Abstract
In a fast evolving field like molecular biology, which produces great amounts of data at an ever increasing pace, it becomes fundamental the development of analysis applications that can keep up with that pace. The Rbbt development framework intends to support the development of complex functionality with strong data processing dependencies, as reusable components, and serving them through a simple and consistent API. This way, the framework promotes reuse and accessibility, and complements other solutions like classic APIs and function libraries or web services. The Rbbt framework currently provides a wide range of functionality from text mining to microarray meta-analysis.
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References
Barrett, T., Suzek, T.O., Troup, D.B., Wilhite, S.E., Ngau, W.C., Ledoux, P., Rudnev, D., Lash, A.E., Fujibuchi, W., Edgar, R.: NCBI GEO: mining millions of expression profiles–database and tools. Nucleic acids research 33(Database Issue), D562 (2005)
Kudo, T.: Crf++: Yet another crf toolkit (2005)
Lafferty, J.D., McCallum, A., Pereira, F.C.N.: Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data. In: Proc. of the Eighteenth International Conference on Machine Learning table of contents, pp. 282–289 (2001)
Leaman, R., Gonzalez, G.: Banner: An executable survey of advances in biomedical named entity recognition. In: Pacific Symposium on Biocomputing, vol. 13, pp. 652–663, Citeseer (2008)
Morgan, A., Lu, Z., Wang, X., Cohen, A., Fluck, J., Ruch, P., Divoli, A., Fundel, K., Leaman, R., Hakenberg, J., et al.: Overview of BioCreative II gene normalization. Genome Biology 9(Suppl. 2), S3 (2008)
Nogales-Cadenas, R., Carmona-Saez, P., Vazquez, M., Vicente, C., Yang, X., Tirado, F., Carazo, J.M., Pascual-Montano, A.: GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Research (2009)
Settles, B.: ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics 21(14), 3191 (2005)
Settles, B., Collier, N., Ruch, P., Nazarenko, A.: Biomedical Named Entity Recognition using Conditional Random Fields and Rich Feature Sets. In: COLING 2004 International Joint workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP) 2004, pp. 107–110 (2004)
Smith, L., Tanabe, L., Ando, R., Kuo, C.J., Chung, I.F., Hsu, C.N., Lin, Y.S., Klinger, R., Friedrich, C., Ganchev, K., et al.: Overview of BioCreative II gene mention recognition. Genome Biology 9(Suppl. 2), S2 (2008)
Vazquez, M., Carmona-Saez, P., Nogales-Cadenas, R., Chagoyen, M., Tirado, F., Carazo, J.M., Pascual-Montano, A.: SENT: semantic features in text. Nucleic Acids Research 37(Web Server issue), W153 (2009)
Vazquez, M., Nogales-Cadenas, R., Arroyo, J., Botas, P., Garca, R., Carazo, J.M., Tirado, F., Pascual-Montano, A., Carmona-Saez, P.: MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures (Under submission), http://marq.dacya.ucm.es
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Vázquez, M., Nogales, R., Carmona, P., Pascual, A., Pavón, J. (2010). Rbbt: A Framework for Fast Bioinformatics Development with Ruby. In: Rocha, M.P., Riverola, F.F., Shatkay, H., Corchado, J.M. (eds) Advances in Bioinformatics. Advances in Intelligent and Soft Computing, vol 74. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13214-8_26
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DOI: https://doi.org/10.1007/978-3-642-13214-8_26
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