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Supporting Information © Copyright Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, 2007 Supporting Information Supplementary Table 1 Table 1 Structure Similarity Scitegic Biospectra* Protein COSTART MedDRA Descriptor Measure Keys* Co-invest* Co-citation* Co-citation* ISIS keys Ward NA 4.68e-070 0.05605 2.443e-005 0.0006525 ISIS keys Cosine NA NA 9.095e-219 NA 7.568e-137 ISIS keys Euclidean NA NA NA 1.799e-086 1.27e-115 Table 2 Structure Similarity ISIS Biospectra* Protein COSTART MedDRA Descriptor Measure Keys* Co-invest* Co-citation* Co-citation* Scitegic keys Ward NA 0.04715 NA NA NA Scitegic keys Cosine NA NA NA NA NA Scitegic keys Euclidean NA NA NA NA NA Table 3 Structure Similarity ISIS Scitegic Protein COSTART MedDRA Descriptor Measure Keys* Keys* Co-invest* Co-citation* Co-citation* Biospectra Ward 4.68e-070 0.04715 4.272e-108 3.68e-118 0.0002087 Biospectra Cosine NA NA 5.34e-015 3.125e-069 9.523e-006 Biospectra Euclidean NA NA 9.533e-122 0+ 2.695e-165 Table 4 Biospectra pair- Cosine ISIS Scitegic Protein COSTART MedDRA wise distances CCS± Keys Keys Co-invest Co-citation Co-citation 565,516 (100%) CCS > 0 NA NA 5.34e-015 3.125e-069 9.523e-006 452,388 (80.0%) CCS > 0.1 NA NA 0.1186 1.77e-053 4.50e-039 60,098 (10.8%) CCS > 0.3 NA NA 1.752e-070 0.03791 7.701e-016 25,862 (4.6%) CCS > 0.5 2.999e-038 1.174e-118 1.194e-066 1.702e-091 3.277e-062 5,076 (0.90%) CCS > 0.7 2.716e-012 3.855e-011 3.465e-005 5.936e-018 2.563e-007 Table 5 ISIS key pair- Cosine Biospectra Scitegic Protein COSTART MedDRA wise distances CCS± Keys Co-invest Co-citation Co-citation 565,516 (100%) CCS > 0 NA NA 9.095e-219 NA 7.568e-137 214,537 (37.9%) CCS > 0.5 NA NA NA 9.938-192 NA 41,792 (7.4%) CCS > 0.65 0.1876 NA NA 2.034e-142 6.262e-244 18,471 (3.3%) CCS > 0.70 3.093e-046 NA NA 1.812e-168 1.457e-163 1512 (0.27%) CCS > 0.85 3.771e-008 6.723e-085 7.661e-007 3.516e-015 1.819e-013 Table 6 Scitegic pair- Cosine Biospectra ISIS Protein COSTART MedDRA wise distances CCS± Keys Co-invest Co-citation Co-citation 565,516 (100%) CCS > 0 NA NA NA NA NA 375,629 (66.4%) CCS > 0.2 NA NA NA NA NA 27,631 (4.9%) CCS > 0.3 7.963e-025 NA NA 6.169e-300 NA 8187 (1.5%) CCS > 0.35 2.048e-031 NA 3.006e-163 2.951e-163 2.709e-177 3834 (0.68%) CCS > 0.4 2.395e-010 5.446e-215 1.077e-045 1.851e-059 9.671e-080 * Statistical significance (p-values) of 565,516 pair wise distance comparisons of 1064 medicines using three molecular structure descriptors (biospectra, ISIS and Scitegic keys) and three system-wide drug-effect descriptors (protein co-investigation frequency, COSTART and MedDRA co-citation). + Statistical significance (p = 9.436e- 291) was obtained for 563,392 (99.6%) of the comparisons. ± Confidence in cluster similarity [0 (least similar) to 1(most similar)]. Supplementary Figure 1 Supplementary Figure 1a.

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