COEUS: “semantic web in a box” for biomedical applications

Journal of Biomedical Semantics

José Luís Oliveira¹  Pedro Lopes¹ 

[1] DETI/IEETA, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, 3810 – 193, Portugal

关键词: Biomedical semantics;    Biomedical applications;    Web services;    Linked data;    Rapid application deployment;    Semantic web framework;   

Others  :  824938
DOI  :  10.1186/2041-1480-3-11

 received in 2012-03-21, accepted in 2012-11-05,  发布年份 2012

【 摘 要 】

Background

As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter’s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited.

Results

COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a “semantic web in a box” approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer.

Conclusions

The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/ webcite.

【 授权许可】

   
2012 Lopes and Oliveira; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Cannata N, Merelli E, Altman RB: Time to organize the bioinformatics resourceome. PLoS Comput Biology 2005, 1:e76.
• [2]Maojo V, Martin Sanchez F: Bioinformatics: towards new directions for public health. Methods Inf Med 2004, 43:208-214.
• [3]Pop M, Salzberg SL: Bioinformatics challenges of new sequencing technology. Trends Genet 2008, 24:142-149.
• [4]Goble C, Stevens R: State of the nation in data integration for bioinformatics. J Biomed Inform 2008, 41:687-693.
• [5]Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB: Bioinformatics challenges for personalized medicine. Bioinformatics 2011, 27:1741-1748.
• [6]Moore JH, Asselbergs FW, Williams SM: Bioinformatics challenges for genome-wide association studies. Bioinformatics 2010, 26:445-455.
• [7]Slater T, Bouton C, Huang ES: Beyond data integration. Drug Discov Today 2008, 13:584-589.
• [8]Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M: BiologicalNetworks 2.0 - an integrative view of genome biology data. BMC Bioinformatics 2010, 11:610. BioMed Central Full Text
• [9]Hepp M: Semantic Web and semantic Web services: father and son or indivisible twins? Internet Computing, IEEE 2006, 10:85-88.
• [10]Wilkinson M, Vandervalk B, McCarthy L: The semantic automated discovery and integration (SADI) web service design-pattern, API and reference implementation. J Biomed Semantics 2011, 2:8. BioMed Central Full Text
• [11]Cannata N, Schroder M, Marangoni R, Romano P: A Semantic Web for bioinformatics: goals, tools, systems, applications. BMC Bioinformatics 2008, 9:S1.
• [12]Shaban-Nejad A, Baker C, Haarslev V, Butler G: The fungalweb ontology: semantic web challenges in bioinformatics and genomics. In The Semantic Web - ISWC 2005; Nov 2005; Galway, Ireland. Edited by Gil Y, Motta E, Benjamins V, Musen M. Berlin / Heidelberg: Springer; 2005:1063-1066.
• [13]Bumans G, Cerans K: RDB2OWL: a practical approach for transforming RDB data into RDF/OWL. In 6th International Conference on Semantic Systems. Graz, Austria: ACM; 2010:1-3.
• [14]Hazber M, Yang J, Jin Q: Towards integration rules of mapping from relational databases to semantic web ontology. In 2010 International Conference on Web Information Systems and Mining. Sanya, China: IEEE Computer Society; 2010:335-339.
• [15]Sahoo SS, Halb W, Hellmann S, Idehen K, Thibodeau T Jr, Auer S, Sequeda J, Ezzat A: A survey of current approaches for mapping of relational databases to RDF. W3C 2009.
• [16]Shufeng Z: Tool for translating relational databases schema into ontology for semantic web. In Second International Workshop on Education Technology and Computer Science (ETCS). Edited by Guangwu M, Haiyun L, Huaiwei Z. Wuhan, China: IEEE Computer Society; 2010:198-201.
• [17]Bizer C, Heath T, Idehen K, Berners-Lee T: Linked data on the web. In Proceedings of the 17th international conference on World Wide Web (WWW'08). ACM; 2008:1265-1266.
• [18]Ring HZ, Kwok P-Y, Cotton RG: Human Variome Project: an international collaboration to catalogue human genetic variation. Pharmacogenomics 2006, 7:969-972.
• [19]Via M, Gignoux C, Burchard EG: The 1000 Genomes Project: new opportunities for research and social challenges. Genome Medicine 2010, 2:1-3. BioMed Central Full Text
• [20]Webb AJ, Thorisson GA, Brookes AJ: An informatics project and online "Knowledge Centre" supporting modern genotype-to-phenotype research. Hum Mutat 2011, 32:543-550.
• [21]Dias G, Vicente F-J, Oliveira JL, Martin-Sánchez F: Integrating medical and genomic data: a sucessful example for rare diseases. In The 20th International Congress of the European Federation for Medical Informatics (MIE 2006). Stud Health Technol Inform 124:125-130.
• [22]Arrais J, Pereira J, Oliveira JL: GeNS: A biological data integration platform. In ICBB 2009, International Conference on Bioinformatics and Biomedicine; Venice. Edited by Brojack B. WASET, World Academy of Science, Engineering and Technology; 2009.
• [23]Auer S, Dietzold S, Lehmann J, Hellmann S, Aumueller D: Triplify: light-weight linked data publication from relational databases. In 8th international conference on World Wide Web. Madrid, Spain: ACM; 2009:621-630.
• [24]Bizer C, Cyganiak R: D2R Server - Publishing Relational Databases on the Semantic Web. International Semantic Web Conference (ISWC 2006) 2006.
• [25]Belleau F, Nolin M-A, Tourigny N, Rigault P, Morissette J: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 2008, 41:706-716.
• [26]Bizer C, Lehmann J, Kobilarov G, Auer S, Becker C, Cyganiak R, Hellmann S: DBpedia - A crystallization point for the web of data. Web Semant: Sci, Serv Agents World Wide Web 2009, 7:154-165.
• [27]Kiryakov A, Ognyanov D, Manov D: OWLIM – A pragmatic semantic repository for OWL. In Web Information Systems Engineering Workshops (WISE 2005). Edited by Dean M, Guo Y, Jun W, Kaschek R, 657 Krishnaswamy S, Pan Z, Sheng Q. Berlin / Heidelberg: Springer; 2005:182-192.
• [28]Swertz M, Dijkstra M, Adamusiak T, van der Velde J, Kanterakis A, Roos E, Lops J, Thorisson G, Arends D, Byelas G, et al.: The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinformatics 2010, 11:S12.
• [29]Almeida J, Deus H, Maass W: S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics 2010, 11:387. BioMed Central Full Text
• [30]Couto F, Silva M: Disjunctive shared information between ontology concepts: application to Gene Ontology. J Biomed Semant 2011, 2:5. BioMed Central Full Text
• [31]Morsey M, Lehmann J, Auer S, Ngomo ACN: Usage-Centric Benchmarking of RDF Triple Stores. In Twenty-Sixth AAAI Conference on Artificial Intelligence (AAAI-12). Toronto, Ontario, Canada; 2012:2134-2140.
• [32]Morsey M, Lehmann J, Auer S, Ngonga ACN: DBpedia SPARQL benchmark– performance assessment with real queries on real data. The Semantic Web Conference (ISWC 2011); Lecture Notes in Computer Science 2011, 454-469.
• [33]Mironov V, Seethappan N, Blonde W, Antezana E, Lindi B, Kuiper M: Benchmarking triple stores with biological data. In Semantic Web Applications and Tools for Life Sciences (SWAT4LS), Berlin, Germany; 2010.
• [34]Cheung K-H, Frost HR, Marshall MS, Prudhommeaux E, Samwald M, Zhao J, Paschke A: A journey to Semantic Web query federation in the life sciences. BMC Bioinformatics 2009, 10(Suppl 10):S10. BioMed Central Full Text