OBIB-a novel ontology for biobanking

Journal of Biomedical Semantics

Volumn 7, Issue 1, 2016, Pages

  Brochhausen, Mathias ^a   Zheng, Jie ^b   Birtwell, David ^c   Williams, Heather ^c   Masci, Anna Maria ^d   Ellis, Helena Judge ^e   Stoeckert, Christian J ^b  

^a UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e DUKE UNIVERSITY   (United States)

Author keywords

Biobanking; Biorepository; Ontologies; Terminology

Indexed keywords

BIOBANK; BIOLOGICAL ONTOLOGY;

BIOLOGICAL ONTOLOGIES; BIOLOGICAL SPECIMEN BANKS;

EID: 84964864472     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/s13326-016-0068-y     Document Type: Article

References (25)

1. Cho SY, Hong EJ, Nam JM, Han B, Chu C, Park O. Opening of the national biobank of Korea as the infrastructure of future biomedical science in Korea. Osong Public Health Res Perspect. 2012;3:177-84.
2. Watts G. UK Biobank opens it data vaults to researchers. BMJ. 2012;344:e2459.
3. Yuille M, van Ommen GJ, Bréchot C, et al. Biobanking for Europe. Brief Bioinform. 2008;9:14-24.
4. Pang C, Hendriksen D, Dijkstra M, et al. BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. J Am Med Inform Assoc. 2015;22:65-75.
5. Izzo M, Mortola F, Arnulfo G, Fato MM, Varesio L. A digital repository with an extensible data model for biobanking and genomic analysis management. BMC Genomics. 2014;15 Suppl 3:S3.
6. Spjuth O, Krestyaninova M, Hastings J, et al. Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research. Eur J Hum Genet. 2015.
7. Andrade AQ, Kreuzthaler M, Hastings J, Krestyaninova M, Schulz S. Requirements for semantic biobanks. Stud Health Technol Inform. 2012;180:569-73.
8. Brochhausen M, Fransson MN, Kanaskar NV, et al. Developing a semantically rich ontology for the biobank-administration domain. J Biomed Semantics. 2013;4:23.
9. Norlin L, Fransson MN, Eriksson M, et al. A minimum data set for sharing biobank samples, information, and data: MIABIS. Biopreserv Biobank. 2012;10:343-8.
10. Smith B, Ashburner M, Rosse C, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007;25:1251-5.
11. Brinkman RR, Courtot M, Derom D, et al. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010;1 Suppl 1:S7.
12. Grenon P, Smith B, Goldberg L. Biodynamic ontology: applying BFO in the biomedical domain. Stud Health Technol Inform. 2004;102:20-38.
13. Arp R, Smith B, Spear AD. Building ontologies with basic formal ontology. Cambridge: The MIT Press; 2015.
14. Smith B, Ceusters W. Ontological realism: a methodology for coordinated evolution of scientific ontologies. Appl Ontol. 2010;5:139.
15. Zheng J, Xiang Z, Stoeckert Jr CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014;30(9):1340-2.
16. Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Research Notes. 2010;3:175.
17. Lin Y, Harris MR, Manion FJ, et al. Development of a BFO-Based Informed Consent Ontology (ICO). Houston: Proceedings of the 5th International Conference on Biomedical Ontology; 2014. http://ceur-ws.org/Vol-1327/icbo2014_paper_54.pdf. Accessed 28 April 2016.
18. Whetzel PL, Noy NF, Shah NH, 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. 2011;39:W541-5.
19. Dumontier M, Baker CJ, Baran J, et al. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J Biomed Semantics. 2014;5:14.
20. Cañas AJ, Hill G, Carff R, et al. CmapTools: a knowledge modeling and sharing environment, Concept maps: theory, methodology, technology. Pamplona: Proceedings of the first international conference on concept mapping; 2004. http://cmc.ihmc.us/papers/cmc2004-283.pdf. Accessed 28 April 2016.
21. Bizer C, Seaborne A. D2RQ-treating non-RDF databases as virtual RDF graphs, Proceedings of the 3rd international semantic web conference. 2004.
22. Fransson MN, Rial-Sebbag E, Brochhausen M, Litton JE. Toward a common language for biobanking. Eur J Hum Genet. 2015;23:22-8.
23. National Cancer Institute - Biorepositories and Biospecimen Research Branch. Lifecycle of Biospecimens. http://biospecimens.cancer.gov/researchnetwork/lifecycle.asp. Accessed 28 April 2016.
24. Almeida MB, Slaughter L, Brochhausen M. Towards an ontology of document acts: Introducing a document act template for healthcare. Berlin, New York, Heidelberg: OTM 2012 Workshops, LNCS 7567; 2012. p. 420-5.
25. Brochhausen M, Almeida MA, Slaughter L. Towards a formal representation of document acts and the resulting legal entities. In: Ingthorsson RD, Svennerlind C, Almäng J, editors. Johanssonian Investigations. Frankfurt: Ontos; 2013. p. 120-39.