Abstract
The field of translational biomedical informatics seeks to integrate knowledge from basic science, directed research into diseases, and clinical insights into a form that can be used to discover effective treatments of diseases. We demonstrate methods and tools to generate RDF representations of a commonly used experimental description format, MAGE-TAB, mappings of MAGE documents to two general-purpose provenance representations, OPM (Open Provenance Model) and PML (Proof Markup Language). We show through a use case simulation that the data represented in MAGE documents can be completely represented in OPM and PML through use of round trip analysis of certain examples. The success in mapping MAGE documents into general-purpose provenance models shows that promise in the implementation of the translational research provenance vision.
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References
Zerhouni, E.A.: Translational and clinical science–time for a new vision. New England Journal of Medicine 353(15), 1621 (2005)
Zerhouni, E.A.: US biomedical research: basic, translational, and clinical sciences. Jama 294(11), 1352 (2005)
Payne, P.R.O., Johnson, S.B., Starren, J.B., Tilson, H.H., Dowdy, D.: Breaking the translational barriers: the value of integrating biomedical informatics and translational research. Journal of Investigative Medicine 53(4), 192 (2005)
Kim, J., Deelman, E., Gil, Y., Mehta, G., Ratnakar, V.: Provenance trails in the Wings/Pegasus system. Concurrency and Computation: Practice and Experience 20(5), 587–597 (2008)
Zhao, J., Goble, C., Stevens, R., Turi, D.: Mining taverna’s semantic web of provenance. Concurrency and Computation: Practice and Experience 20(5), 463–472 (2008)
Scheidegger, C., Koop, D., Santos, E., Vo, H., Callahan, S., Freire, J., Silva, C.: Tackling the provenance challenge one layer at a time. Concurrency And Computation 20(5), 473 (2008)
Benjamini, Y., Hochberg, Y.: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological), 289–300 (1995)
Goble, C.: Position statement: Musings on provenance, workflow and (Semantic web) annotations for bioinformatics. In: Workshop on Data Derivation and Provenance, Chicago (2002)
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C., Causton, H., et al.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature genetics 29(4), 365–372 (2001)
Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Muertter, R.N., Edgar, R.: NCBI GEO: archive for high-throughput functional genomic data. Nucl. Acids Res. 37(suppl. 1), D885–D890 (2009)
Parkinson, H., Kapushesky, M., Kolesnikov, N., Rustici, G., Shojatalab, M., Abeygunawardena, N., Berube, H., Dylag, M., Emam, I., Farne, A., et al.: ArrayExpress update–from an archive of functional genomics experiments to the atlas of gene expression. In: Nucleic Acids Research (2008)
Berman, J., Edgerton, M., Friedman, B.: The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data. BMC Medical Informatics and Decision Making 3(1), 5 (2003)
Moreau, L., Miles, S., Missier, P., Simmhan, Y., Futrelle, J., Myers, J., Stephan, E., Kwasnikowska, N., den Bussche, J.V., Freire, J., et al.: The open provenance model (v1. 1) (2009)
McGuinness, D., Ding, L., Pinheiro da Silva, P., Chang, C.: Pml 2: A modular explanation interlingua. In: Proceedings of AAAI, vol. 7 (2007)
Davidson, S.B., Freire, J.: Provenance and scientific workflows: challenges and opportunities. In: Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data, pp. 1345–1350 (2008)
Moreau, L., Kwasnikowska, N., Van den Bussche, J.: The Foundations of the Open Provenance Model (2009)
Rayner, T., Rocca-Serra, P., Spellman, P., Causton, H., Farne, A., Holloway, E., Irizarry, R., Liu, J., Maier, D., Miller, M., Petersen, K., Quackenbush, J., Sherlock, G., Stoeckert, C., White, J., Whetzel, P., Wymore, F., Parkinson, H., Sarkans, U., Ball, C., Brazma, A.: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7(1), 489 (2006)
Bian, X., Klemm, J., Basu, A., Hadfield, J., Srinivasa, R., Parnell, T., Miller, S., Mason, W., Kokotov, D., Duncan, M., et al.: Data submission and curation for caArray, a standard based microarray data repository system (2009)
Stokes, T., Torrance, J., Li, H., Wang, M.: ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC bioinformatics 9(Suppl 6), S18 (2008)
Farquhar, A., Fikes, R., Rice, J.: The ontolingua server: A tool for collaborative ontology construction. International Journal of Human-Computers Studies 46(6), 707–727 (1997)
Antkiewicz, M., Czarnecki, K.: Framework-specific modeling languages with round-trip engineering. In: Wang, J., Whittle, J., Harel, D., Reggio, G. (eds.) MoDELS 2006. LNCS, vol. 4199, p. 692. Springer, Heidelberg (2006)
Missier, P., Belhajjame, K., Zhao, J., Goble, C.: Data lineage model for Taverna workflows with lightweight annotation requirements. In: Freire, J., Koop, D., Moreau, L. (eds.) IPAW 2008. LNCS, vol. 5272, pp. 17–30. Springer, Heidelberg (2008)
Whetzel, P., Parkinson, H., Causton, H., Fan, L., Fostel, J., Fragoso, G., Game, L., Heiskanen, M., Morrison, N., Rocca-Serra, P., et al.: The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22(7), 866 (2006)
McCusker, J.P., McGuinness, D.L.: Representing high throughput biomedical experiments using the open provenance model. Technical report, Technical Report TW-2010-14, Tetherless World Constellation, Rensselaer Polytechnic Institute, USA (2010)
Shannon, P., Markiel, A., Ozier, O., Baliga, N., Wang, J., Ramage, D., Amin, N., Schwikowski, B., Ideker, T.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research 13(11), 2498 (2003)
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McCusker, J.P., McGuinness, D.L. (2010). Explorations into the Provenance of High Throughput Biomedical Experiments. In: McGuinness, D.L., Michaelis, J.R., Moreau, L. (eds) Provenance and Annotation of Data and Processes. IPAW 2010. Lecture Notes in Computer Science, vol 6378. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-17819-1_15
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DOI: https://doi.org/10.1007/978-3-642-17819-1_15
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