SCAI Bioinformatics has a longtime working experience on the automated extraction of information from biomedical literature. Based on our experience in the field of biological information extraction (cf. BER and ProMiner ), we recently extended the scope of our research towards chemical entity recognition.

Here some references on this topic:

Chemical Structure Recognition:

  • Framework for Extracting Rotation Invariant Features for Image Classification and an Application using Haar Wavelets; S. Akle, M.-E. Algorri and M. Zimmermann; WSEAS Intern. Conferences, Univ. of Cambridge, February 2008.
  • Chemical Structure Recognition via an expert system guided graph exploration; Peter Kral; Diploma Thesis; Ludwig-Maximilians-Universitaet, Muenchen, 2007. Download [PDF, ZIP 2.8 MB]
  • Combating Illiteracy in Chemistry: Towards Computer-Based Chemical Structure Reconstruction; M. Zimmermann, C. M. Friedrich and M. E. Algorri; 1st German Conference on Chemoinformatics, (2005), Goslar.
  • CSR - Chemical Structure Recognition from Images; Y. Wang, L. T. Bui Thi, C. M. Friedrich, M. Zimmermann, M. Algorri, H. Noltemeier, M. Hofmann; German Conference on Bioinformatics (GCB 2005), Hamburg
  • Combating Illiteracy in Chemistry: Towards Computer-Based Chemical Structure Reconstruction; M. Zimmermann, Le T. Bui Thi, M. Hofmann; ERCIM News No. 60, (2005) 40-41. Download [PDF, 217 KB]
  • Graph-Rekonstruktion im Rahmen chemischer Strukturrepraesentationen; Le Thuy Bui Thi; Diplomarbeit; Bayerische Julius-Maximilians-Universitaet, Wuerzburg, 2005. Download [PDF, 1.2 MB]
  • Kekule: Ocr-optical chemical (structure) recognition; R. McDaniel and Jason R. Balmuth. J. Chem. Inf. Comput. Sci., 32(4):373-378, 1992.
  • Chemical Literature Data Extraction: The CLiDE Project; P. Ibison, M. Jacquot, F. Kam, A. G. Neville, R.W. Simpson, C. Tonnelier, T. Venczel and A.P. Johnson, J. Chem. Inf. Comput. Sci., vol. 33(3): 338-344, 1993.
  • Optical recognition of chemical graphics; S. Boyer, Document Analysis and Recognition, Proceedings of the Second International Conference on Publication, 627-631, 20-22 Oct 1993.

Information Extraction:

  • Identification of New Drug Classification Terms in Textual Resources; C. Kolarik, M. Hofmann-Apitius, M. Zimmermann and J. Fluck; ISMB/ECCB, (2007), Vienna.
  • Mining chemical structural information from the drug literature; D.L. Banville, DDT(2006), 11(1):35-42, 2006.
  • Information extraction in the life sciences: perspectives for medicinal chemistry, pharmacology and toxicology; M. Zimmermann, J. Fluck, le T. BuiThi, C. Kolarik, K. Kumpf, M. Hofmann; Curr Top Med Chem. (2005); 5(8):785-96. PMID: 16101418 Download [PDF, 165 KB]
  • Information Extraction Technologies for the Life Science Industry; J. Fluck, M. Zimmermann, G. Kurapkat, M. Hofmann; Drug Discovery Today-Technologies (2005), 2(3):217-24. Download [PDF, 278 KB]

Selected Talks: