Display options
Cite
Brinkman RR, Courtot M, Derom D, et al. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010;1:S7doi: 10.1186/2041-1480-1-S1-S7.
Brinkman, R. R., Courtot, M., Derom, D., Fostel, J. M., He, Y., Lord, P., Malone, J., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S. A., Soldatova, L. N., Stoeckert, C. J., Turner, J. A., Zheng, J. (2010). Modeling biomedical experimental processes with OBI. Journal of biomedical semantics, 1S7. https://doi.org/10.1186/2041-1480-1-S1-S7
Brinkman, Ryan R, et al. "Modeling biomedical experimental processes with OBI." Journal of biomedical semantics vol. 1 (2010): S7. doi: https://doi.org/10.1186/2041-1480-1-S1-S7
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010 Jun 22;1:S7. doi: 10.1186/2041-1480-1-S1-S7. PMID: 20626927; PMCID: PMC2903726.
Copy Download .nbib Format: NLM
Share it on

J Biomed Semantics. 2010 Jun 22;1:S7. doi: 10.1186/2041-1480-1-S1-S7.

Modeling biomedical experimental processes with OBI.

Journal of biomedical semantics

Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N Soldatova, Christian J Stoeckert, Jessica A Turner, Jie Zheng,

Affiliations

  1. British Columbia Cancer Agency, Vancouver, Canada. [email protected].

PMID: 20626927 PMCID: PMC2903726 DOI: 10.1186/2041-1480-1-S1-S7

Abstract

BACKGROUND: Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval.

RESULTS: The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI.

CONCLUSION: We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components.

AVAILABILITY: OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl.

References

  1. Nucleic Acids Res. 2008 Jan;36(Database issue):D440-4 - PubMed
  2. Nucleic Acids Res. 2008 Jan;36(Database issue):D923-8 - PubMed
  3. OMICS. 2006 Summer;10(2):199-204 - PubMed
  4. Stud Health Technol Inform. 2004;102:20-38 - PubMed
  5. J R Soc Interface. 2006 Dec 22;3(11):795-803 - PubMed
  6. PLoS Biol. 2005 Mar;3(3):e91 - PubMed
  7. Neuroinformatics. 2008 Sep;6(3):175-94 - PubMed
  8. Nat Biotechnol. 2007 Nov;25(11):1251-5 - PubMed
  9. Bioinformatics. 2006 Jul 15;22(14):e464-71 - PubMed
  10. Nature. 2002 Jul 25;418(6896):413-7 - PubMed
  11. AMIA Annu Symp Proc. 2006;:909 - PubMed
  12. Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15 - PubMed
  13. BMC Bioinformatics. 2009 Apr 27;10:125 - PubMed
  14. Bioinformatics. 2006 Apr 1;22(7):866-73 - PubMed
  15. Nat Genet. 2000 May;25(1):25-9 - PubMed
  16. Science. 2009 Apr 3;324(5923):85-9 - PubMed
  17. Genome Biol. 2005;6(5):R46 - PubMed

Publication Types

Grant support