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First commit to move to new ODK

Files that dont affect the old system
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matentzn committed Feb 21, 2019
1 parent f52b145 commit 73c34c2e341417cefaf5aabefd498cbfa201efbe
Showing with 1,359,908 additions and 9 deletions.
  1. +4 −0 .gitignore
  2. +6,039 −0 imports/chebi_import.json
  3. +2,037 −0 imports/chebi_import.obo
  4. +110,677 −0 imports/clo_import.json
  5. +36,058 −0 imports/clo_import.obo
  6. +94,254 −0 imports/go_import.json
  7. +29,830 −0 imports/go_import.obo
  8. +10,404 −0 imports/ncbitaxon_import.json
  9. +3,733 −0 imports/ncbitaxon_import.obo
  10. +2,351 −0 imports/pato_import.json
  11. +899 −0 imports/pato_import.obo
  12. +57,650 −0 imports/pr_import.json
  13. +18,306 −0 imports/pr_import.obo
  14. +7,151 −0 imports/ro_import.json
  15. +2,628 −0 imports/ro_import.obo
  16. +253,294 −0 imports/uberon_import.json
  17. +91,444 −0 imports/uberon_import.obo
  18. +36 −0 patterns/definitions.owl
  19. +37 −0 patterns/pattern.owl
  20. +19,976 −0 reports/cl-obo-report.tsv
  21. +6,039 −0 src/ontology/imports/chebi_import.json
  22. +110,677 −0 src/ontology/imports/clo_import.json
  23. +36,058 −0 src/ontology/imports/clo_import.obo
  24. +94,254 −0 src/ontology/imports/go_import.json
  25. +10,404 −0 src/ontology/imports/ncbitaxon_import.json
  26. +3,733 −0 src/ontology/imports/ncbitaxon_import.obo
  27. +2,351 −0 src/ontology/imports/pato_import.json
  28. +57,650 −0 src/ontology/imports/pr_import.json
  29. +7,151 −0 src/ontology/imports/ro_import.json
  30. +253,294 −0 src/ontology/imports/uberon_import.json
  31. +2,413 −0 src/ontology/reports/basic-report.tsv
  32. +19,976 −0 src/ontology/reports/cl-obo-report.tsv
  33. +9 −0 src/ontology/reports/class-count-by-prefix.tsv
  34. +2,780 −0 src/ontology/reports/edges.tsv
  35. +136 −0 src/ontology/reports/obsoletes.tsv
  36. +4,525 −0 src/ontology/reports/synonyms.tsv
  37. +1,437 −0 src/ontology/reports/xrefs.tsv
  38. +1 −1 src/ontology/run.sh
  39. +2 −0 src/ontology/test
  40. +0 −2 src/patterns/data/clustering/abnormal.tsv
  41. +35 −0 src/patterns/data/clustering/abnormalAnatomicalEntity.ofn
  42. +2 −0 src/patterns/data/clustering/abnormalAnatomicalEntity.tsv
  43. +7 −0 src/patterns/data/clustering/abnormalAnatomicalEntity.txt
  44. +0 −2 src/patterns/data/default/abnormal.tsv
  45. +35 −0 src/patterns/data/default/abnormalAnatomicalEntity.ofn
  46. +2 −0 src/patterns/data/default/abnormalAnatomicalEntity.tsv
  47. +7 −0 src/patterns/data/default/abnormalAnatomicalEntity.txt
  48. +27 −2 src/patterns/definitions.owl
  49. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/X_X_capable_of_X.yaml
  50. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/X_bearer_of_X.yaml
  51. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/X_capable_of_X.yaml
  52. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/X_has_plasma_membrane_part_X.yaml
  53. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/X_part_of_X.yaml
  54. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/abnormalCell.yaml
  55. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/epithelial_cell_part_of_X.yaml
  56. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/fibroblast_part_of_X.yaml
  57. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/glandular_epithelial_cell_part_of_X.yaml
  58. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/secretory_cell_capable_of_X.yaml
  59. 0 src/patterns/{dosdp-patterns → dosdp-pattern-workshop}/smooth_muscle_cell_part_of_X.yaml
  60. +49 −0 src/patterns/dosdp-patterns/abnormalAnatomicalEntity.yaml
  61. +1 −1 src/patterns/dosdp-patterns/external.txt
  62. +27 −1 src/patterns/pattern.owl
  63. +18 −0 src/patterns/pattern_owl_seed.txt
@@ -15,3 +15,7 @@ src/ontology/ed_definitions_merged.owl
src/ontology/patterns
*.tmp.obo
*.tmp.owl
src/ontology/cl-base.json
src/ontology/cl-base.obo
src/ontology/cl.json
src/patterns/all_pattern_terms.txt
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