Tunable machine vision-based strategy for automated annotation of chemical databases

Journal of Chemical Information and Modeling

Volumn 49, Issue 8, 2009, Pages 1993-2001

  Park, Jungkap ^a   Rosania, Gus R ^a   Saltou, Kazuhiro ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER VISION; EXPERT SYSTEMS; INTELLIGENT DATABASES; MOLECULES; TEXT MINING;

ANNOTATION PERFORMANCE; CHEMICAL SIMILARITY; CONVERSION ACCURACIES; PUBLICLY ACCESSIBLE; RECALL AND PRECISION; SCIENTIFIC KNOWLEDGE; SCIENTIFIC LITERATURE; STRUCTURE DIAGRAMS;

MOLECULAR GRAPHICS;

ARTICLE; ARTIFICIAL INTELLIGENCE; BIBLIOGRAPHIC DATABASE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; FACTUAL DATABASE; MOLECULAR LIBRARY;

ARTIFICIAL INTELLIGENCE; DATABASES, BIBLIOGRAPHIC; DATABASES, FACTUAL; MOLECULAR STRUCTURE; SMALL MOLECULE LIBRARIES; SOFTWARE;

EID: 69549097794     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900029v     Document Type: Article

References (54)

1. Agrafiotis, D. K.; Lobanov, V. S.; Salemme, F. R. Combinatorial informatics in the post-genomics era. Nat. Rev. Drug Discovery 2002, 1, 337-346.
2. (2) Schreiber, S. L. Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 2000, 287, 1964-1969. (Pubitemid 30158663)
3. Dobson, C. M. Chemical space and biology. Nature 2004, 432, 824-828.
4. Schreiber, S. L. The small-molecule approach to biology: chemical genetics and diversity-oriented organic synthesis make possible the systematic exploration of biology. Chem. Eng. News 2003, 87, 51-61.
5. (5) Miller, M. A. Chemical database techniques in drug discovery. Nat. Rev. Drug Discovery 2002, 1, 220-227. (Pubitemid 37361425)
6. Jonsdottir, S. O.; Jorgensen, F. S.; Burnak, S. Prediction methods and databases within cheminformatics: emphasis on drugs and drug candidates. Bioinformatics 2005, 21, 2145-2160.
7. (7) Rosania, G. R.; Crippen, G.; Woolf, P.; States, D.; Shedden, K. A Cheminformatic Toolkit for Mining Biomedical Knowledge. Pharm. Res. 2007, 24, 1791-1802. (Pubitemid 47389234)
8. (8) Weisgerber, D. W. Chemical Abstracts Service Chemical Registry System: History, Scope, and Impacts. J. Am. Soc. Inf. Sci. 1997, 48, 349-360. (Pubitemid 127614265)
9. (9) Kaiser, J. Chemists want NIH to curtail database. Science 2005, 308, 774. (Pubitemid 40629230)
10. Wishart, D. S.; Knox, C.; Guo, A. C.; Shrivastava, S.; Hassanali, M.; Stothard, P.; Chang, Z.; Woolsey, J. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2007, 34, 668-672.
11. eMolecules. http://www.emolecules.com (accessed May 12, 2009).
12. SciFinder. http://www.cas.org/SCIFINDER/SCHOLAR/ (accessed May 12, 2009).
13. IDdb3. http://www.iddb3.com (accessed May 12, 2009).
14. SureChem. http://www.surechem.org (accessed May 12, 2009).
15. Chen, J.; Swamidass, S. J.; Dou, Y.; Bruand, J.; Baldi, P. ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics 2005, 21, 4133-4139.
16. (16) Baker, M. Open-access chemistry databases evolving slowly but not surely. Nat. Rev. Drug Discovery 2006, 5, 707-708. (Pubitemid 44323694)
17. (17) Banville, D. L. Mining chemical structural information from the drug literature. Drug Discovery Today 2006, 11, 35-42. (Pubitemid 43227850)
18. (18) Krallinger, M.; Erhardt, R. A.; Valencia, A. Text-mining approaches in molecular biology and biomedicine. Drug Discovery Today 2005, 10, 439-445. (Pubitemid 40450274)
19. Fukuda, K.; Tamura, A.; Tsunoda, T.; Takagi, T. Toward information extraction: identifying protein names from biological papers. Proceedings of Pacific Symposium on Biocomputing, Hawaii, U.S.A., Jan 4- 9, 1998; pp 707-718.
20. (20) Krauthammer, M.; Rzhetsky, A.; Morozov, P.; Friedman, C. Using BLAST for identifying gene and protein names in journal articles. Gene 2000, 259, 245-252. (Pubitemid 32119256)
21. Tanabe, L.; Wilbur, W. J. Tagging gene and protein names in biomedical text. Bioinformatics 2002, 18, 1124-1132.
22. (22) Kemp, N.; Lynch, M. Extraction of Information from the Text of Chemical Patents. 1. Identification of Specific Chemical Names. J. Chem. Inf. Comput. Sci. 1998, 38, 544-551. (Pubitemid 128571182)
23. Wilbur, W. J.; Hazard G. F.; Divita, G.; Mork, J. G.; Aronson, A. R.; Browne, A. C. Analysis of Biomedical Text for Chemical Names: a comparison of Three Methods. Proceedings of the AMIA Symposium, Washington, D.C, U.S.A., Nov 7-11, 1999; ppl76-180.
24. Corbett, P.; Murray-Rust, P. High-Throughput Identification of Chemistry in Life Science Texts. CompLifie 2006, 107-118, LNBI 4216.
25. Lexichem. http://www.eyesopen.com/products/toolkits/lexichem.html (accessed May 12, 2009).
26. ACD/Name to Structure, http://www.acdlabs.com/products/name-lab/ rename/batch.html (accessed May 12, 2009).
27. Brecher, J. Name=Struct: A Practical Approach to the Sorry State of Real-Life Chemical Nomenclature. J. Chem. Infi. Comput. Sci. 1999, 39, 943-950.
28. IBM Chemical Search Alpha, https://chemsearch.almaden.ibm.com/ chemsearch/SearchServlet (accessed May 12, 2009).
29. Rhodes, J.; Boyer, S.; Kreulen, J.; Chen, Y.; Ordonez, P. Mining Patents Using Molecular Similarity Search. Proceedings of Pacific Symposium on Biocomputing, Hawaii, U.S.A., Jan 3-7, 2007; pp 304-315.
30. Zimmermann, M.; Fluck, J.; Friedrich, C. M.; Hofmann-Apitius, M. A Critical Review of Information Extraction Technologies in Chemistry. Presented at The International Conference in Trends for Scientific Information Professionals [Online], Barcelona, Spain, Oct 21-24, 2007. Fraunhofer SCAI Web site, http://www.scai.fraunhofer.de/ fileadmin/images/bio/chemoCR/Talks/Martin- Hofmann-Apitius-ICIC- talk.pdf (accessed May 20, 2008).
31. Simon, A.; Johnson, P. Recent Advances in the CLiDE Project: Logical Layout Analysis of Chemical Documents. J. Chem. Inf. Comput. Sci. 1997, 32, 109-116.
32. Gkoutos, G. V.; Rzepa, H.; Clark, R. M.; Adjei, O.; Johal, H. Chemical Machine Vision: Automated Extraction of Chemical Metadata from Raster Images. J. Chem. Inf. Comput. Sci. 2003, 43, 1342-1355.
33. McDaniel, J. R.; Balmuth, J. R. Kekule: OCR - Optical Chemical (Structure) Recognition. J. Chem. Inf. Comput. Sci. 1992, 32, 373-378.
34. Casey, R.; Boyer, S.; Healey, P.; Miller, A.; Oudot, B.; Zilles, K. Optical Recognition of Chemical Graphics Proceedings of the Second International Conference on Document Analysis and Recognition, Tsukuba Science City, Japan, Oct 20-22, 1993; pp 627-632.
35. Ibison, P.; Jacquot, M.; Kam, F.; Neville, A. G.; Simpson, R. W.; Tonnelier, C.; Venczel, T.; Johnson, A. P. Chemical Literature Data Extraction: The CLiDE Project. J. Chem. Inf. Comput. Sci. 1993, 33, 338-1334
36. Valko, A. T.; Johnson, A. P. CLiDE Pro: The Latest Generation of CLiDE, a Tool for Optical Chemical Structure Recognition. J. Chem. Inf. Comput. Sci. 2009, 49 (4), 780-787.
37. Algorri, M. E.; Zimmermann, M.; Hofmann-Apitius, M. Automatic Recognition of Chemical Images. In ENC 2007: Eighth Mexican International Conference on Current Trends in Computer Science, Morelia, Mexico, Sep 24-28, 2007; IEEE Computer Soc: Los Alamitos, California, U.S.A., 2007; pp 41-46.
38. Algorri, M. E.; Zimmermann, M.; Hofmann-Apitius, M. Reconstruction of Chemical Molecules from Images. In Proceedings of Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Lyon, France, Aug 22-26, 2007; IEEE: New York, 2007; pp 4609-4612.
39. Filippov, I. V.; Nicklaus, M. C. Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution. J. Chem. Inf. Model. 2009, 49 (3), 740-743.
40. Park, J.; Rosania, G. R.; Shedden, K. A.; Nguyen, M.; Lyu, N.; Saitou, K. Automated Extraction of Chemical Structure Information from Digital Raster Images. Chem. Cent. J. [Online] 2009, 3, Article 4. http://journal. chemistrycentral.com/content/3/l/4 (accessed Mar 22, 2009).
41. Willett, P. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
42. Sheridan, R. P.; Kearsley, S. K. Why do we need so many chemical similarity search methods. Drug Discovery Today 2002, 7, 903-911.
43. PubChem Substructure Fingerprint V1.2, 2007. NCBI PubChem WebSite, ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem- fingerprints.txt (accessed Mar 22, 2009).
44. PubMed. http://www.ncbi.nlm.nih.gov/pubmed/ (accessed May 11, 2009).
45. Adobe PDF. http://partners.adobe.com/public/developer/pdf/index- reference.html (accessed May 11, 2009).
46. ChemDraw Software, http://www.cambridgesoft.com/software/ ChemDraw/ (accessed May 11, 2009).
47. PubChem database, http://pubchem.ncbi.nlm.nih.gov/ (accessed May 11, 2009).
48. Zhou, Y.; Zhou, B.; Chen, K.; Yan, S. F.; King, F. J.; Jiang, S.; Winzeler, E. A. Large-Scale Annotation of Small-Molecule Librar- ies Using Public Databases. J. Chem. Inf. Model. 2007, 47, 1386-1394.
49. Open source code for generating PubChem Fingerprint provided by the NIH Chemical Genomics Center, http://ncgc.nih.gov/pub/openhts/ code/NCGC-PubChemFP. java.txt (accessed May 11, 2009).
50. ChemAxon's JChem toolkits, http://www.chemaxon.com/jchem/intro/ index.html (accessed May 11, 2009).
51. Pub SOAP for PubChem. http://pubchem.ncbi.nlm.nih.gov/pug-soap/ pug-soap-help.html (accessed May 11, 2009).
52. Medical Subject Headings (MeSH). http://www.nlm.nih.gov/mesh/ (accessed May 11, 2009).
53. Baker, M. Open-access chemistry databases evolving slowly but not surely. Nat. Rev. Drug Discovery 2006, 5, 707-708. (Pubitemid 44323694)
54. Singh, S. B.; Hull, R. D.; Fluder, E. M. Text Influenced Molecular Indexing (TIMI): A Literature Database Mining Approach that Handles Text and Chemistry. J. Chem. Inf. Comput. Sci. 2003, 43, 743-752.