Information extraction from chemical patents

• Autorzy: Bergmann S. , Romberg M. , Klenner A. , Zimmermann M.
• Języki publikacji: PL

Abstrakty

EN

The development of new chemicals or pharmaceuticals is preceded by an indepth analysis of published patents in this field. This information retrieval is a costly and time inefficient step when done by a human reader, yet it is mandatory for potential success of an investment. The goal of the research project UIMA-HPC is to automate and hence speed-up the process of knowledge mining about patents. Multi-threaded analysis engines, developed according to UIMA (Unstructured Information Management Architecture) standards, process texts and images in thousands of documents in parallel. UNICORE (UNiform Interface to COmputing Resources) workflow control structures make it possible to dynamically allocate resources for every given task to gain best cpu-time/realtime ratios in an HPC environment.

Słowa kluczowe

EN

information extraction; chemical patents; HPC; workflows; UNICORE; UIMA

• Wydawca: Wydawnictwa AGH
• Czasopismo: Computer Science
• Rocznik: 2012
• Tom: Vol. 13 (2)
• Strony: 21--32
• Opis fizyczny: Bibliogr. 13 poz., rys., wykr., tab.

Twórcy

autor

Bergmann S.

• Forschungszentrum Julich GmbH, 52425 Julich, Germany

autor

Romberg M.

• Forschungszentrum Julich GmbH, 52425 Julich, Germany

autor

Klenner A.

• Fraunhofer-Institute for Algorithms and Scientific Computing, 53754 Sankt Augustin, Germany

autor

Zimmermann M.

• Fraunhofer-Institute for Algorithms and Scientific Computing, 53754 Sankt Augustin, Germany

Bibliografia

• [1] Algorri M.-E., Zimmermann M., Friedrich C. M., Akle S., Hofmann-Apitius M.: Reconstrucition of chemical molecules from images. [in:] Conference Proceedings of the International Conference of IEEE Engineering in Medicine and Biology Society, vol. 2007 of Proceedings of Annual International Conference of the 30 Sandra Bergmann, Mathilde Romberg, Alexander Klenner, Marc Zimmermann IEEE Engineering in Medicine and Biology Society, pp. 4609–4612. Department of Digital Systems, Instituto Tecnologico Autonomo de Mexico, Mexico City. [e-mail], 2007.
• [2] Banville D. L.: Mining chemical structural information from the drug literature. Drug discovery today, 11(1–2):35–42, January 2006.
• [3] Demuth B., Schuller B., Holl S., Daivandy J., Giesler A., Huber V., Sild S.: The unicore rich client: Facilitating the automated execution of scientific workflows. [in:] e-Science (e-Science), 2010 IEEE Sixth International Conference on, pp. 238–245, dec. 2010.
• [4] Filippov I. V., Nicklaus M. C.: Optical structure recognition software to recover chemical information: OSRA, an open source solution. Journal of chemical information and modeling, 49(3):740–3, March 2009.
• [5] Hettne K. M., Stierum R. H., Schuemie M. J., Hendriksen P. J. M., Schijvenaars B. J. A., Mulligen E. M. V., Kleinjans J., Kors J. A.: A dictionary to identify small molecules and drugs in free text. Bioinformatics (Oxford, England), 25(22):2983–91, November 2009.
• [6] J. Yuan M.: Watson and healthcare: How natural language processing and semantic search could revolutionize clinical decision support. developerWorks, April 2011.
• [7] Jessop D. M., Adams S. E., Murray-Rust P.: Mining chemical information from Open patents. Journal of cheminformatics, 3(1):40, October 2011.
• [8] Kolluru B., Hawizy L., Murray-Rust P., Tsujii J., Ananiadou S.: Using workflows to explore and optimise named entity recognition for chemistry. PloS one, 6(5):e20181, January 2011.
• [9] Ogren P., Bethard S.: Building test suites for UIMA components. [in:] Proceedings of the Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing (SETQA-NLP 2009), pp. 1–4, Boulder, Colorado, June 2009. Association for Computational Linguistics.
• [10] Park J., Rosania G. R., Shedden K. A., Nguyen M., Lyu N., Saitou K.: Automated extraction of chemical structure information from digital raster images. Chemistry Central journal, 3:4, January 2009.
• [11] Streit A., Bergmann S., Breu R., Daivandy J., Demuth B., Giesler A., Hagemeier B., Holl S., Huber V., Mallmann D., Memon A. S., Memon M. S., Menday R., Rambadt M., Riedel M., Romberg M., Schuller B., Lippert T.: UNICORE 6– A European Grid Technology, vol. 18. 2009.
• [12] Warr W. A.: Chemoinformatics and Computational Chemical Biology, vol. 672 of Methods in Molecular Biology. Humana Press, Totowa, NJ, 2011.
• [13] Zimmermann M., Fluck J., Thi L. T. B., Kol´arik C., Kumpf K., Hofmann M.: Information extraction in the life sciences: perspectives for medicinal chemistry, pharmacology and toxicology. Current Topics in Medicinal Chemistry, 5(8):785–796, 2005.