Identification of chemical images and conversion to structure-searchable information

Chemical Information Mining: Facilitating Literature-Based Discovery

Volumn , Issue , 2008, Pages 45-76

  Peter Johnson, A ^a   Valkó, Anikó T ^b  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b Hobberley Lodge   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85055516321     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420076509     Document Type: Chapter

References (47)

1. Aho, A. V., J. E. Hopcroft, and J. D. Ullman. 1983. Data Structures and Algorithms. Reading, MA: Addison-Wesley.
2. Akle, S., M. E. Algorri, C. Friedrich, and M. Zimmermann. 2007. Chemical OCR. Fraunhofer SCAI Internal report.
3. Algorri, M. E., M. Zimmermann, and M. Hofmann-Apitius. 2007a. Automatic recognition of chemical images. Eighth Mexican International Conference on Current Trends in Computer Science, (ENC 2007):41-46.
4. Algorri, M. E., M. Zimmermann, and M. Hofmann-Apitius. 2007b. Reconstruction of chemical molecules from images. Engineering in Medicine and Biology Society, 2007. EMBS 2007. 29th Annual International Conference of the IEEE, pp. 4609-4612.
5. Algorri, M. E., M. Zimmermann, M. Hofmann-Apitius, and C. Friedrich. 2007c. Turning a Binary Image into a Vector Graph by Analyzing the Texture of Discrete Directions. Fraunhofer SCAI Internal report.
6. Baird, H. S. 1994. Background structure in document images. Int. J. Pattern Recognit. Artif. Intell. 8:1013-1030.
7. Barnard, J. M., M. F. Lynch, and S. M. Welford. 1981. Computer storage and retrieval of generic structures in chemical patents. 2. GENSAL, a formal language for the description of generic chemical structures. J. Chem. Inf. Comput. Sci. 21(3):151-161.
8. Barnard, J. M., M. F. Lynch, and S. M. Welford. 1982. Computer storage and retrieval of generic structures in chemical patents. 4. An extended connection table representation for generic structures. J. Chem. Inf. Comput. Sci. 22(3):160-164.
9. Borman, S. 1992. New computer program reads, interprets chemical structures. Chem. Eng. News 70(4):17-19.
10. Casey, R., S. Boyer, P. Healey, A. Miller, B. Oudot, and K. Zilles. 1993. Optical Recognition of Chemical Graphics. Proc. 2nd Int. Conf. on Doc. Anal. and Recogn. (ICDAR’93), pp. 627-631.
11. Chowdhury, G. C., and M. F. Lynch. 1992a. Automatic interpretation of the texts of chemical patent abstracts. 1. Lexical analysis and categorization. J. Chem. Inf. Comput. Sci. 32(5):463-467.
12. Chowdhury, G. C., and M. F. Lynch. 1992b. Automatic interpretation of the texts of chemical patent abstracts. 2. Processing and results. J. Chem. Inf. Comput. Sci. 32(5):468-473.
13. Contreras, M. L., C. Allendes, L. T. Alvarez, and R. Rozas. 1990. Computational perception and recognition of digitized molecular structures. J. Chem. Inf. Comput. Sci. 30(3):302-307.
14. Duda, R. O., and P. E. Hart. 1972. Use of the Hough transform to detect lines and curves in pictures. Graphics Image Process. 1 (2):409-418.
15. Fan, K. C., C. H. Liu, and Y. K. Wang. 1994. Segmentation and classification of mixed text/graphics/image documents. Pattern Recogn. Lett. 15(12):1201-1209.
16. Fisanick, W. 1990. The Chemical Abstracts Service generic chemical (Markush) structure storage and retrieval capability. 1. Basic concepts. J. Chem. Inf. Comput. Sci. 30(2):145-154.
17. Fletcher, L. A., and R. Kasturi. 1988. A robust algorithm for text string separation from mixed text/graphics images. IEEE Trans. Pattern Anal. Mach. Intell. 10(6):294-308.
18. Gkoutos, G. V., H. Rzepa, R. M. Clark, O. Adjei, and H. Johal. 2003. Chemical machine vision: automated extraction of chemical metadata from raster images. J. Chem. Inf. Comput. Sci. 43(5):1342-1355.
19. Govindan, V. K., and A. P. Shivaprasad. 1990. Character recognition: a review. Pattern Recognit. 23(7):671-683.
20. Ibison, P. 1992. Internal Report in Image Group. Maxwell Institute.
21. Ibison, P., M. Jacquot, F. Kam, et al. 1993. Chemical literature data extraction: the CLiDE Project. J. Chem. Inf. Comput. Sci. 33(3):338-344.
22. Ibison, P., F. Kam, R. W. Simpson, C. Tonnelier, T. Venczel, and A. P. Johnson. 1992. Chemical structure recognition and generic text interpretation in the CLiDE Project. Online Inf. 92:131-142.
23. Illingworth, J., and J. Kitter. 1988. The adaptive Hough transform. Comput. Vision Graphics Image Process. 44(2):87-116.
24. Itoh, N., and H. Takahashi. 1990. A handwritten numeral verification method using distribution maps of structural features. Proc. SPIE Image Communications and Workstations, p. 1258.
25. Ittner, D. J., and H. S. Baird. 1993. Language-free layout analysis. Proc. 2nd Int. Conf. on Anal. and Recogn. (ICDAR’93), pp. 331-340.
26. Jain, A., and S. Bhattacharjee. 1992. Text segmentation using gabor filters for automatic document processing. Machine Vision Applications 5:169-184.
27. Kam, F. 1994. Automated Extraction of Chemical Information from the Chemical Literature. PhD Dissertation, School of Chemistry, University of Leeds, U.K.
28. Kam, F., R. W. Simpson, C. Tonnelier, T. Venczel, and A. P. Johnson. 1992. Chemical literature data extraction. Bond crossing in single and multiple structures. Int. Chem. Inf. Conf., pp. 113-126.
29. Karl, P. 2007. Chemical structure recognition via an expert system guided graph exploration. Master’s thesis, Ludwig-Maximilians-Universitaet, Munich, Germany.
30. Krishnamoorthy, M., G. Nagy, S. Seth, and M. Viswanathan. 1993. Syntactic segmentation and labeling of digitized pages from technical journals. IEEE Trans. Pattern Anal. Mach. Intell. 15(7):737-747.
31. Loening, K. L. 1988. Poster session: conventions, practices, and pitfalls in drawing chemical structures. Chem. Structures Int. Lang. Chem., pp. 415-423.
32. Lynch, M. F., J. M. Barnard, and S. M. Welford. 1981. Computer storage and retrieval of generic structures in chemical patents. 1. Introduction and general strategy. J. Chem. Inf. Comput. Sci. 21(3):148-150.
33. McDaniel, J. R., and J. R. Balmuth. 1992. Kekule: OCR-optical chemical (structure) recognition. J. Chem. Inf. Comput. Sci. 32(4):373-378.
34. Naccache, N. J., and R. Shinghal. 1984. An investigation into the skeletonization approach of Hildtich. IEEE Trans. Syst., Man Cyber 3(2):409-418.
35. Nagy, G., S. Seth, and M. Viswanathan. 1992. A prototype document image analysis system for technical journals. Computer 25:10-22.
36. O’Gorman, L., and R. Kasturi. 1993. The document spectrum for page layout analysis. IEEE Trans. Pattern Anal. Mach. Intell. 15(11):1162-1173.
37. Pavlidis, T. 1968. Computer recognition of figures through decomposition. J. Inf. Control 12:526-537.
38. Saitoh, T., T. Yamaai, and M. Tachikawa. 1994. Document image segmentation and layout analysis. IEICE Trans. Inf. Systems 77(7):778-784.
39. Simon, A. 1996. Image Analysis and Content Retrieval of Printed Chemistry Documents. PhD Dissertation, School of Chemistry, University of Leeds, U.K.
40. Simon, A., and A. P. Johnson. 1997. Recent advances in the CLiDE Project: logical layout analysis of chemical documents. J. Chem. Inf. Comput. Sci. 37(1):109-116.
41. Simon, A., J. C. Pret, and A. P. Johnson. 1995. (Chem)DeTeX Automatic generation of a markup language description of (chemical) documents from bitmap images. Proc. 3rd Int. Conf. on Doc. Anal. and Recogn. (ICDAR’95), pp. 458-461.
42. Sklansky, J., and V. Gonzalez. 1980. Fast polygonal approximation of digitized curves. Pattern Recogn. 12:327-331.
43. Smith, R. W. 1987. Compuer processing of line images: a survey. Pattern Recogn. 1(2):7-15.
44. Tetsuo, A., D. Z. Chen, N. Katoh, and T. Tokuyama. 1996. Polynomial-time solutions to image segmentation. Proc. Seventh Ann. ACM-SIAM Symp. Discrete Algorithms, pp. 104-113.
45. Tsujimoto, S., and H. Asada. 1992. Major components of a complete text reading system. Proc. IEEE 80(7):1133-1149.
46. Venczel, T. 1993. Recognition of Primitives. PhD Dissertation, School of Chemistry, University of Leeds, U.K.
47. Zimmermann, M., T. Bui Thi Le, and M. Hofmann-Apitius. 2005. Combating illiteracy in chemistry: towards computer-based chemical structure reconstruction. ERCIM News (60):40-41.