR, Musen MA, Noy NF. Bioportal as a dataset of linked biomedical ontologies and terminologies in RDF. Semantic Web 2013; 4: 277-84.
- 33 Dos Reis JC, Pruski C, Reynaud-Delaître C. State-of-the-art on mapping maintenance and challenges towards a fully automatic approach. Expert Systems with Applications 2015; 42: 1465-78.
- 34 Gal A, Anaby-tavor A, Trombetta A, Montesi D. A framework for modeling and evaluating automatic semantic reconciliation. The VLDB Journal 2005; 14: 50-67.
- 35 Zurawski M, Smaill A, Robertson D. Bounded Ontological Consistency for Scalable Dynamic Knowledge Infrastructures. In: Domingue J, Anutariya C. editors. ASWC. LNCS ed.: Springer; 2008. p. 212-26.
- 36 Mccann R, Alshebli B, Le Q, Nguyen H, Vu L, Doan A. Mapping Maintenance for Data Integration Systems. VLDB ‘05 Proceedings of the 31st International Conference on very large data bases; 2005 p. 1018-29.
- 37 Colazzo D, Sartiani C. Detection of corrupted schema mappings in XML data integration systems. ACM Transactions on Internet Technology 2009; 9: 1-53.
- 38 Abdul-Rahman, Mawlood-Yunis. Fault-tolerant Semantic Mappings Among Heterogeneous and Distributed Local Ontologies. Proceedings of the 2nd international workshop on Ontologies and information systems for the semantic web; 2008 p. 31-8.
- 39 Li A, Miao J, Jia Y. Research on Broken Mappings Detecting Method Based on Fuzzy Aggregation Operators in Deep Web Integration Environment. 2010 International Conference on E-Business and E-Government. IEEE; 2010 p. 125-8.
- 40 Meilicke C, Stuckenschmidt H, Tamilin A. Reasoning Support for Mapping Revision. Journal of Logic and Computation 2008; 19: 807-29.
- 41 Nikitina N, Rudolph S, Glimm B. Reasoning-supported interactive revision of knowledge bases. The twenty-second international joint conference on artificial intelligence, IJCAI’11. AAAI Press; 2011. p. 1027-32.
- 42 Jimenez-Ruiz E, Grau BC. Logmap: Logic-based and scalable ontology matching. The Semantic Web--ISWC 2011. Spinger; 2011. p. 273-88.
- 43 Fagin R, Kolaitis PG, Popa L, Tan W-C. Schema Mapping Evolution Through Composition and Inversion. Data-Centric Systems and Applications. Springer-Verlag; 2011. p. 191-222.
- 44 An Y, Hu X, Song I-Y. Maintaining Mappings between Conceptual Models and Relational Schemas. Journal of Database Management 2010; 21: 36-68.
- 45 Tang F, and Tang R. Minimizing Influence of Ontology Evolution In Ontology-based Data Access System. IEEE International Conference on Progress in Informatics and Computing (PIC); 2010 p. 10-4.
- 46 Maedche A, Motik B, Silva N, Volz R. MAFRA - A MApping FRAmework for Distributed Ontologies in the Semantic Web. Knowledge engineering and knowledge management: ontologies and the semantic web. Springer; 2002. p. 235-50.
- 47 Martins H, Silva N. A User-Driven and a Semantic-Based Ontology Mapping Evolution Approach. 11th International Conference on Enterprise Information Systems. Milan; 2009. p. 6-10.
- 48 Dos Reis JC, Dinh D, Pruski C, Da Silveira M, Reynaud-Delaître C. Mapping Adaptation Actions for the Automatic Reconciliation of Dynamic Ontologies. ACM International Conference on Information and Knowledge Management (CIKM 2013). San Francisco: ACM; 2013. p. 599-608.
- 49 Gross A, Dos Reis JC, Hartung M, Pruski C, Rahm E. Semi-Automatic Adaptation of Mappings between Life Science Ontologies. Data Integration in the Life Sciences (DILS 2013). Montreal, Canada: Springer-Verlag; 2013 p. 90-104.
- 50 Dos Reis JC, Pruski C, Da Silveira M, Reynaud-Delaître C. Characterizing Semantic Mappings Adaptation via Biomedical KOS Evolution: A Case Study Investigating SNOMED CT and ICD. AMIA 2013 Annual Symposium. Washington, DC (USA): 2013. p. 333-42.
- 51 Hussain S, Sun H, Sinaci AA, Erturkmen GB, Mead C, Gray AJ. et al. A Framework for Evaluating and Utilizing Medical Terminology Mappings. e-Health - For Continuity of Care - Proceedings of MIE2014, the 25th European Medical Informatics Conference. Istanbul, Turkey: IOS Press; 2014. p. 594-8.
- 52 Dos Reis JC, Da Silveira M, Dinh D, Pruski C, Reynaud-Delaitre C. Requirements for Implementing Mapping Adaptation Systems. WETICE Conference (WETICE), 2014 IEEE 23rd International; 2014 p. 405-10.
- 53 Ananiadou S, Pyysalo S, Tsujii JI, Kell DB. Event extraction for systems biology by text mining the literature. Trends Biotechnol 2010; 28: 381-90.
- 54 Roberts A, Gaizauskas R, Hepple M, Demetriou G, Guo Y, Roberts I. et al. A semantically annotated corpus of clinical texts. Biomed Inform 2009; 42: 950-66.
- 55 Mowery D, Jordan P, Wiebe J, Harkema H, Dowling J, Chapman WW. Semantic Annotation of Clinical Events for Generating a Problem List. AMIA Annu Symp Proc 2013 p. 1032-41.
- 56 Gross A, Hartung M, Kirsten T, Rahm E. Estimating the Quality of Ontology-based Annotations by Considering Evolutionary Changes. 6th Data Integration in the Life Sciences (DILS); 2009 p. 71-87.
- 57 Ensembl genome databases. http://www.ensembl.org/index.html , Last accessed in 11/11/2014.
- 58 UniProtKB / Swiss-Prot Database. http://www.uniprot.org/uniprot/?query=*&fil= , Last accessed in 11/11/2014.
- 59 Gillis J, Pavlidis P. Assessing identity, redundancy and confounds in gene ontology annotations over time. Bioinformatics 2013; 29: 476-82.
- 60 Skunca N, Altenhoff A, Dessimoz C. Quality of computationally inferred gene ontology annotations. PLoS Computl Biol 2012: 8.
- 61 Gross A, Hartung M, Prüfer K, Kelso J, Rahm E. Impact of Ontology Evolution on Functional Analyses. Bioinformatics 2012; 28: 2671-7.
- 62 Park YR, Kim J, Lee HW, Yoon YJ, Kim JH. GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products. BMC Bioinformatics; 2011: 12.
- 63 National Center for Biotechnology Information Taxonomy. http://www.ncbi.nlm.nih.gov/taxonomy , Last accessed in 11/11/2014.
- 64 Köpke J, Eder J. Semantic Invalidation of Annotations Due to Ontology Evolution. OTM Conferences. Hersonissos, Crete, Greece: Springer; 2011. p. 763-80.
- 65 Maynard D, Peters W, d’Aquin M, Sabou M. Change Management for Metadata Evolution. Proceedings of the International Workshop on Ontology Dynamics (IWOD-07); 2007 p. 27-40.
- 66 Volz J, Bizer C, Gaedke M, Kobilarov G. Discovering and maintaining links on the web of data. International Semantic Web Conference (ISWC). Washington, DC. Berlin, Heidelberg: Springer; 2009. p. 650-65.
- 67 Popitsch N, Haslhofer B. DSNotify–A solution for event detection and link maintenance in dynamic datasets. Web Semantics: Science, Services and Agents on the World Wide Web 2011; 9: 266-83.
- 68 Rogozan D. Gestion de l’évolution d’une onto-logie : méthodes et outils pour un référencement sémantique évolutif fondé sur une analyse des changements entre versions d’une ontologie. [Managing ontology evolution: methods and tools for an evolving semantic referring based on an analysis of ontology version changes] PhD Thesis. Rouen: INSA; 2008
- 69 Luong P-H, Dieng-Kuntz R. A Rule-based Approach for Semantic Annotation Evolution. Computational Intelligence 2007; 23: 320-38.
- 70 Luong P-h, Dieng-Kuntz R, Boucher A. Managing semantic annotations evolution in the CosWEM system. Proc 3rd National Symp on Research, Development and Application of Information and Communication Technology,. 2006 p. 215-23.
- 71 Corby O, Dieng-Kuntz R, and Faron-Zucker C. Querying the Semantic Web with the CORESE Search Engine. 16th European Conference on Artificial Intelligence (ECAI’2004). Valencia, Spain: IOS Press; 2004. p. 705-9.
- 72 Tudorache T, Nyulas CI, Noy NF, and Musen MA. Using Semantic Web in ICD-11: Three Years Down the Road. The Semantic Web--ISWC 2013; 2013 p. 195-211.
- 73 Rodrigues JM, Schulz S, Rector A, Spackman K, Üstün B, Chute CG. et al. Do we need a Common Ontology between ICD 11 and SNOMED CT to ensure Seamless Re-Use and Semantic Interoperability?. Stud Health Technol Inform 2013; 192: 343-6.
- 74 Musen MA, Middleton B, Greenes RA. Clinical decision-support systems. Biomedical informatics. Springer; 2014. p. 643-74.
- 75 Burgun A. Desiderata for domain reference ontologies in biomedicine. J Biomed Inform 2006; 39: 307-13.
- 76 Ben Abacha A, Da Silveira M, Pruski C. Medical Ontology Validation through Question Answering. Artificial Intelligence in Medicine. Murcia, Spain: Springer; 2013. p. 196-205.
- 77 Liang S, Stevens R, Scott D, Rector A. Automatic Verbalisation of SNOMED Classes Using OntoVerbal. In: Peleg M, Lavrač N, Combi C. editors. Artificial Intelligence in Medicine. Berlin, Heidelberg: Springer; 2011. p. 338-42.