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| A Biomedical Ontology Repository and Platform Focused on Precision Medicine |
| Guo Jingwen, Yang Sheng, Shi Furen, Shao Chen, Zhang Lulu, Wang Heng*, Yang Xiaolin* |
| Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China |
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Abstract In the past decade, ontology has been widely used in biomedical data analysis, search, integration and reuse. As ontology itself is a specific type of data, the amount of ontologies has also increased rapidly. In order to promote the integration of precision medicine data sets and provide ontology resource service for domestic users, we constructed MedPortal, an ontology repository and platform. Reusing NCBO BioPortal technology, we constructed MedPortal software framework. We selected precision medicine-related ontologies and built MedPortal ontology repository. Further, we modified some original code in order that MedPortal could run smoothly in the new network environment. Now MedPortal ontology repository has been successfully constructed. So far, 42 biomedical ontologies have been imported into MedPortal, mappings among which have also been created. Several ontology services including term search, ontology mapping, and data annotation are provided through websites and REST API, accessible at: http://medportal.bmicc.cn. MedPortal will be of help to biomedical data integration.
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Received: 10 February 2017
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[1] 贺林. 新医学是解决人类健康问题的真正钥匙——需“精准”理解奥巴马的“精准医学计划”[J]. 遗传, 2015, 37(6):613-614.
[2] Collins F S, Varmus H. A new initiative on precision medicine[J]. New England Journal of Medicine, 2015, 372(9):793-795.
[3] Servant N, Roméjon J, Gestraud P, et al. Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial[J]. Frontiers in Genetics, 2014, 5:152-152.
[4] Pesquita C, Ferreira J D, Couto F M, et al. The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources[J]. Journal of Biomedical Semantics, 2014, 5(1):1-7.
[5] Huang Jingshan, Fernando G, Strachan H J, et al. OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data[J]. Journal of Biomedical Semantics, 2016, 7(1):1-17.
[6] Mate S, Köpcke F, Toddenroth D, et al. Ontology-based data integration between clinical and research systems[J]. Plos One, 2015, 10(1):e0116656-e0116656.
[7] Smith B, Ashburner M, Rosse C, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration[J]. Nat Biotech, 2007, 25(11): 1251-1255.
[8] Ong E, Xiang Zuoshuang, Zhao Bin, et al. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration[J]. Nucleic Acids Research, 2016, 45(Database issue):D347-D352.
[9] Côté R, Reisinger F, Martens L, et al. The Ontology Lookup Service: bigger and better[J]. Nucleic Acids Research, 2010, 38(Web Server issue):W155.
[10] Whetzel P L, Shah N H, Noy N F, et al. BioPortal: ontologies and integrated data resources at the click of a mouse[J]. Nucleic Acids Research, 2009, 37(suppl_2):170-173.
[11] Salvadores M, Alexander P R, Musen M A, et al. BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF[J]. Semantic Web, 2013,4(3):277.
[12] Whetzel P L, Noy N F, Shah 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[J]. Nucleic Acids Research, 2011,39(suppl 2): W541-W545.
[13] Vemonet. Importing UMLS To Virtual Appliance[EB/OL]. https://www.bioontology.org/wiki/index.php/Importing_UMLS_To_Virtual_Appliance.
[14] Horridge M, Bechhofer S. The OWL API: a Java API for working with OWL 2 ontologies[C]//Patel-Schneider P F. Proceedings of the 6th International Conference on OWL: Experiences and Directions(OWLED 2009). Chantilly, VA, United States;Hoekstra R, Patel-Schneider P F, 2009: 47-56.
[15] Graybeal. NCBO Virtual Appliance[EB/OL]. https://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance.
[16] Arp R, Smith B. Function, role, and disposition in Basic Formal Ontology[J]. Nature Precedings, 2008.
[17] Ceusters W, Smith B. Aboutness: Towards foundations for the information artifact ontology[C]//Proceedings of the 6th International Conference on Biomedical Ontology (ICBO). Lisbon: ICBO2015 Program Committee, 2015: 47-51.
[18] Bandrowski A, Brinkman R, Brochhausen M, et al. The Ontology for Biomedical Investigations[J]. Plos One, 2016, 11(4).
[19] Consortium T G O. Gene Ontology Consortium: going forward[J]. Nucleic Acids Research, 2015, 43(Database issue):1049-1056.
[20] BodenreiderO. The Unified Medical Language System (UMLS): integrating biomedical terminology[J]. Nucleic Acids Research, 2004, 32(suppl 1): D267-D270.
[21] Shao Chen. Urinary Protein Biomarker Database: A useful tool for biomarker discovery[J]. Advances in Experimental Medicine & Biology, 2015, 845(845):195-203.
[22] Lapatas V, Stefanidakis M, Jimenez R C, et al. Data integration in biological research: an overview[J]. Journal of Biological Research-Thessaloniki, 2015, 22(1):1-16.
[23] Jonquet C, Dzalé-Yeumo E, Arnaud E, et al. AgroPortal: A proposition for ontology-based services in the agronomic domain[C]//XXIV Plant and Animal Genome Conference. San Diego: The Plant & Animal Genome Organizing Committee, 2016: P0343.
[24] Jonquet C, Toulet A, Arnaud E, et al. Reusing the NCBO BioPortal technology for agronomy to build AgroPortal[C]//International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). Corvallis: ICBO and BioCreative, 2016: D203.
[25] Jonquet C, Lependu P, Falconer S, et al. NCBO Resource Index: Ontology-based search and mining of biomedical resources[J]. Web Semantics: Science, Services and Agents on the World Wide Web, 2011, 9(3): 316-324.
[26] Jonquet C, Emonet V, Musen MA. Roadmap for a multilingual BioPortal[C]//Proceedings of the Fourth Workshop on the Multilingual Semantic Web. Portoroz: MSW4 Program Committee, 2015: 15-26. |
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