Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. Number of phenotypes associated with genes through articles in the AMELIE knowledgebase.
  • Fig. S2. The accelerated accumulation of curatable facts in Mendelian genomics.
  • Fig. S3. Replication of AMELIE’s causative gene ranking performance on 56 clinical patients from Stanford and Manton.
  • Fig. S4. Cross-validation of AMELIE’s causative gene ranking performance on 681 simulated patients.
  • Fig. S5. Essence of the AMELIE interface at https://AMELIE.stanford.edu.
  • Table S1. Full-text gene extraction statistics.
  • Table S2. Extraction statistics from the 100 most used journals.
  • Table S3. Simulated patient details.
  • Table S4. DDD patient details.
  • Table S5. Searching for top-ranked AMELIE articles in OMIM.
  • Table S6. Stanford and Manton clinical patient details.
  • Table S7. Simulated patient gene ranking results.
  • Table S8. Most important features for patients with top-ranked causative genes.
  • Table S9. AMELIE classifier feature ablation results.
  • Table S10. DisGeNET gene ranking results.
  • Table S11. Regular expression patterns used to parse variant type from OMIM allelic variant entries.
  • Table S12. Phenotypes extracted from full-text articles by AMELIE, indicating whether the phenotype was extracted correctly or not.
  • Table S13. Assignment of features to feature groups.
  • References (4160)

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Other Supplementary Material for this manuscript includes the following: