Computational polypharmacology with text mining and ontologies

Current Pharmaceutical Biotechnology

Volumn 12, Issue 3, 2011, Pages 449-457

  Plake, Conrad ^a   Schroeder, Michael ^a  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Drug target interaction; Lead identification; Ontologies; Semantic similarity; Target identification; Text mining

Indexed keywords

LISURIDE; NILUTAMIDE; OMEGA 3 FATTY ACID;

ARTICLE; BLOOD CLOTTING; BLOOD VISCOSITY; CLINICAL FEATURE; COST CONTROL; DRUG DESIGN; DRUG DEVELOPMENT; DRUG TARGETING; INFORMATION PROCESSING; LITERATURE; METAPHYSICS; METHODOLOGY; ONTOLOGY; RAYNAUD PHENOMENON; SIGNAL TRANSDUCTION; TEXT MINING; VASOCONSTRICTION;

COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, BIBLIOGRAPHIC; DATABASES, FACTUAL; DRUG DISCOVERY; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PHARMACEUTICAL PREPARATIONS;

DUDLEYA EDULIS;

EID: 79551679202     PISSN: 13892010     EISSN: 18734316     Source Type: Journal    
DOI: 10.2174/138920111794480624     Document Type: Article

References (62)

1. Adams, C.P.; Brantner, V.V. Estimating the cost of new drug development: is it really 802 million dollars? Health. Aff. (Millwood), 2006, 25(2), 420-428.
2. Lage, K.; Karlberg, E.O.; Størling, Z.M.; Olason, P.I.; Pedersen, A.G.; Rigina, O.; Hinsby, A.M.; Türmer, Z.; Pociot, F.; Tommerup, N.; Moreau, Y.; Brunak, S. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat. Biotechnol., 2007, 25(3), 309-316.
3. Davis, F.P.; Sali, A. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput. Biol., 2010, 6(2), e1000668.
4. Shahian, T.; Lee, G.M.; Lazic, A.; Arnold, L.A.; Velusamy, P.; Roels, C.M.; Guy, R.K.; Craik, C.S. Inhibition of a viral enzyme by a small-molecule dimer disruptor. Nat. Chem. Biol., 2009, 5(9), 640-646.
5. Hopkins, A.L. Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol., 2008, 4(11), 682-690.
6. Janga, S.C.; Tzakos, A. Structure and organization of drug-target networks: insights from genomic approaches for drug discovery. Mol. Biosyst., 2009, 5(12), 1536-1548.
7. Gloeckner, C.; Garner, A.L.; Mersha, F.; Oksov, Y.; Tricoche, N.; Eubanks, L.M.; Lustigman, S.; Kaufmann, G.F.; Janda, K.D. Repositioning of an existing drug for the neglected tropical disease on-chocerciasis. Proc. Natl. Acad. Sci., 2010, 107(8), 3424-3429.
8. Keiser, M.J.; Setola, V.; Irwin, J.J.; Laggner, C.; Abbas, A.I.; Hufeisen, S.J.; Jensen, N.H.; Kuijer, M.B.; Matos, R.C.; Tran, T.B.; Whaley, R.; Glennon, R.A.; Hert, J.; Thomas, K.L.H.; Edwards, D.D.; Shoichet, B.K.; Roth, B.L. Predicting new molecular targets for known drugs. Nature, 2009, 462(7270), 175-181.
9. Krallinger, M.; Valencia, A. Text-mining and information retrieval services for molecular biology. Genome Biol., 2005, 6(7), 224.
10. Swanson, D.R. Medical literature as a potential source of new knowledge. Bull. Med. Libr. Assoc., 1990, 78(1), 29-37.
11. Swanson, D.R. Fish oil, raynaud's syndrome, and undiscovered public knowledge. Perspect. Biol. Med., 1986, 30(1), 7-18.
12. DiGiacomo, R.A.; Kremer, J.M.; Shah, D.M. Fish-oil dietary supplementation in patients with Raynaud's phenomenon: a double-blind, controlled, prospective study. Am. J. Med., 1989, 86(2), 158-164.
13. Campillos, M.; Kuhn, M.; Gavin, A.; Jensen, L.J.; Bork, P. Drug target identification using side-effect similarity. Science, 2008, 321(5886), 263-266.
14. Tsoi, L.C.; Boehnke, M.; Klein, R.L.; Zheng, W.J. Evaluation of genome-wide association study results through development of ontology fingerprints. Bioinformatics, 2009, 25(10), 1314-1320.
15. Washington, N.L.; Haendel, M.A.; Mungall, C.J.; Ashburner, M.; Westerfield, M.; Lewis, S.E. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol., 2009, 7:e1000247.
16. Ashburner, M.; Ball, C.A.; Blake, J.A.; Botstein, D.; Butler, H.; Cherry, J.M.; Davis, A.P.; Dolinski, K.; Dwight, S.S.; Eppig, J.T.; Harris, M.A.; Hill, D.P.; Issel-Tarver, L.; Kasarskis, A; Lewis, S.; Matese, J.C.; Richardson, J.E.; Ringwald, M.; Rubin, G.M.; Sherlock, G. Gene ontology: tool for the unification of biology. Nat. Genet., 2000, 25(1), 25-29.
17. Pesquita, C.; Faria, D.; Falco, A.O.; Lord, P.; Couto, F.M. Semantic similarity in biomedical ontologies. PLoS Comput. Biol., 2009, 5(7), e1000443.
18. Barrell, D.; Dimmer, E.; Huntley, R.P.; Binns, D.; O'Donovan, C.; Apweiler, R. The GOA database in 2009-an integrated gene ontology annotation resource. Nucleic Acids Res., 2009, 37(Database issue), D396-D403.
19. Winnenburg, R.; Wächter, T.; Plake, C.; Doms, A.; Schroeder, M. Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies? Brief. Bioinform., 2008, 9(6), 466-478.
20. Du, P.; Feng, G.; Flatow, J.; Song, J.; Holko, M.; Kibbe, W.A.; Lin, S.M. From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics, 2009, 25(12), i63-i68.
21. Robinson, P.N.; Köhler, S.; Bauer, S.; Seelow, D.; Horn, D.; Mundlos, S. The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet., 2008, 83(5), 610-615.
22. Smith, C.L.; Eppig, J.T. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Inter-discip. Rev. Syst. Biol. Med., 2009, 1(3), 390-399.
23. Rector, A.L.; Rogers, J.E.; Zanstra, P.E.; Haring, E.V.D. OpenGalen: Open Source Medical Terminology and Tools. AMIA Annu. Symp. Proc., Washington, DC, USA, 2003, p. 982.
24. Stearns, M.Q.; Price, C.; Spackman, K.A.; Wang, A.Y. Snomed Clinical Terms: Overview of the Development Process and Project Status. Proc. AMIA Symp., La Jolla, CA, USA, 2001, pp. 662-666.
25. Clarke, C.L.A.; Cormack, G.V.; Lynam, T.R. Exploiting redundancy in question answering. In: SIGIR'01: Proceedings of the 24th annual international ACM SIGIR conference on Research and development in information retrieval; New Orleans, Louisiana, USA; ACM, 2001.
26. Hirschman, L.; Colosimo, M; Morgan, A.; Yeh, A. Overview of biocreative task 1b: normalized gene lists. BMC Bioinformatics, 2005, 6(Suppl. 1), S11.
27. Morgan, A.A.; Lu, Z.; Wang, X.; Cohen, A.M.; Fluck, J.; Ruch, P.; Divoli, A.; Fundel, K.; Leaman, R.; Hakenberg, J.; Sun, C.; Liu, H.; Torres, R.; Krauthammer, M.; Lau, W.W.; Liu, H.; Hsu, C.; Schuemie, M.; Cohen, K.B.; Hirschman, L. Overview of biocreative II gene normalization. Genome Biol., 2008, 9(Suppl. 2), S3.
28. Hakenberg, J.; Plake, C.; Leaman, R.; Schroeder, M.; Gonzalez, G. Inter-species normalization of gene mentions with GNAT. Bioin-formatics, 2008, 24(16), i126-i132.
29. Wren, J.D. A scalable machine-learning approach to recognize chemical names within large text databases. BMC Bioinformatics, 2006, 7(Suppl. 2), S3.
30. Klinger, R.; Kolrik, C.; Fluck, J.; Hofmann- Apitius, M.; Friedrich, C.M. Detection of IUPAC and IUPAC-like chemical names. Bioin-formatics, 2008, 24(13), i268-i276.
31. Schuemie, M.J.; Jelier, R.; Kors, J.A. Peregrine: Lightweight Gene Name Normalization by Dictionary Lookup. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop; Madrid, Spain; 2007; pp. 131-133.
32. Hettne, K.M.; Stierum, R.H.; Schuemie, M.J.; Hendriksen, P.J.M.; Schijvenaars, B.J.A.; van Mulligen, E.M.; Kleinjans, J.; Kors, J.A. A dictionary to identify small molecules and drugs in free text. Bio-informatics, 2009, 25(22), 2983-2991.
33. Couto, F.M.; Silva, M.J.; Coutinho, P.M. Finding genomic ontology terms in text using evidence content. BMC Bioinformatics, 2005, 6(Suppl. 1), S21.
34. Ruch, P. Automatic assignment of biomedical categories: toward a generic approach. Bioinformatics, 2006, 22(6), 658-664.
35. Doms, A.; Schroeder, M. GoPubMed: exploring PubMed with the gene ontology. Nucleic Acids Res., 2005, 33(Web Server issue), W783-786.
36. Liu, H.; Teller, V.; Friedman, C. A multi-aspect comparison study of supervised word sense disambiguation. J. Am. Med. Inform. As-soc., 2004, 11(4), 320-331.
37. Alexopoulou, D.; Andreopoulos, B.; Dietze, H.; Doms, A.; Gan-don, F.; Hakenberg, J.; Khelif, K.; Schroeder, M.; Wächter, T. Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. BMC Bioinformatics, 2009, 10, 28.
38. Ananiadou, S.; McNaught, J., Eds. Text Mining for Biology and Biomedicine; Artech House, Inc., Norwood, MA, USA, 2005.
39. Wishart, D.S.; Knox, C.; Guo, A.C.; Cheng, D.; Shrivastava, S.; Tzur, D.; Gautam, B.; Hassanali, M. Drugbank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 2008, 36(Database issue), D901-D906.
40. Günther, S.; Kuhn, M.; Dunkel, M.; Campillos, M.; Senger, C.; Petsalaki, E.; Ahmed, J.; Urdiales, E.G.; Gewiess, A.; Jensen, L.J.; Schneider, R.; Skoblo, R.; Russell, R.B.; Bourne, P.E.; Bork, P.; Preissner, R. SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res., 2008, 36(Database issue), D919-D922.
41. Hernandez-Boussard, T.; Whirl-Carrillo, M.; Hebert, J.M.; Gong, L.; Owen, R.; Gong, M.; Gor, W.; Liu, F.; Truong, C.; Whaley, R.; Woon, M.; Zhou, T.; Altman, R.B.; Klein, T.E. The pharmacoge-netics and pharmacogenomics knowledge base: accentuating the knowledge. Nucleic Acids Res., 2008, 36(Database issue), D913-D918.
42. Kuhn, M.; von Mering, C.; Campillos, M.; Jensen, L.J.; Bork, P. Stitch: interaction networks of chemicals and proteins. Nucleic Acids Res., 2008, 36(Database issue), D684-D688.
43. Kuhn, M.; Campillos, M.; Letunic, I.; Jensen, L.J.; Bork, P. A side effect resource to capture phenotypic effects of drugs. Mol. Syst. Biol., 2010, 6, 343.
44. van Driel, M.A.; Bruggeman, J.; Vriend, G.; Brunner, H.G.; Le-unissen, J.A.M. A text-mining analysis of the human phenome. Eur. J. Hum. Genet., 2006, 14(5), 535-542.
45. McGary, K.L.; Park, T.J.; Woods, J.O.; Cha, H.J.; Wallingford, J.B.; Marcotte, E.M. Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc. Natl. Acad. Sci. USA, 2010, 107(14), 6544-6549.
46. Rihel, J.; Prober, D.A.; Arvanites, A.; Lam, K.; Zimmerman, S.; Jang, S.; Haggarty, S.J.; Kokel, D.; Rubin, L.L.; Peterson, R.T.; Schier, A.F. Zebrafish behavioral profiling links drugs to biological targets and rest/wake regulation. Science, 2010, 327(5963), 348-351.
47. Zhu, S.; Okuno, Y.; Tsujimoto, G.; Mamitsuka, H. A probabilistic model for mining implicit'chemical compound-gene' relations from literature. Bioinformatics, 2005, 21(Suppl. 2), ii245-ii251.
48. Plake, C.; Schiemann, T.; Pankalla, M.; Hakenberg, J.; Leser, U. AliBaba: PubMed as a graph. Bioinformatics, 2006, 22(19), 2444-2445.
49. Rebholz-Schuhmann, D.; Kirsch, H.; Arregui, M.; Gaudan, S.; Riethoven, M.; Stoehr, P. Ebimed-text crunching to gather facts for proteins from medline. Bioinformatics, 2007, 23(2):e237-e244.
50. Garten, Y.; Altman, R.B. Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics, 2009, 10(Suppl. 2), S6.
51. Chen, F.; Mackey, A.J.; Vermunt, J.K.; Roos, D.S. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One, 2007, 2(4), e383.
52. Vanunu, O.; Magger, O.; Ruppin, E.; Shlomi, T.; Sharan, R. Associating genes and protein complexes with disease via network propagation. PLoS Comput. Biol., 2010, 6(1), e1000641.
53. Camon, E.B.; Barrell, D.G.; Dimmer, E.C.; Lee, V.; Magrane, M.; Maslen, J.; Binns, D.; Apweiler, R. An evaluation of GO annotation retrieval for Biocreative and GOA. BMC Bioinformatics, 2005, 6(Suppl. 1), S17.
54. Krallinger, M.; Erhardt, R.A.; Valencia, A. Text-mining approaches in molecular biology and biomedicine. Drug Discov. Today, 2005, 10(6), 439-445.
55. Wren, J.D. In: Automating literature-based lead discovery. In: Frontieres in Drug Design & Discovery, 1st ed.; Caldwell, G.W.; Rahman, A.; Springer, B.A., Eds.; Bentham Science Publishers, United Arab Emirates, 2005; pp. 267-286.
56. Agarwal, P.; Searls, D.B. Literature mining in support of drug discovery. Brief. Bioinform., 2008, 9(6), 479-492.
57. Jensen, L.J.; Saric, J.; Bork, P. Literature mining for the biologist: from information retrieval to biological discovery. Nat. Rev. Genet., 2006, 7(2), 119-129.
58. Rubin, D.L.; Thorn, C.F.; Klein, T.E.; Altman, R.B. A statistical approach to scanning the biomedical literature for pharmacogenet-ics knowledge. J. Am. Med. Inform. Assoc., 2005, 12(2), 121-129.
59. Rindflesch, T.C.; Tanabe, L.; Weinstein, J.N.; Hunter, L. Edgar: extraction of drugs, genes and relations from the biomedical literature. Pac. Symp. Biocomput., 2000, 517-528.
60. Stevens, R.; Goble, C.A.; Bechhofer, S. Ontology-based knowledge representation for bioinformatics. Brief. Bioinform., 2000, 1(4), 398-414.
61. Bakheet, T.M.; Doig, A.J. Properties and identification of human protein drug targets. Bioinformatics, 2009, 25(4), 451-457.
62. Smith, B.; Ashburner, M.; Rosse, C.; Bard, J.; Bug, W.; Ceusters, W.; Goldberg, L.J.; Eilbeck, K.; Ireland, A.; Mungall, C.J.; Consortium, O.B.I.; Leontis, N.; Rocca-Serra, P.; Ruttenberg, A.; Sansone, S.; Scheuermann, R.H.; Shah, N.; Whetzel, P.L.; Lewis, S. The OBO foundry: coordinated evolution of ontologies to support bio-medical data integration. Nat. Biotechnol., 2007, 25(11), 1251-1255.