Optical structure recognition software to recover chemical information: OSRA, an open source solution

Journal of Chemical Information and Modeling

Volumn 49, Issue 3, 2009, Pages 740-743

  Filippov, Igor V ^a   Nicklaus, Marc C ^b  

^a SAIC FREDERICK INC   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMAGE PROCESSING; MOLECULAR GRAPHICS; MOLECULAR STRUCTURE; OPEN SYSTEMS; OPTICAL DATA PROCESSING;

AUTOMATED PROCESSING; CHEMICAL INFORMATION; GRAPHICAL INFORMATION; GRAPHICAL REPRESENTATIONS; OPEN SOURCE TOOLS; OPEN-SOURCE SOLUTIONS; OPTICAL STRUCTURES; STRUCTURAL INFORMATION;

OPEN SOURCE SOFTWARE;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER GRAPHICS; COMPUTER PROGRAM;

COMPUTER GRAPHICS; MOLECULAR STRUCTURE; SOFTWARE;

EID: 65249117009     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800067r     Document Type: Article

References (22)

1. Heller, S.; Stein, S.; Tchekhovskoi, D. InChI: Open access/open source and the IUPAC international chemical identifier. Abstr. Pap. Am. Chem. Soc. 2005, 230, 1025-1026.
2. Murray-Rust, P.; Rzepa, H. Chemical markup, XML, and the worldwide web. 1. Basic principles. J. Chem. Inf. Comput. Sci. 1999, 39, 928-942.
3. Contreras, M.; Allendes, C.; Alvarez, L.; Rozas, R. Computational perception and recognition of digitized molecular structures. J. Chem. Inf. Comput. Sci. 1990, 30, 302-307.
4. Casey, R.; Boyer, S.; Healey, P.; Miller, A.; Oudot, B.; Zilles, K. Optical Recognition of Chemical Graphics. Proceedings of the 2nd International Conference on Document Analysis and Recognition; Tsukiba Science City, Japan, October 1993; IEEE: Piscataway, NJ, 1993; 627-632.
5. McDaniel, J.; Balmuth, J. Kekule - OCR optical chemical (structure) recognition. J. Chem. Inf. Comput. Sci. 1992, 32, 373-378.
6. Ibison, P.; Jacquot, M.; Kam, F.; Neville, A.; Simpson, R.; Tonnelier, C.; Venczel, T.; Johnson, A. Chemical Literature Data Extraction - The CLiDE Project. J. Chem. Inf. Comput. Sci. 1993, 33, 338-344.
7. Zimmermann, M.; Thi, L.; Hofmann, M. Combating illiteracy in chemistry: Towards computer-based chemical structure reconstruction. ERCIM News 2005, 60, 40-41.
8. Zimmermann, M. Large scale evaluation of chemical structure recognition. Proceedings of the 4th Text Mining Symposium in Life Sciences; October 9-10, 2006; Fraunhofer SCAI: Germany, 2006.
9. Michigan Alliance for Cheminformatic Exploration. http://www-personal. umich.edu/grosania/MACE071806OSANIA.ppt. (accessed September 26, 2008).
10. ImageMagick: Convert, Edit, and Compose Images. http://www. imagemagick.org/script/index.php. (accessed September 26, 2008).
11. Ghostscript, Ghostview and GSView. http://pages.cs.wisc.edu/ghost/. (accessed September 26, 2008).
12. OSRA: Optical Structure Recognition, http://cactus.nci.nih.gov/osra. (accessed September 26, 2008).
13. OSRA: Optical Structure Recognition. http://cactus.nci.nih.gov/cgi-bin/ osra/index.cgi. (accessed September 26, 2008).
14. SourceForge.net: OSRA. http://sourceforge.net/projects/osra/. (accessed September 26, 2008).
15. GREYCstoration. http://www.greyc.ensicaen.fr/dtschump/greycstoration/. (accessed September 26, 2008).
16. Cychosz, J. M. Efficient binary image thinning using neighborhood maps. In Graphics gems IV; Academic Press Professional, Inc.: San Diego, CA, 1994; pp 465-473.
17. Peter Selinger: Potrace. http://potrace.sourceforge.net/. (accessed September 26, 2008).
18. Optical Character Recognition (GOCR). http://sourceforge.net/projects/ jocr/. (accessed September 26, 2008).
19. Ocrad-GNU Project-Free Software Foundation (FSF). http://www. gnu.org/software/ocrad/ocrad.html. (accessed September 26, 2008).
20. Sitzmann, M.; Filippov, I. V.; Nicklaus, M. C. Internet resources integrating many small-molecule databases. SAR QSAR Environ. Res. 2008, 19, 1-9.
21. Xemistry Chemoinformatics. http://www.xemistry.com/. (accessed September 26, 2008).
22. Filippov, I. V.; Nicklaus, M. C. Optical structure recognition application. Proceedings of the 236th ACS National Meeting; Philadelphia, PA, August 17-21, 2008; American Chemical Society: Washington, DC, 2008.