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  1. dict_new_dppo/alt_hpoid.json +0 -0
  2. dict_new_dppo/id_word_map.json +0 -0
  3. dict_new_dppo/lable.vocab +1 -0
  4. dict_new_dppo/noabb_lemma.dic +0 -0
  5. dict_new_dppo/obo.json +0 -0
  6. dict_new_dppo/word_id_map.json +0 -0
  7. dict_new_fyeco/alt_hpoid.json +408 -0
  8. dict_new_fyeco/id_word_map.json +1876 -0
  9. dict_new_fyeco/lable.vocab +425 -0
  10. dict_new_fyeco/noabb_lemma.dic +947 -0
  11. dict_new_fyeco/obo.json +0 -0
  12. dict_new_fyeco/word_id_map.json +2847 -0
  13. dict_new_hpo/alt_hpoid.json +0 -0
  14. dict_new_hpo/id_word_map.json +0 -0
  15. dict_new_hpo/lable.vocab +0 -0
  16. dict_new_hpo/noabb_lemma.dic +0 -0
  17. dict_new_hpo/obo.json +0 -0
  18. dict_new_hpo/word_id_map.json +0 -0
  19. src/__pycache__/Transformer_keras.cpython-37.pyc +0 -0
  20. src/__pycache__/abbre_resolution.cpython-37.pyc +0 -0
  21. src/__pycache__/combine_result.cpython-37.pyc +0 -0
  22. src/__pycache__/dic_ner.cpython-37.pyc +0 -0
  23. src/__pycache__/ml_ner.cpython-37.pyc +0 -0
  24. src/__pycache__/nn_model.cpython-37.pyc +0 -0
  25. src/__pycache__/nn_represent.cpython-37.pyc +0 -0
  26. src/__pycache__/post_processing.cpython-37.pyc +0 -0
  27. src/__pycache__/restore_index.cpython-37.pyc +0 -0
  28. src/__pycache__/ssplit_tokenzier.cpython-37.pyc +0 -0
  29. src/__pycache__/tagging_text.cpython-37.pyc +0 -0
  30. src/abbre_resolution.py +434 -0
  31. src/combine_result.py +102 -0
  32. src/dic_ner.py +164 -0
  33. src/ml_ner.py +578 -0
  34. src/nn_model.py +150 -0
  35. src/nn_represent.py +338 -0
  36. src/post_processing.py +58 -0
  37. src/restore_index.py +109 -0
  38. src/ssplit_tokenzier.py +45 -0
  39. src/tagging_text.py +102 -0
dict_new_dppo/alt_hpoid.json ADDED
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dict_new_dppo/id_word_map.json ADDED
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dict_new_dppo/lable.vocab ADDED
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dict_new_dppo/noabb_lemma.dic ADDED
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dict_new_dppo/obo.json ADDED
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dict_new_dppo/word_id_map.json ADDED
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dict_new_fyeco/alt_hpoid.json ADDED
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+ "FYECO:0000328": "FYECO:0000328",
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+ "FYECO:0000329": "FYECO:0000329",
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+ "FYECO:0000330": "FYECO:0000330",
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+ "FYECO:0000331": "FYECO:0000331",
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+ "FYECO:0000332": "FYECO:0000332",
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+ "FYECO:0000333": "FYECO:0000333",
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+ "FYECO:0000334": "FYECO:0000334",
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+ "FYECO:0000335": "FYECO:0000335",
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+ "FYECO:0000336": "FYECO:0000336",
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+ "FYECO:0000337": "FYECO:0000337",
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+ "FYECO:0000338": "FYECO:0000338",
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+ "FYECO:0000339": "FYECO:0000339",
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+ "FYECO:0000340": "FYECO:0000340",
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+ "FYECO:0000341": "FYECO:0000341",
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+ "FYECO:0000342": "FYECO:0000342",
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+ "FYECO:0000343": "FYECO:0000343",
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+ "FYECO:0000344": "FYECO:0000344",
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+ "FYECO:0000345": "FYECO:0000345",
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+ "FYECO:0000346": "FYECO:0000346",
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+ "FYECO:0000347": "FYECO:0000347",
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+ "FYECO:0000348": "FYECO:0000348",
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+ "FYECO:0000349": "FYECO:0000349",
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+ "FYECO:0000350": "FYECO:0000350",
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+ "FYECO:0000351": "FYECO:0000351",
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+ "FYECO:0000352": "FYECO:0000352",
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+ "FYECO:0000353": "FYECO:0000353",
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+ "FYECO:0000354": "FYECO:0000354",
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+ "FYECO:0000355": "FYECO:0000355",
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+ "FYECO:0000356": "FYECO:0000356",
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+ "FYECO:0000357": "FYECO:0000357",
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+ "FYECO:0000358": "FYECO:0000358",
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+ "FYECO:0000359": "FYECO:0000359",
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+ "FYECO:0000360": "FYECO:0000360",
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+ "FYECO:0000361": "FYECO:0000361",
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+ "FYECO:0000362": "FYECO:0000362",
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+ "FYECO:0000363": "FYECO:0000363",
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+ "FYECO:0000364": "FYECO:0000364",
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+ "FYECO:0000365": "FYECO:0000365",
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+ "FYECO:0000367": "FYECO:0000367",
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+ "FYECO:0000368": "FYECO:0000368",
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+ "FYECO:0000369": "FYECO:0000369",
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+ "FYECO:0000371": "FYECO:0000371",
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+ "FYECO:0000372": "FYECO:0000372",
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+ "FYECO:0000373": "FYECO:0000373",
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+ "FYECO:0000374": "FYECO:0000374",
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+ "FYECO:0000375": "FYECO:0000375",
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+ "FYECO:0000376": "FYECO:0000376",
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+ "FYECO:0000377": "FYECO:0000377",
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+ "FYECO:0000378": "FYECO:0000378",
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+ "FYECO:0000379": "FYECO:0000379",
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+ "FYECO:0000380": "FYECO:0000380",
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+ "FYECO:0000381": "FYECO:0000381",
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+ "FYECO:0000382": "FYECO:0000382",
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+ "FYECO:0000383": "FYECO:0000383",
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+ "FYECO:0000384": "FYECO:0000384",
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+ "FYECO:0000385": "FYECO:0000385",
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+ "FYECO:0000386": "FYECO:0000386",
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+ "FYECO:0000387": "FYECO:0000387",
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+ "FYECO:0000388": "FYECO:0000388",
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+ "FYECO:0000389": "FYECO:0000389",
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+ "FYECO:0000390": "FYECO:0000390",
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+ "FYECO:0000391": "FYECO:0000391",
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+ "FYECO:0000392": "FYECO:0000392",
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+ "FYECO:0000393": "FYECO:0000393",
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+ "FYECO:0000394": "FYECO:0000394",
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+ "FYECO:0000395": "FYECO:0000395",
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+ "FYECO:0000396": "FYECO:0000396",
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+ "FYECO:0000397": "FYECO:0000397",
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+ "FYECO:0000398": "FYECO:0000398",
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+ "FYECO:0000399": "FYECO:0000399",
372
+ "FYECO:0000400": "FYECO:0000400",
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+ "FYECO:0000401": "FYECO:0000401",
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+ "FYECO:0000402": "FYECO:0000402",
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+ "FYECO:0000404": "FYECO:0000404",
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+ "FYECO:0000405": "FYECO:0000405",
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+ "FYECO:0000406": "FYECO:0000406",
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+ "FYECO:0000407": "FYECO:0000407",
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+ "FYECO:0000408": "FYECO:0000408",
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+ "FYECO:0000409": "FYECO:0000409",
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+ "FYECO:0000410": "FYECO:0000410",
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+ "FYECO:0000411": "FYECO:0000411",
383
+ "FYECO:0000412": "FYECO:0000412",
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+ "FYECO:0000413": "FYECO:0000413",
385
+ "FYECO:0000414": "FYECO:0000414",
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+ "FYECO:0000415": "FYECO:0000415",
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+ "FYECO:0000416": "FYECO:0000416",
388
+ "FYECO:0000417": "FYECO:0000417",
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+ "FYECO:0000418": "FYECO:0000418",
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+ "FYECO:0000419": "FYECO:0000419",
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+ "FYECO:0000420": "FYECO:0000420",
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+ "FYECO:0000421": "FYECO:0000421",
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+ "FYECO:0000422": "FYECO:0000422",
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+ "FYECO:0000423": "FYECO:0000423",
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+ "FYECO:0000424": "FYECO:0000424",
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+ "FYECO:0000425": "FYECO:0000425",
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+ "FYECO:0000426": "FYECO:0000426",
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+ "FYECO:0000427": "FYECO:0000427",
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+ "FYECO:0000428": "FYECO:0000428",
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+ "FYECO:0000429": "FYECO:0000429",
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+ "FYECO:0000430": "FYECO:0000430",
402
+ "FYECO:0000431": "FYECO:0000431",
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+ "FYECO:0000432": "FYECO:0000432",
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+ "FYECO:0000433": "FYECO:0000433",
405
+ "FYECO:0000434": "FYECO:0000434",
406
+ "FYECO:0000435": "FYECO:0000435",
407
+ "FYECO:0000436": "FYECO:0000436"
408
+ }
dict_new_fyeco/id_word_map.json ADDED
@@ -0,0 +1,1876 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "FYECO:0000001": [
3
+ "fission yeast phenotype condition",
4
+ "phenotype condition"
5
+ ],
6
+ "FYECO:0000002": [
7
+ "temperature"
8
+ ],
9
+ "FYECO:0000003": [
10
+ "expression level"
11
+ ],
12
+ "FYECO:0000004": [
13
+ "high temperature",
14
+ "33 degree celsius",
15
+ "33 degrees celsius",
16
+ "34 degree celsius",
17
+ "34 degrees celsius",
18
+ "35 degree celsius",
19
+ "35 degrees celsius",
20
+ "36 degree celsius",
21
+ "36 degrees celsius",
22
+ "37 degree celsius",
23
+ "37 degrees celsius",
24
+ "38 degree celsius",
25
+ "38 degrees celsius",
26
+ "39 degree celsius",
27
+ "39 degrees celsius",
28
+ "40 degree celsius",
29
+ "40 degrees celsius",
30
+ "41 degree celsius",
31
+ "41 degrees celsius",
32
+ "42 degree celsius",
33
+ "42 degrees celsius",
34
+ "43 degree celsius",
35
+ "43 degrees celsius"
36
+ ],
37
+ "FYECO:0000005": [
38
+ "standard temperature",
39
+ "25 degree celsius",
40
+ "25 degrees celsius",
41
+ "26 degree celsius",
42
+ "26 degrees celsius",
43
+ "27 degree celsius",
44
+ "27 degrees celsius",
45
+ "28 degree celsius",
46
+ "28 degrees celsius",
47
+ "29 degree celsius",
48
+ "29 degrees celsius",
49
+ "30 degree celsius",
50
+ "30 degrees celsius",
51
+ "31 degree celsius",
52
+ "31 degrees celsius",
53
+ "32 degree celsius",
54
+ "32 degrees celsius",
55
+ "normal temperature"
56
+ ],
57
+ "FYECO:0000006": [
58
+ "low temperature",
59
+ "17 degree celsius",
60
+ "17 degrees celsius",
61
+ "18 degree celsius",
62
+ "18 degrees celsius",
63
+ "19 degree celsius",
64
+ "19 degrees celsius",
65
+ "20 degree celsius",
66
+ "20 degrees celsius",
67
+ "21 degree celsius",
68
+ "21 degrees celsius",
69
+ "22 degree celsius",
70
+ "22 degrees celsius",
71
+ "23 degree celsius",
72
+ "23 degrees celsius",
73
+ "24 degree celsius",
74
+ "24 degrees celsius",
75
+ "cold"
76
+ ],
77
+ "FYECO:0000007": [
78
+ "overexpression"
79
+ ],
80
+ "FYECO:0000008": [
81
+ "knockdown"
82
+ ],
83
+ "FYECO:0000009": [
84
+ "group growth medium",
85
+ "grouping growth medium"
86
+ ],
87
+ "FYECO:0000010": [
88
+ "absence of chemical"
89
+ ],
90
+ "FYECO:0000018": [
91
+ "absence of chemical"
92
+ ],
93
+ "FYECO:0000011": [
94
+ "grouping limit",
95
+ "grouping limited"
96
+ ],
97
+ "FYECO:0000013": [
98
+ "group define medium",
99
+ "grouping defined medium"
100
+ ],
101
+ "FYECO:0000015": [
102
+ "sporulation medium",
103
+ "malt extract medium",
104
+ "mat medium",
105
+ "mating medium",
106
+ "spa medium"
107
+ ],
108
+ "FYECO:0000016": [
109
+ "high glucose mm",
110
+ "high glucose minimal medium"
111
+ ],
112
+ "FYECO:0000021": [
113
+ "+ limited adenine"
114
+ ],
115
+ "FYECO:0000022": [
116
+ "absence of p - factor"
117
+ ],
118
+ "FYECO:0000023": [
119
+ "presence of 3',5 ' - cyclic amp"
120
+ ],
121
+ "FYECO:0000024": [
122
+ "+ sugar"
123
+ ],
124
+ "FYECO:0000025": [
125
+ "+ sorbitol"
126
+ ],
127
+ "FYECO:0000026": [
128
+ "+ vanadate",
129
+ "sodium orthovanadate add",
130
+ "sodium orthovanadate added"
131
+ ],
132
+ "FYECO:0000027": [
133
+ "presence of mat pheromone",
134
+ "presence of mating pheromone"
135
+ ],
136
+ "FYECO:0000028": [
137
+ "+ tbc"
138
+ ],
139
+ "FYECO:0000030": [
140
+ "+ ion",
141
+ "+ ions"
142
+ ],
143
+ "FYECO:0000031": [
144
+ "+ k ion",
145
+ "+ k ions",
146
+ "potassium ion add",
147
+ "potassium ions added"
148
+ ],
149
+ "FYECO:0000032": [
150
+ "+ cl ion",
151
+ "+ cl ions",
152
+ "chloride ion add",
153
+ "chloride ions added"
154
+ ],
155
+ "FYECO:0000033": [
156
+ "+ cd ion",
157
+ "+ cd ions",
158
+ "cadmium ion add",
159
+ "cadmium ions added"
160
+ ],
161
+ "FYECO:0000034": [
162
+ "+ ca ion",
163
+ "+ ca ions",
164
+ "ca ion add",
165
+ "ca ions added",
166
+ "calcium ion add",
167
+ "calcium ions added"
168
+ ],
169
+ "FYECO:0000035": [
170
+ "+ cu ion",
171
+ "+ cu ions",
172
+ "copper ion add",
173
+ "copper ions added"
174
+ ],
175
+ "FYECO:0000036": [
176
+ "+ pb ion",
177
+ "+ pb ions",
178
+ "lead ion add",
179
+ "lead ions added"
180
+ ],
181
+ "FYECO:0000037": [
182
+ "+ bi ion",
183
+ "+ bi ions",
184
+ "bismuth ion add",
185
+ "bismuth ions added"
186
+ ],
187
+ "FYECO:0000038": [
188
+ "+ mg ion",
189
+ "+ mg ions",
190
+ "magnesium ion add",
191
+ "magnesium ions added"
192
+ ],
193
+ "FYECO:0000039": [
194
+ "+ p - factor",
195
+ "p factor add",
196
+ "p factor added"
197
+ ],
198
+ "FYECO:0000040": [
199
+ "+ m - factor",
200
+ "m factor add",
201
+ "m factor added"
202
+ ],
203
+ "FYECO:0000041": [
204
+ "sugar alcohol add",
205
+ "sugar alcohol added"
206
+ ],
207
+ "FYECO:0000042": [
208
+ "+ fatty acid"
209
+ ],
210
+ "FYECO:0000043": [
211
+ "+ palmitic acid"
212
+ ],
213
+ "FYECO:0000044": [
214
+ "+ myristic acid"
215
+ ],
216
+ "FYECO:0000045": [
217
+ "+ pentadecanoic acid"
218
+ ],
219
+ "FYECO:0000046": [
220
+ "+ margaric acid"
221
+ ],
222
+ "FYECO:0000047": [
223
+ "+ stearic acid"
224
+ ],
225
+ "FYECO:0000048": [
226
+ "+ petroselinic acid"
227
+ ],
228
+ "FYECO:0000049": [
229
+ "+ oleic acid"
230
+ ],
231
+ "FYECO:0000050": [
232
+ "+ linoleic acid"
233
+ ],
234
+ "FYECO:0000051": [
235
+ "+ linolenic acid"
236
+ ],
237
+ "FYECO:0000052": [
238
+ "+ arachidic acid"
239
+ ],
240
+ "FYECO:0000053": [
241
+ "+ melissic acid"
242
+ ],
243
+ "FYECO:0000054": [
244
+ "glycerol mm",
245
+ "glycerol minimal medium"
246
+ ],
247
+ "FYECO:0000077": [
248
+ "glycerol mm",
249
+ "glycerol minimal medium"
250
+ ],
251
+ "FYECO:0000055": [
252
+ "m and p factor produce",
253
+ "m and p factor produced",
254
+ "presence of m - factor and p - factor",
255
+ "presence of mat pheromone",
256
+ "presence of mating pheromones"
257
+ ],
258
+ "FYECO:0000056": [
259
+ "+ 3,5 - cyclic amp"
260
+ ],
261
+ "FYECO:0000057": [
262
+ "3 ' 5 ' - cyclic amp produce",
263
+ "3 ' 5 ' - cyclic amp produced"
264
+ ],
265
+ "FYECO:0000058": [
266
+ "+ mat pheromone",
267
+ "+ mating pheromone"
268
+ ],
269
+ "FYECO:0000059": [
270
+ "chemical add or exclude",
271
+ "chemical added or excluded",
272
+ "chemical add",
273
+ "chemical added",
274
+ "chemical",
275
+ "chemicals"
276
+ ],
277
+ "FYECO:0000017": [
278
+ "chemical add or exclude",
279
+ "chemical added or excluded",
280
+ "chemical add",
281
+ "chemical added",
282
+ "chemical",
283
+ "chemicals"
284
+ ],
285
+ "FYECO:0000019": [
286
+ "chemical add or exclude",
287
+ "chemical added or excluded",
288
+ "chemical add",
289
+ "chemical added",
290
+ "chemical",
291
+ "chemicals"
292
+ ],
293
+ "FYECO:0000020": [
294
+ "chemical add or exclude",
295
+ "chemical added or excluded",
296
+ "chemical add",
297
+ "chemical added",
298
+ "chemical",
299
+ "chemicals"
300
+ ],
301
+ "FYECO:0000060": [
302
+ "chemical produce",
303
+ "chemical produced"
304
+ ],
305
+ "FYECO:0000061": [
306
+ "+ xenobiotic substrate"
307
+ ],
308
+ "FYECO:0000062": [
309
+ "absence of nitrogen"
310
+ ],
311
+ "FYECO:0000063": [
312
+ "absence of 3 ' 5 ' - cyclic amp"
313
+ ],
314
+ "FYECO:0000064": [
315
+ "+ inositol"
316
+ ],
317
+ "FYECO:0000065": [
318
+ "absence of adenine"
319
+ ],
320
+ "FYECO:0000066": [
321
+ "absence of inositol"
322
+ ],
323
+ "FYECO:0000067": [
324
+ "+ lauric acid"
325
+ ],
326
+ "FYECO:0000068": [
327
+ "+ vaccenic acid"
328
+ ],
329
+ "FYECO:0000069": [
330
+ "+ caffeine"
331
+ ],
332
+ "FYECO:0000070": [
333
+ "absence of uracil"
334
+ ],
335
+ "FYECO:0000071": [
336
+ "+ 1 - na - pp1",
337
+ "1 - na - pp1 present",
338
+ "4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine add",
339
+ "4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine added",
340
+ "4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine present"
341
+ ],
342
+ "FYECO:0000072": [
343
+ "glycerol mm with trace glucose",
344
+ "glycerol main carbon source + very low glucose mm",
345
+ "glycerol minimal medium with trace glucose"
346
+ ],
347
+ "FYECO:0000073": [
348
+ "dha minimal medium",
349
+ "dihydroxyacetone mm",
350
+ "dihydroxyactone minimal medium"
351
+ ],
352
+ "FYECO:0000074": [
353
+ "+ nad+"
354
+ ],
355
+ "FYECO:0000075": [
356
+ "+ nadp+"
357
+ ],
358
+ "FYECO:0000076": [
359
+ "+ dihydroxyacetone",
360
+ "dha add",
361
+ "dha added"
362
+ ],
363
+ "FYECO:0000078": [
364
+ "+ h2o2",
365
+ "hydrogen peroxide add",
366
+ "hydrogen peroxide added"
367
+ ],
368
+ "FYECO:0000079": [
369
+ "+ thiabendazole",
370
+ "tbz add",
371
+ "tbz added"
372
+ ],
373
+ "FYECO:0000080": [
374
+ "group rich medium",
375
+ "grouping rich medium"
376
+ ],
377
+ "FYECO:0000081": [
378
+ "low glucose yes",
379
+ "low glucose rich medium",
380
+ "low glucose ye"
381
+ ],
382
+ "FYECO:0000082": [
383
+ "+ arginine"
384
+ ],
385
+ "FYECO:0000084": [
386
+ "+ glutamate"
387
+ ],
388
+ "FYECO:0000085": [
389
+ "+ glutamine"
390
+ ],
391
+ "FYECO:0000086": [
392
+ "+ ornithine"
393
+ ],
394
+ "FYECO:0000087": [
395
+ "+ pro",
396
+ "proline add",
397
+ "proline added"
398
+ ],
399
+ "FYECO:0000088": [
400
+ "+ 2 - og",
401
+ "2 - og present",
402
+ "2 - oxoglutarate add",
403
+ "2 - oxoglutarate added",
404
+ "2 - oxoglutarate present"
405
+ ],
406
+ "FYECO:0000089": [
407
+ "+ na oleate",
408
+ "sodium oleate add",
409
+ "sodium oleate added"
410
+ ],
411
+ "FYECO:0000090": [
412
+ "+ limited nitrogen",
413
+ "nitrogen starvation"
414
+ ],
415
+ "FYECO:0000091": [
416
+ "+ cisplatin"
417
+ ],
418
+ "FYECO:0000092": [
419
+ "+ na ion",
420
+ "+ na ions",
421
+ "sodium ion add",
422
+ "sodium ions added"
423
+ ],
424
+ "FYECO:0000093": [
425
+ "+ li ion",
426
+ "+ li ions",
427
+ "lithium ion add",
428
+ "lithium ions added"
429
+ ],
430
+ "FYECO:0000094": [
431
+ "group sequential growth condition",
432
+ "grouping sequential growth conditions"
433
+ ],
434
+ "FYECO:0000095": [
435
+ "24 - 48h nitrogen starvation follow by 4 - 7 day recovery in rich medium",
436
+ "24 - 48h nitrogen starvation followed by 4 - 7 day recovery in rich medium"
437
+ ],
438
+ "FYECO:0000096": [
439
+ "24 - 48h nitrogen starvation follow by 5 - 12h recovery in rich medium",
440
+ "24 - 48h nitrogen starvation followed by 5 - 12h recovery in rich medium"
441
+ ],
442
+ "FYECO:0000097": [
443
+ "24 - 48h nitrogen starvation follow by 12 - 24h recovery in rich medium",
444
+ "24 - 48h nitrogen starvation followed by 12 - 24h recovery in rich medium"
445
+ ],
446
+ "FYECO:0000098": [
447
+ "72h - 7days nitrogen starvation follow by 12 - 24h recovery in rich medium",
448
+ "72h - 7days nitrogen starvation followed by 12 - 24h recovery in rich medium"
449
+ ],
450
+ "FYECO:0000099": [
451
+ "72h - 7days nitrogen starvation follow by 4 - 7 day recovery in rich medium",
452
+ "72h - 7days nitrogen starvation followed by 4 - 7 days recovery in rich medium"
453
+ ],
454
+ "FYECO:0000100": [
455
+ "water medium"
456
+ ],
457
+ "FYECO:0000101": [
458
+ "medium texture"
459
+ ],
460
+ "FYECO:0000102": [
461
+ "agar plate",
462
+ "agar plates",
463
+ "solid agar plate",
464
+ "solid agar plates"
465
+ ],
466
+ "FYECO:0000103": [
467
+ "liquid culture"
468
+ ],
469
+ "FYECO:0000104": [
470
+ "low glucose mm",
471
+ "low glucose minimal medium"
472
+ ],
473
+ "FYECO:0000105": [
474
+ "+ limited thiamine"
475
+ ],
476
+ "FYECO:0000106": [
477
+ "+ thiamine"
478
+ ],
479
+ "FYECO:0000107": [
480
+ "+ aminopyrimidine"
481
+ ],
482
+ "FYECO:0000108": [
483
+ "+ thiazole"
484
+ ],
485
+ "FYECO:0000109": [
486
+ "group excess",
487
+ "grouping excess"
488
+ ],
489
+ "FYECO:0000110": [
490
+ "nitrogen starvation and recovery",
491
+ "recovery from nitrogen depletion",
492
+ "recovery from nitrogen starvation"
493
+ ],
494
+ "FYECO:0000111": [
495
+ "+ limited myo - inositol",
496
+ "limited inositol add",
497
+ "limited inositol added"
498
+ ],
499
+ "FYECO:0000112": [
500
+ "+ limited phosphate"
501
+ ],
502
+ "FYECO:0000113": [
503
+ "+ calcofluor white"
504
+ ],
505
+ "FYECO:0000114": [
506
+ "+ cyclosporin a"
507
+ ],
508
+ "FYECO:0000115": [
509
+ "+ gtp",
510
+ "+ guanosine triphosphate"
511
+ ],
512
+ "FYECO:0000116": [
513
+ "group heat shock",
514
+ "grouping heat shock"
515
+ ],
516
+ "FYECO:0000117": [
517
+ "heat shock and recovery at normal temperature",
518
+ "heat shock for 20 - 30 min at 48 degree c , preceeded and follow by growth at normal temperature",
519
+ "heat shock for 20 - 30 min at 48 degrees c , preceeded and followed by growth at normal temperature"
520
+ ],
521
+ "FYECO:0000118": [
522
+ "+ glutathione",
523
+ "gsh add",
524
+ "gsh added",
525
+ "l - gamma - glutamyl - l - cysteinylglycine add",
526
+ "l - gamma - glutamyl - l - cysteinylglycine added"
527
+ ],
528
+ "FYECO:0000119": [
529
+ "+ n - acetyl - l - cysteine",
530
+ "acetylcysteine add",
531
+ "acetylcysteine added",
532
+ "nac add",
533
+ "nac added"
534
+ ],
535
+ "FYECO:0000120": [
536
+ "group absent",
537
+ "grouping absent"
538
+ ],
539
+ "FYECO:0000121": [
540
+ "+ methylamine"
541
+ ],
542
+ "FYECO:0000122": [
543
+ "group growth timing",
544
+ "grouping growth timing"
545
+ ],
546
+ "FYECO:0000123": [
547
+ "growth to stationary phase"
548
+ ],
549
+ "FYECO:0000124": [
550
+ "growth to late exponential phase"
551
+ ],
552
+ "FYECO:0000125": [
553
+ "growth to exponential phase"
554
+ ],
555
+ "FYECO:0000126": [
556
+ "glucose mm",
557
+ "glucose minimal medium",
558
+ "normal glucose minimal medium",
559
+ "normal glucose mm",
560
+ "sd medium",
561
+ "standard glucose minimal medium"
562
+ ],
563
+ "FYECO:0000014": [
564
+ "glucose mm",
565
+ "glucose minimal medium",
566
+ "normal glucose minimal medium",
567
+ "normal glucose mm",
568
+ "sd medium",
569
+ "standard glucose minimal medium"
570
+ ],
571
+ "FYECO:0000127": [
572
+ "nitrogen absent",
573
+ "nitrogen exclude",
574
+ "nitrogen excluded",
575
+ "nitrogen free",
576
+ "nitrogen starvation"
577
+ ],
578
+ "FYECO:0000128": [
579
+ "ph"
580
+ ],
581
+ "FYECO:0000129": [
582
+ "high ph",
583
+ "ph 6.8"
584
+ ],
585
+ "FYECO:0000130": [
586
+ "high ph",
587
+ "ph 6.8"
588
+ ],
589
+ "FYECO:0000131": [
590
+ "+ ubiquinone q6",
591
+ "coenzyme q6 add",
592
+ "coenzyme q6 added"
593
+ ],
594
+ "FYECO:0000132": [
595
+ "group experimental environment",
596
+ "grouping experimental environment"
597
+ ],
598
+ "FYECO:0000133": [
599
+ "oxygen level"
600
+ ],
601
+ "FYECO:0000134": [
602
+ "anaerobic environment",
603
+ "- oxygen",
604
+ "anaerobiosis",
605
+ "minus oxygen"
606
+ ],
607
+ "FYECO:0000135": [
608
+ "semi - aerobic environment",
609
+ "hypoxia",
610
+ "hypoxic environment",
611
+ "limited o atom",
612
+ "limited o atoms",
613
+ "limited oxygen",
614
+ "reduce oxygen level",
615
+ "reduced oxygen level",
616
+ "semi aerobic environment",
617
+ "semi - anaerobic environment",
618
+ "semiaerobic environment",
619
+ "semianaerobic environment"
620
+ ],
621
+ "FYECO:0000136": [
622
+ "raffinose ye",
623
+ "raffinose rich medium"
624
+ ],
625
+ "FYECO:0000137": [
626
+ "yes",
627
+ "complex medium",
628
+ "glucose rich medium",
629
+ "normal glucose rich medium",
630
+ "standard dextrose rich medium",
631
+ "standard glucose rich medium"
632
+ ],
633
+ "FYECO:0000012": [
634
+ "yes",
635
+ "complex medium",
636
+ "glucose rich medium",
637
+ "normal glucose rich medium",
638
+ "standard dextrose rich medium",
639
+ "standard glucose rich medium"
640
+ ],
641
+ "FYECO:0000138": [
642
+ "glycerol ye",
643
+ "glycerol rich medium",
644
+ "glycerol sole carbon source rich medium",
645
+ "glycerol sole carbon source ye",
646
+ "non - fermentable glycerol sole carbon source rich medium",
647
+ "nonfermentable glycerol sole carbon source rich medium"
648
+ ],
649
+ "FYECO:0000083": [
650
+ "glycerol ye",
651
+ "glycerol rich medium",
652
+ "glycerol sole carbon source rich medium",
653
+ "glycerol sole carbon source ye",
654
+ "non - fermentable glycerol sole carbon source rich medium",
655
+ "nonfermentable glycerol sole carbon source rich medium"
656
+ ],
657
+ "FYECO:0000139": [
658
+ "glycerol and ethanol rich medium",
659
+ "glycerol + ethanol ye",
660
+ "glycerol and ethanol ye",
661
+ "non - fermentable glycerol and ethanol rich medium",
662
+ "nonfermentable glycerol and ethanol rich medium"
663
+ ],
664
+ "FYECO:0000140": [
665
+ "in vitro"
666
+ ],
667
+ "FYECO:0000141": [
668
+ "in vivo"
669
+ ],
670
+ "FYECO:0000142": [
671
+ "+ ade",
672
+ "+ adenine"
673
+ ],
674
+ "FYECO:0000143": [
675
+ "+ antimycin a",
676
+ "respiratory chain inhibitor"
677
+ ],
678
+ "FYECO:0000144": [
679
+ "sucrose ye",
680
+ "sucrose rich medium"
681
+ ],
682
+ "FYECO:0000145": [
683
+ "maltose mm",
684
+ "maltose minimal medium"
685
+ ],
686
+ "FYECO:0000146": [
687
+ "trehalose mm",
688
+ "trehalose minimal medium"
689
+ ],
690
+ "FYECO:0000147": [
691
+ "sucrose mm",
692
+ "sucrose minimal medium"
693
+ ],
694
+ "FYECO:0000148": [
695
+ "galactose rich medium with trace glucose",
696
+ "non - fermentable galactose and very low glucose rich medium",
697
+ "nonfermentable galactose and very low glucose rich medium",
698
+ "ypgala"
699
+ ],
700
+ "FYECO:0000149": [
701
+ "+ 1 - dnj",
702
+ "1 - deoxynojirimycin add",
703
+ "1 - deoxynojirimycin added",
704
+ "deoxynojirimycin add",
705
+ "deoxynojirimycin added",
706
+ "dnj add",
707
+ "dnj added"
708
+ ],
709
+ "FYECO:0000150": [
710
+ "calcium absent"
711
+ ],
712
+ "FYECO:0000151": [
713
+ "+ mn ion",
714
+ "+ mn ions",
715
+ "manganese ion add",
716
+ "manganese ions added",
717
+ "mn2+ add",
718
+ "mn2+ added"
719
+ ],
720
+ "FYECO:0000152": [
721
+ "+ mannose"
722
+ ],
723
+ "FYECO:0000153": [
724
+ "+ diethyl maleate",
725
+ "diethyl maleate add",
726
+ "diethyl maleate added"
727
+ ],
728
+ "FYECO:0000154": [
729
+ "+ ethanolamine",
730
+ "2 - aminoethanol add",
731
+ "2 - aminoethanol added",
732
+ "eta add",
733
+ "eta added",
734
+ "mea add",
735
+ "mea added",
736
+ "monoethanolamine add",
737
+ "monoethanolamine added"
738
+ ],
739
+ "FYECO:0000155": [
740
+ "+ choline"
741
+ ],
742
+ "FYECO:0000156": [
743
+ "rhodamine - phalloidin add",
744
+ "rhodamine - phalloidin added",
745
+ "rhodamine phalloidin"
746
+ ],
747
+ "FYECO:0000157": [
748
+ "growth to stationary phase in rich medium follow by transfer to h2o",
749
+ "growth to stationary phase in rich medium followed by transfer to h2o"
750
+ ],
751
+ "FYECO:0000158": [
752
+ "group growth to stationary phase",
753
+ "grouping growth to stationary phase"
754
+ ],
755
+ "FYECO:0000159": [
756
+ "growth to stationary phase in rich medium follow by transfer to minimal medium",
757
+ "growth to stationary phase in rich medium followed by transfer to minimal medium"
758
+ ],
759
+ "FYECO:0000160": [
760
+ "+ tacrolimus",
761
+ "fk506 add",
762
+ "fk506 added",
763
+ "tacrolimus add",
764
+ "tacrolimus added"
765
+ ],
766
+ "FYECO:0000029": [
767
+ "+ tacrolimus",
768
+ "fk506 add",
769
+ "fk506 added",
770
+ "tacrolimus add",
771
+ "tacrolimus added"
772
+ ],
773
+ "FYECO:0000161": [
774
+ "hoechst stain add",
775
+ "hoechst stain added",
776
+ "bisbenzimide add",
777
+ "bisbenzimide added"
778
+ ],
779
+ "FYECO:0000162": [
780
+ "high glucose yes",
781
+ "high glucose rich medium"
782
+ ],
783
+ "FYECO:0000163": [
784
+ "fitc - conjugate lectin add",
785
+ "fitc - conjugated lectin added"
786
+ ],
787
+ "FYECO:0000164": [
788
+ "anti - tubulin antibody add",
789
+ "anti - tubulin antibodies added",
790
+ "anti - tubulin antibody added"
791
+ ],
792
+ "FYECO:0000165": [
793
+ "+ na2s",
794
+ "sodium sulfide add",
795
+ "sodium sulfide added"
796
+ ],
797
+ "FYECO:0000166": [
798
+ "+ nacl",
799
+ "sodium chloride add",
800
+ "sodium chloride added"
801
+ ],
802
+ "FYECO:0000167": [
803
+ "+ sd",
804
+ "+ sds",
805
+ "sodium dodecyl sulfate add",
806
+ "sodium dodecyl sulfate added"
807
+ ],
808
+ "FYECO:0000168": [
809
+ "heat shock and recovery at high temperature",
810
+ "heat shock for 20 - 30 min at 48 degree c , preceeded and follow by growth at high temperature",
811
+ "heat shock for 20 - 30 min at 48 degrees c , preceeded and followed by growth at high temperature"
812
+ ],
813
+ "FYECO:0000169": [
814
+ "+ limited ethanolamine"
815
+ ],
816
+ "FYECO:0000170": [
817
+ "+ hu",
818
+ "hydroxyurea add",
819
+ "hydroxyurea added"
820
+ ],
821
+ "FYECO:0000171": [
822
+ "sorbitol absent"
823
+ ],
824
+ "FYECO:0000172": [
825
+ "+ zn ion",
826
+ "+ zn ions",
827
+ "zinc ion add",
828
+ "zinc ions added"
829
+ ],
830
+ "FYECO:0000173": [
831
+ "+ zncl2",
832
+ "zinc chloride add",
833
+ "zinc chloride added"
834
+ ],
835
+ "FYECO:0000174": [
836
+ "+ fecl2",
837
+ "iron chloride add",
838
+ "iron chloride added",
839
+ "iron dichloride add",
840
+ "iron dichloride added",
841
+ "iron ( ii ) chloride"
842
+ ],
843
+ "FYECO:0000175": [
844
+ "+ cdcl2",
845
+ "+ cadmium chloride"
846
+ ],
847
+ "FYECO:0000176": [
848
+ "+ edta",
849
+ "edta add",
850
+ "edta added",
851
+ "ethylenediaminetetraacetic acid add",
852
+ "ethylenediaminetetraacetic acid added"
853
+ ],
854
+ "FYECO:0000177": [
855
+ "+ limited zinc",
856
+ "limited zn add",
857
+ "limited zn added"
858
+ ],
859
+ "FYECO:0000178": [
860
+ "+ meet",
861
+ "+ met",
862
+ "m add",
863
+ "m added",
864
+ "methionine add",
865
+ "methionine added"
866
+ ],
867
+ "FYECO:0000179": [
868
+ "+ cysteine",
869
+ "c add",
870
+ "c added",
871
+ "cys add",
872
+ "cys added"
873
+ ],
874
+ "FYECO:0000180": [
875
+ "+ limit sulfur",
876
+ "+ limited sulfur",
877
+ "limited sulphur add",
878
+ "limited sulphur added"
879
+ ],
880
+ "FYECO:0000181": [
881
+ "+ glucose"
882
+ ],
883
+ "FYECO:0000182": [
884
+ "+ asparagine",
885
+ "asn add",
886
+ "asn added"
887
+ ],
888
+ "FYECO:0000183": [
889
+ "+ alpha - tocopherol",
890
+ "vitamin e add",
891
+ "vitamin e added"
892
+ ],
893
+ "FYECO:0000184": [
894
+ "+ cucl2",
895
+ "copper chloride add",
896
+ "copper chloride added"
897
+ ],
898
+ "FYECO:0000185": [
899
+ "+ limited sodium"
900
+ ],
901
+ "FYECO:0000186": [
902
+ "+ feso4",
903
+ "iron sulfate add",
904
+ "iron sulfate added",
905
+ "iron sulphate add",
906
+ "iron sulphate added"
907
+ ],
908
+ "FYECO:0000187": [
909
+ "pantothenate absent"
910
+ ],
911
+ "FYECO:0000188": [
912
+ "+ pantothenate"
913
+ ],
914
+ "FYECO:0000189": [
915
+ "+ limited pantothenate"
916
+ ],
917
+ "FYECO:0000190": [
918
+ "dapi add",
919
+ "dapi added",
920
+ "4',6 - diamidino - 2 - phenylindole add",
921
+ "4',6 - diamidino - 2 - phenylindole added"
922
+ ],
923
+ "FYECO:0000191": [
924
+ "+ biotin"
925
+ ],
926
+ "FYECO:0000192": [
927
+ "biotin absent"
928
+ ],
929
+ "FYECO:0000193": [
930
+ "+ dethiobiotin",
931
+ "desthiobiotin add",
932
+ "desthiobiotin added"
933
+ ],
934
+ "FYECO:0000194": [
935
+ "+ limited biotin"
936
+ ],
937
+ "FYECO:0000195": [
938
+ "+ limited dethiobiotin",
939
+ "limited desthiobiotin add",
940
+ "limited desthiobiotin added"
941
+ ],
942
+ "FYECO:0000196": [
943
+ "glucose mm , urea nitrogen source",
944
+ "glucose minimal medium , urea nitrogen source",
945
+ "standard glucose minimal medium , urea nitrogen source"
946
+ ],
947
+ "FYECO:0000197": [
948
+ "+ limited nickel"
949
+ ],
950
+ "FYECO:0000198": [
951
+ "+ ni ion",
952
+ "+ ni ions",
953
+ "nickel ion add",
954
+ "nickel ions added"
955
+ ],
956
+ "FYECO:0000199": [
957
+ "+ lys",
958
+ "lysine add",
959
+ "lysine added"
960
+ ],
961
+ "FYECO:0000200": [
962
+ "+ peptone"
963
+ ],
964
+ "FYECO:0000201": [
965
+ "ypd",
966
+ "glucose rich medium , peptone / ye nitrogen source"
967
+ ],
968
+ "FYECO:0000202": [
969
+ "chill cell",
970
+ "chilled cells",
971
+ "cold",
972
+ "ice"
973
+ ],
974
+ "FYECO:0000203": [
975
+ "diploid cell",
976
+ "diploid cells",
977
+ "2n cell",
978
+ "2n cells"
979
+ ],
980
+ "FYECO:0000204": [
981
+ "diploid cell",
982
+ "diploid cells",
983
+ "2n cell",
984
+ "2n cells"
985
+ ],
986
+ "FYECO:0000205": [
987
+ "+ na2so4",
988
+ "sodium sulfate add",
989
+ "sodium sulfate added"
990
+ ],
991
+ "FYECO:0000206": [
992
+ "+ cscl",
993
+ "caesium chloride add",
994
+ "caesium chloride added",
995
+ "cesium chloride add",
996
+ "cesium chloride added"
997
+ ],
998
+ "FYECO:0000207": [
999
+ "+ kcl",
1000
+ "potassium chloride add",
1001
+ "potassium chloride added"
1002
+ ],
1003
+ "FYECO:0000208": [
1004
+ "+ nh4cl",
1005
+ "ammonium chloride add",
1006
+ "ammonium chloride added"
1007
+ ],
1008
+ "FYECO:0000209": [
1009
+ "+ biochanin a",
1010
+ "bca add",
1011
+ "bca added"
1012
+ ],
1013
+ "FYECO:0000210": [
1014
+ "+ limit glucose",
1015
+ "+ limited glucose"
1016
+ ],
1017
+ "FYECO:0000211": [
1018
+ "+ mm",
1019
+ "+ mms",
1020
+ "methyl methanesulfonate add",
1021
+ "methyl methanesulfonate added"
1022
+ ],
1023
+ "FYECO:0000212": [
1024
+ "+ ethanol"
1025
+ ],
1026
+ "FYECO:0000213": [
1027
+ "non - fermentable carbon source medium",
1028
+ "non - fermentable carbon sources medium"
1029
+ ],
1030
+ "FYECO:0000214": [
1031
+ "+ mgcl2",
1032
+ "magnesium chloride add",
1033
+ "magnesium chloride added"
1034
+ ],
1035
+ "FYECO:0000215": [
1036
+ "low ph"
1037
+ ],
1038
+ "FYECO:0000216": [
1039
+ "growth < 24 hr",
1040
+ "growth < 24 hrs",
1041
+ "growth < 24 hour",
1042
+ "growth < 24 hours",
1043
+ "overnight culture"
1044
+ ],
1045
+ "FYECO:0000217": [
1046
+ "growth > 24 hr",
1047
+ "growth > 24 hrs",
1048
+ "growth > 24 hour",
1049
+ "growth > 24 hours"
1050
+ ],
1051
+ "FYECO:0000218": [
1052
+ "+ beta - estradiol"
1053
+ ],
1054
+ "FYECO:0000219": [
1055
+ "nitrogen source shift , proline to glutamate"
1056
+ ],
1057
+ "FYECO:0000220": [
1058
+ "nitrogen source shift , glutamate to proline"
1059
+ ],
1060
+ "FYECO:0000221": [
1061
+ "nitrogen source shift"
1062
+ ],
1063
+ "FYECO:0000222": [
1064
+ "+ nocodazole"
1065
+ ],
1066
+ "FYECO:0000223": [
1067
+ "+ 1 - nm - pp1"
1068
+ ],
1069
+ "FYECO:0000224": [
1070
+ "+ his",
1071
+ "histidine add",
1072
+ "histidine added"
1073
+ ],
1074
+ "FYECO:0000225": [
1075
+ "+ ura",
1076
+ "uracil add",
1077
+ "uracil added"
1078
+ ],
1079
+ "FYECO:0000226": [
1080
+ "+ leu",
1081
+ "leucine add",
1082
+ "leucine added"
1083
+ ],
1084
+ "FYECO:0000227": [
1085
+ "permissive temperature"
1086
+ ],
1087
+ "FYECO:0000228": [
1088
+ "semi - permissive temperature",
1089
+ "semipermissive temperature"
1090
+ ],
1091
+ "FYECO:0000229": [
1092
+ "restrictive temperature",
1093
+ "non - permissive temperature",
1094
+ "nonpermissive temperature"
1095
+ ],
1096
+ "FYECO:0000230": [
1097
+ "low nitrogen glucose mm",
1098
+ "low nitrogen glucose minimal medium"
1099
+ ],
1100
+ "FYECO:0000231": [
1101
+ "+ na2so3",
1102
+ "sodium sulfite add",
1103
+ "sodium sulfite added"
1104
+ ],
1105
+ "FYECO:0000232": [
1106
+ "temperature shift , low to standard",
1107
+ "growth at low temperature follow by growth at standard temperature",
1108
+ "growth at low temperature followed by growth at standard temperature"
1109
+ ],
1110
+ "FYECO:0000233": [
1111
+ "uracil absent"
1112
+ ],
1113
+ "FYECO:0000234": [
1114
+ "+ sulfite"
1115
+ ],
1116
+ "FYECO:0000235": [
1117
+ "+ microtubule depolymerizing drug",
1118
+ "+ microtubule depolymerizing drugs"
1119
+ ],
1120
+ "FYECO:0000236": [
1121
+ "maltose ye",
1122
+ "maltose rich medium"
1123
+ ],
1124
+ "FYECO:0000237": [
1125
+ "growth > 48 hr",
1126
+ "growth > 48 hrs",
1127
+ "growth > 48 hour",
1128
+ "growth > 48 hours"
1129
+ ],
1130
+ "FYECO:0000238": [
1131
+ "group condition combination",
1132
+ "grouping condition combinations"
1133
+ ],
1134
+ "FYECO:0000239": [
1135
+ "group starvation and timing",
1136
+ "grouping starvation and timing"
1137
+ ],
1138
+ "FYECO:0000240": [
1139
+ "> 7 day nitrogen starvation",
1140
+ "> 7 days nitrogen starvation"
1141
+ ],
1142
+ "FYECO:0000241": [
1143
+ "28 day nitrogen starvation follow by 10 - 50 hour recovery in minimal medium",
1144
+ "28 days nitrogen starvation followed by 10 - 50 hours recovery in minimal medium"
1145
+ ],
1146
+ "FYECO:0000242": [
1147
+ "+ rapamycin",
1148
+ "+ sirolimus"
1149
+ ],
1150
+ "FYECO:0000243": [
1151
+ "+ lmb",
1152
+ "+ leptomycin b"
1153
+ ],
1154
+ "FYECO:0000244": [
1155
+ "+ 3mb - pp1"
1156
+ ],
1157
+ "FYECO:0000245": [
1158
+ "+ phosphate"
1159
+ ],
1160
+ "FYECO:0000246": [
1161
+ "glucose mm , proline nitrogen source"
1162
+ ],
1163
+ "FYECO:0000247": [
1164
+ "+ cdso4",
1165
+ "+ cadmium sulfate"
1166
+ ],
1167
+ "FYECO:0000248": [
1168
+ "+ lata",
1169
+ "+ latrunculin a"
1170
+ ],
1171
+ "FYECO:0000249": [
1172
+ "+ cuso4",
1173
+ "+ copper ( ii ) sulfate"
1174
+ ],
1175
+ "FYECO:0000250": [
1176
+ "+ agno3",
1177
+ "+ silver nitrate"
1178
+ ],
1179
+ "FYECO:0000251": [
1180
+ "+ amitrole",
1181
+ "+ 3 - amino - 1,2,4 - triazole"
1182
+ ],
1183
+ "FYECO:0000252": [
1184
+ "+ glycerol",
1185
+ "glycerol add",
1186
+ "glycerol added"
1187
+ ],
1188
+ "FYECO:0000253": [
1189
+ "+ limited ammonium",
1190
+ "+ limited nh4cl"
1191
+ ],
1192
+ "FYECO:0000254": [
1193
+ "glucose mm , ammonium nitrogen source"
1194
+ ],
1195
+ "FYECO:0000255": [
1196
+ "arginine absent"
1197
+ ],
1198
+ "FYECO:0000256": [
1199
+ "glycerol mm with trace ethanol"
1200
+ ],
1201
+ "FYECO:0000257": [
1202
+ "+ cycloheximide"
1203
+ ],
1204
+ "FYECO:0000258": [
1205
+ "+ arsenate"
1206
+ ],
1207
+ "FYECO:0000259": [
1208
+ "+ arsenic"
1209
+ ],
1210
+ "FYECO:0000260": [
1211
+ "hu block and release"
1212
+ ],
1213
+ "FYECO:0000261": [
1214
+ "+ cacl2",
1215
+ "+ calcium chloride"
1216
+ ],
1217
+ "FYECO:0000262": [
1218
+ "glucose minimal medium , exclude nitrogen",
1219
+ "glucose minimal medium , excluding nitrogen"
1220
+ ],
1221
+ "FYECO:0000263": [
1222
+ "glucose mm , glutamate nitrogen source",
1223
+ "glucose minimal medium , glutamate nitrogen source",
1224
+ "standard glucose minimal medium , glutamate nitrogen source"
1225
+ ],
1226
+ "FYECO:0000264": [
1227
+ "glucose mm , organic nitrogen source , no inorganic nitrogen"
1228
+ ],
1229
+ "FYECO:0000265": [
1230
+ "> 6 hr in nitrogen starvation",
1231
+ "> 6 hrs in nitrogen starvation",
1232
+ "> 6 hour in nitrogen starvation",
1233
+ "> 6 hours in nitrogen starvation"
1234
+ ],
1235
+ "FYECO:0000266": [
1236
+ "glucose mm , xanthine nitrogen source"
1237
+ ],
1238
+ "FYECO:0000267": [
1239
+ "+ naphthaleneacetic acid"
1240
+ ],
1241
+ "FYECO:0000268": [
1242
+ "+ trichostatin a"
1243
+ ],
1244
+ "FYECO:0000269": [
1245
+ "+ mevalonate"
1246
+ ],
1247
+ "FYECO:0000270": [
1248
+ "+ tev protease"
1249
+ ],
1250
+ "FYECO:0000271": [
1251
+ "+ snp",
1252
+ "+ sodium nitroprusside"
1253
+ ],
1254
+ "FYECO:0000272": [
1255
+ "glucose mm , no nitrogen"
1256
+ ],
1257
+ "FYECO:0000273": [
1258
+ "glucose mm , no glucose"
1259
+ ],
1260
+ "FYECO:0000274": [
1261
+ "glucose mm , adenine nitrogen source"
1262
+ ],
1263
+ "FYECO:0000275": [
1264
+ "competitive culture"
1265
+ ],
1266
+ "FYECO:0000276": [
1267
+ "glucose mm , uracil nitrogen source"
1268
+ ],
1269
+ "FYECO:0000277": [
1270
+ "+ bleomycin"
1271
+ ],
1272
+ "FYECO:0000278": [
1273
+ "glucose mm , isoleucine nitrogen source"
1274
+ ],
1275
+ "FYECO:0000279": [
1276
+ "+ mncl2",
1277
+ "manganese chloride add",
1278
+ "manganese chloride added"
1279
+ ],
1280
+ "FYECO:0000280": [
1281
+ "+ limited leucine"
1282
+ ],
1283
+ "FYECO:0000281": [
1284
+ "+ fecl3",
1285
+ "iron chloride add",
1286
+ "iron chloride added",
1287
+ "iron trichloride add",
1288
+ "iron trichloride added",
1289
+ "iron ( iii ) chloride"
1290
+ ],
1291
+ "FYECO:0000282": [
1292
+ "+ limited aminolevulinic acid",
1293
+ "+ limited ala"
1294
+ ],
1295
+ "FYECO:0000283": [
1296
+ "+ hemin"
1297
+ ],
1298
+ "FYECO:0000284": [
1299
+ "+ thiosulfate"
1300
+ ],
1301
+ "FYECO:0000285": [
1302
+ "cold shock and recovery at normal temperature"
1303
+ ],
1304
+ "FYECO:0000286": [
1305
+ "glucose mm , no adenine"
1306
+ ],
1307
+ "FYECO:0000287": [
1308
+ "+ nigericin"
1309
+ ],
1310
+ "FYECO:0000288": [
1311
+ "temperature shift , high to standard",
1312
+ "growth at high temperature follow by growth at standard temperature",
1313
+ "growth at high temperature followed by growth at standard temperature"
1314
+ ],
1315
+ "FYECO:0000289": [
1316
+ "galactose mm"
1317
+ ],
1318
+ "FYECO:0000290": [
1319
+ "+ carbendazim",
1320
+ "cbz add",
1321
+ "cbz added",
1322
+ "mbc add",
1323
+ "mbc added",
1324
+ "mecarzole add",
1325
+ "mecarzole added"
1326
+ ],
1327
+ "FYECO:0000291": [
1328
+ "temperature block and release"
1329
+ ],
1330
+ "FYECO:0000292": [
1331
+ "nitrogen starvation at normal temperature and shift to high temperature in rich medium"
1332
+ ],
1333
+ "FYECO:0000293": [
1334
+ "temperature shift , low to high"
1335
+ ],
1336
+ "FYECO:0000294": [
1337
+ "temperature shift , high to low"
1338
+ ],
1339
+ "FYECO:0000295": [
1340
+ "two - step temperature shift , low to standard , standard to high"
1341
+ ],
1342
+ "FYECO:0000296": [
1343
+ "glucose mm , phenylalanine nitrogen source"
1344
+ ],
1345
+ "FYECO:0000297": [
1346
+ "+ naaso2",
1347
+ "sodium arsenite add",
1348
+ "sodium arsenite added"
1349
+ ],
1350
+ "FYECO:0000298": [
1351
+ "+ zymolyase"
1352
+ ],
1353
+ "FYECO:0000299": [
1354
+ "+ queuosine"
1355
+ ],
1356
+ "FYECO:0000300": [
1357
+ "temperature shift , standard to high"
1358
+ ],
1359
+ "FYECO:0000301": [
1360
+ "+ queuine"
1361
+ ],
1362
+ "FYECO:0000302": [
1363
+ "+ ammonium iron ( 2+ ) sulfate",
1364
+ "+ ferrous ammonium sulfate ( anhydrous )"
1365
+ ],
1366
+ "FYECO:0000303": [
1367
+ "+ menadione"
1368
+ ],
1369
+ "FYECO:0000304": [
1370
+ "+ tbhp",
1371
+ "tert - butyl hydroperoxide"
1372
+ ],
1373
+ "FYECO:0000305": [
1374
+ "ionize radiation",
1375
+ "ionizing radiation",
1376
+ "gamma irradiation",
1377
+ "gamma radiation"
1378
+ ],
1379
+ "FYECO:0000306": [
1380
+ "two - step temperature shift , standard to low , low to high"
1381
+ ],
1382
+ "FYECO:0000307": [
1383
+ "+ cutin - 1"
1384
+ ],
1385
+ "FYECO:0000308": [
1386
+ "+ doxorubicin",
1387
+ "+ 14 - hydroxydaunomycin",
1388
+ "+ 14 - hydroxydaunorubicine",
1389
+ "+ adriamycin"
1390
+ ],
1391
+ "FYECO:0000309": [
1392
+ "nitrogen starvation follow by heat shock and recovery at normal temperature",
1393
+ "nitrogen starvation followed by heat shock and recovery at normal temperature",
1394
+ "nitrogen starvation follow by heat shock and recovery at permissive temperature",
1395
+ "nitrogen starvation followed by heat shock and recovery at permissive temperature"
1396
+ ],
1397
+ "FYECO:0000310": [
1398
+ "glucose starvation and recovery"
1399
+ ],
1400
+ "FYECO:0000311": [
1401
+ "+ cocl2",
1402
+ "+ cobalt chloride"
1403
+ ],
1404
+ "FYECO:0000312": [
1405
+ "+ sam",
1406
+ "+ s - adenosyl - l - methionine",
1407
+ "+ s - adenosylmethionine"
1408
+ ],
1409
+ "FYECO:0000313": [
1410
+ "+ top - 53"
1411
+ ],
1412
+ "FYECO:0000314": [
1413
+ "+ cpt",
1414
+ "+ camptothecin"
1415
+ ],
1416
+ "FYECO:0000315": [
1417
+ "uv",
1418
+ "ultraviolet light",
1419
+ "uv irradiation"
1420
+ ],
1421
+ "FYECO:0000316": [
1422
+ "+ limited uracil"
1423
+ ],
1424
+ "FYECO:0000317": [
1425
+ "+ urea",
1426
+ "urea add",
1427
+ "urea added"
1428
+ ],
1429
+ "FYECO:0000318": [
1430
+ "+ compactin"
1431
+ ],
1432
+ "FYECO:0000319": [
1433
+ "+ bfa",
1434
+ "+ brefeldin a"
1435
+ ],
1436
+ "FYECO:0000320": [
1437
+ "+ oleate"
1438
+ ],
1439
+ "FYECO:0000321": [
1440
+ "+ copper chelator",
1441
+ "+ tetrathiomolybdate"
1442
+ ],
1443
+ "FYECO:0000322": [
1444
+ "+ bortezomib"
1445
+ ],
1446
+ "FYECO:0000323": [
1447
+ "cold shock and recovery at high temperature"
1448
+ ],
1449
+ "FYECO:0000324": [
1450
+ "+ latb",
1451
+ "+ latrunculin b"
1452
+ ],
1453
+ "FYECO:0000325": [
1454
+ "+ ethylene glycol"
1455
+ ],
1456
+ "FYECO:0000326": [
1457
+ "+ 4 - nqo",
1458
+ "+ 4 - nitroquinoline n - oxide"
1459
+ ],
1460
+ "FYECO:0000327": [
1461
+ "+ mg132",
1462
+ "proteasome inhibitor"
1463
+ ],
1464
+ "FYECO:0000328": [
1465
+ "lnb glucose medium"
1466
+ ],
1467
+ "FYECO:0000329": [
1468
+ "+ formamide"
1469
+ ],
1470
+ "FYECO:0000330": [
1471
+ "+ limited iron"
1472
+ ],
1473
+ "FYECO:0000331": [
1474
+ "glucose mm , arginine nitrogen source",
1475
+ "glucose minimal medium , arginine nitrogen source"
1476
+ ],
1477
+ "FYECO:0000332": [
1478
+ "+ 2 - dg",
1479
+ "2 - deoxy - d - glucose add",
1480
+ "2 - deoxy - d - glucose added",
1481
+ "2 - deoxyglucose add",
1482
+ "2 - deoxyglucose added"
1483
+ ],
1484
+ "FYECO:0000333": [
1485
+ "+ 20 standard aa 's",
1486
+ "22 standard amino acid add",
1487
+ "22 standard amino acids added"
1488
+ ],
1489
+ "FYECO:0000334": [
1490
+ "+ phloxine b"
1491
+ ],
1492
+ "FYECO:0000335": [
1493
+ "+ ap20187"
1494
+ ],
1495
+ "FYECO:0000336": [
1496
+ "+ cerulenin"
1497
+ ],
1498
+ "FYECO:0000337": [
1499
+ "inorganic phosphate absent"
1500
+ ],
1501
+ "FYECO:0000338": [
1502
+ "+ 3 - brb - pp1"
1503
+ ],
1504
+ "FYECO:0000339": [
1505
+ "+ auxin"
1506
+ ],
1507
+ "FYECO:0000340": [
1508
+ "+ iron chelator"
1509
+ ],
1510
+ "FYECO:0000341": [
1511
+ "+ dtt",
1512
+ "+ dithiothreitol"
1513
+ ],
1514
+ "FYECO:0000342": [
1515
+ "+ icrf - 193"
1516
+ ],
1517
+ "FYECO:0000343": [
1518
+ "+ ( nh4 ) 2so4",
1519
+ "+ ammonium sulfate"
1520
+ ],
1521
+ "FYECO:0000344": [
1522
+ "+ mnso4",
1523
+ "+ manganese sulfate"
1524
+ ],
1525
+ "FYECO:0000345": [
1526
+ "zinc starvation follow by zinc shock",
1527
+ "zinc starvation followed by zinc shock"
1528
+ ],
1529
+ "FYECO:0000346": [
1530
+ "synchronous culture"
1531
+ ],
1532
+ "FYECO:0000347": [
1533
+ "+ vanoxerine"
1534
+ ],
1535
+ "FYECO:0000348": [
1536
+ "+ hexestrol"
1537
+ ],
1538
+ "FYECO:0000349": [
1539
+ "+ clomifene",
1540
+ "+ clomiphene"
1541
+ ],
1542
+ "FYECO:0000350": [
1543
+ "+ ketoconazole"
1544
+ ],
1545
+ "FYECO:0000351": [
1546
+ "+ terconazole"
1547
+ ],
1548
+ "FYECO:0000352": [
1549
+ "+ aminolevulinic acid"
1550
+ ],
1551
+ "FYECO:0000353": [
1552
+ "+ agnp",
1553
+ "+ silver nanoparticles"
1554
+ ],
1555
+ "FYECO:0000354": [
1556
+ "+ phleomycin"
1557
+ ],
1558
+ "FYECO:0000355": [
1559
+ "+ r - limonene",
1560
+ "+ ( 4r ) - limonene"
1561
+ ],
1562
+ "FYECO:0000356": [
1563
+ "+ ck - 666"
1564
+ ],
1565
+ "FYECO:0000357": [
1566
+ "+ aspartate",
1567
+ "+ asp"
1568
+ ],
1569
+ "FYECO:0000358": [
1570
+ "yes + galactose",
1571
+ "rich medium with glucose and galactose"
1572
+ ],
1573
+ "FYECO:0000359": [
1574
+ "+ clotrimazole"
1575
+ ],
1576
+ "FYECO:0000360": [
1577
+ "+ terbinafine"
1578
+ ],
1579
+ "FYECO:0000361": [
1580
+ "+ acetaldehyde"
1581
+ ],
1582
+ "FYECO:0000362": [
1583
+ "+ formaldehyde"
1584
+ ],
1585
+ "FYECO:0000363": [
1586
+ "two - step temperature shift , standard to high , high to standard"
1587
+ ],
1588
+ "FYECO:0000364": [
1589
+ "+ diamide",
1590
+ "+ n , n , n ' , n ' - tetramethyldiazene - 1,2 - dicarboxamide"
1591
+ ],
1592
+ "FYECO:0000365": [
1593
+ "mbc block and release"
1594
+ ],
1595
+ "FYECO:0000366": [
1596
+ "single passage culture"
1597
+ ],
1598
+ "FYECO:0000367": [
1599
+ "multiple passage culture"
1600
+ ],
1601
+ "FYECO:0000368": [
1602
+ "+ tamoxifen"
1603
+ ],
1604
+ "FYECO:0000369": [
1605
+ "+ beta - glucanase"
1606
+ ],
1607
+ "FYECO:0000370": [
1608
+ "+ foa",
1609
+ "+ 5 - fluoroorotic acid"
1610
+ ],
1611
+ "FYECO:0000371": [
1612
+ "+ dmso",
1613
+ "+ dimethyl sulfoxide"
1614
+ ],
1615
+ "FYECO:0000372": [
1616
+ "+ manumycin a",
1617
+ "+ manu - a"
1618
+ ],
1619
+ "FYECO:0000373": [
1620
+ "+ thiolutin"
1621
+ ],
1622
+ "FYECO:0000374": [
1623
+ "glucose mm , serine nitrogen source",
1624
+ "glucose minimal medium , serine nitrogen source"
1625
+ ],
1626
+ "FYECO:0000375": [
1627
+ "+ streptonigrin"
1628
+ ],
1629
+ "FYECO:0000376": [
1630
+ "pyruvate mm",
1631
+ "pyruvate minimal medium"
1632
+ ],
1633
+ "FYECO:0000377": [
1634
+ "+ 5 - fu",
1635
+ "+ 5 - fluorouracil"
1636
+ ],
1637
+ "FYECO:0000378": [
1638
+ "+ respiratory chain inhibitor",
1639
+ "+ electron transport chain inhibitor",
1640
+ "+ mitochondrial complex iii / iv inhibitor",
1641
+ "+ respiratory complex iii inhibitor"
1642
+ ],
1643
+ "FYECO:0000379": [
1644
+ "+ diuron",
1645
+ "+ 3 - ( 3,4 - dichlorophenyl ) - 1,1 - dimethylurea",
1646
+ "+ respiratory chain inhibitor"
1647
+ ],
1648
+ "FYECO:0000380": [
1649
+ "+ nan3",
1650
+ "+ respiratory chain inhibitor",
1651
+ "+ sodium azide"
1652
+ ],
1653
+ "FYECO:0000381": [
1654
+ "thiamine absent"
1655
+ ],
1656
+ "FYECO:0000382": [
1657
+ "fructose mm",
1658
+ "fructose minimal medium"
1659
+ ],
1660
+ "FYECO:0000383": [
1661
+ "wild type cell of opposite mating type add to culture",
1662
+ "wild type cells of opposite mating type added to culture",
1663
+ "mat with wt",
1664
+ "mating with wt"
1665
+ ],
1666
+ "FYECO:0000384": [
1667
+ "isogenic cell of opposite mating type add to culture",
1668
+ "isogenic cells of opposite mating type added to culture",
1669
+ "self mating"
1670
+ ],
1671
+ "FYECO:0000385": [
1672
+ "+ fluconazole"
1673
+ ],
1674
+ "FYECO:0000386": [
1675
+ "cpt block and release"
1676
+ ],
1677
+ "FYECO:0000387": [
1678
+ "+ tebuconazole"
1679
+ ],
1680
+ "FYECO:0000388": [
1681
+ "+ mpa",
1682
+ "+ mycophenolic acid"
1683
+ ],
1684
+ "FYECO:0000389": [
1685
+ "glucose mm , sulfate sulfur source",
1686
+ "glucose minimal medium , sulfate sulfur source",
1687
+ "glucose minimal medium , sulphate sulphur source",
1688
+ "glucose mm , sulphate sulphur source"
1689
+ ],
1690
+ "FYECO:0000390": [
1691
+ "+ torin1",
1692
+ "torin1"
1693
+ ],
1694
+ "FYECO:0000391": [
1695
+ "+ echinocandin"
1696
+ ],
1697
+ "FYECO:0000392": [
1698
+ "+ caspofungin"
1699
+ ],
1700
+ "FYECO:0000393": [
1701
+ "+ caspofungin sld"
1702
+ ],
1703
+ "FYECO:0000394": [
1704
+ "+ caspofungin ld"
1705
+ ],
1706
+ "FYECO:0000395": [
1707
+ "+ micafungin"
1708
+ ],
1709
+ "FYECO:0000396": [
1710
+ "+ micafungin sld"
1711
+ ],
1712
+ "FYECO:0000397": [
1713
+ "+ micafungin ld"
1714
+ ],
1715
+ "FYECO:0000398": [
1716
+ "+ anidulafungin"
1717
+ ],
1718
+ "FYECO:0000399": [
1719
+ "+ anidulafungin sld"
1720
+ ],
1721
+ "FYECO:0000400": [
1722
+ "+ anidulafungin ld"
1723
+ ],
1724
+ "FYECO:0000401": [
1725
+ "transient amino acid starvation < 1 hour"
1726
+ ],
1727
+ "FYECO:0000402": [
1728
+ "xylose add",
1729
+ "xylose added"
1730
+ ],
1731
+ "FYECO:0000404": [
1732
+ "+ zinc sulfate",
1733
+ "+ zinc sulphate"
1734
+ ],
1735
+ "FYECO:0000405": [
1736
+ "+ ile",
1737
+ "isoleucine add",
1738
+ "isoleucine added"
1739
+ ],
1740
+ "FYECO:0000406": [
1741
+ "+ val",
1742
+ "valine add",
1743
+ "valine added"
1744
+ ],
1745
+ "FYECO:0000407": [
1746
+ "+ benzamidine",
1747
+ "benzamidine add",
1748
+ "benzamidine added"
1749
+ ],
1750
+ "FYECO:0000408": [
1751
+ "+ canavanin",
1752
+ "canavanin add",
1753
+ "canavanin added"
1754
+ ],
1755
+ "FYECO:0000409": [
1756
+ "+ 2,2 ' - dipyridyl",
1757
+ "2,2 ' - dipyridyl add",
1758
+ "2,2 ' - dipyridyl added"
1759
+ ],
1760
+ "FYECO:0000410": [
1761
+ "+ 3,4 - dihydrocoumarin",
1762
+ "3,4 - dihydrocoumarin add",
1763
+ "3,4 - dihydrocoumarin added"
1764
+ ],
1765
+ "FYECO:0000411": [
1766
+ "+ egtazic acid",
1767
+ "egtazic acid add",
1768
+ "egtazic acid added",
1769
+ "egta add",
1770
+ "egta added"
1771
+ ],
1772
+ "FYECO:0000412": [
1773
+ "+ tunicamycin",
1774
+ "tunicamycin add",
1775
+ "tunicamycin added"
1776
+ ],
1777
+ "FYECO:0000413": [
1778
+ "+ valproic acid",
1779
+ "valproic acid add",
1780
+ "valproic acid added"
1781
+ ],
1782
+ "FYECO:0000414": [
1783
+ "xylose ye",
1784
+ "xylose rich medium"
1785
+ ],
1786
+ "FYECO:0000415": [
1787
+ "+ tea tree oil",
1788
+ "tea tree oil add",
1789
+ "tea tree oil added"
1790
+ ],
1791
+ "FYECO:0000416": [
1792
+ "glucose mm , cysteine nitrogen source",
1793
+ "glucose minimal medium , cysteine nitrogen source",
1794
+ "standard glucose minimal medium , cysteine nitrogen source"
1795
+ ],
1796
+ "FYECO:0000417": [
1797
+ "glucose mm , methionine nitrogen source",
1798
+ "glucose minimal medium , methionine nitrogen source",
1799
+ "standard glucose minimal medium , methionine nitrogen source"
1800
+ ],
1801
+ "FYECO:0000418": [
1802
+ "leucine absent"
1803
+ ],
1804
+ "FYECO:0000419": [
1805
+ "+ ethyl methanesulfonate"
1806
+ ],
1807
+ "FYECO:0000420": [
1808
+ "+ ferrichrome"
1809
+ ],
1810
+ "FYECO:0000421": [
1811
+ "+ ( 8e,10s ) - 10 - hydroxy - 8 - octadecenoic acid",
1812
+ "+ ( r , z ) - 10 - hydroxyoctadec - 8 - enoic acid"
1813
+ ],
1814
+ "FYECO:0000422": [
1815
+ "no glucose yes"
1816
+ ],
1817
+ "FYECO:0000423": [
1818
+ "+ ciclopirox olamine"
1819
+ ],
1820
+ "FYECO:0000424": [
1821
+ "+ amorolfine"
1822
+ ],
1823
+ "FYECO:0000425": [
1824
+ "x - ray",
1825
+ "x - rays",
1826
+ "x ray",
1827
+ "x rays"
1828
+ ],
1829
+ "FYECO:0000426": [
1830
+ "glucose mm , lysine nitrogen source",
1831
+ "glucose minimal medium , lysine nitrogen source",
1832
+ "standard glucose minimal medium , lysine nitrogen source"
1833
+ ],
1834
+ "FYECO:0000427": [
1835
+ "fructose ye",
1836
+ "fructose rich medium"
1837
+ ],
1838
+ "FYECO:0000428": [
1839
+ "ethanol ye",
1840
+ "ethanol rich medium"
1841
+ ],
1842
+ "FYECO:0000429": [
1843
+ "ye with trace glucose",
1844
+ "very low glucose ye",
1845
+ "rich medium with trace glucose"
1846
+ ],
1847
+ "FYECO:0000430": [
1848
+ "mm with trace glucose",
1849
+ "very low glucose mm",
1850
+ "minimal medium with trace glucose"
1851
+ ],
1852
+ "FYECO:0000431": [
1853
+ "+ itraconazole"
1854
+ ],
1855
+ "FYECO:0000432": [
1856
+ "galactose ye",
1857
+ "galactose rich medium"
1858
+ ],
1859
+ "FYECO:0000433": [
1860
+ "mannitol ye",
1861
+ "mannitol rich medium"
1862
+ ],
1863
+ "FYECO:0000434": [
1864
+ "transient hydroxyurea treatment",
1865
+ "acute hydroxyurea treatment"
1866
+ ],
1867
+ "FYECO:0000435": [
1868
+ "+ cccp",
1869
+ "an experimental condition in which carbonyl cyanide m - chlorophenyl hydrazone be add to the medium or assay buffer in excess compare to standard medium or assay buffer .",
1870
+ "an experimental condition in which carbonyl cyanide m - chlorophenyl hydrazone was added to the medium or assay buffer in excess compared to standard medium or assay buffers ."
1871
+ ],
1872
+ "FYECO:0000436": [
1873
+ "+ fccp",
1874
+ "carbonyl cyanide m - chlorophenyl hydrazone"
1875
+ ]
1876
+ }
dict_new_fyeco/lable.vocab ADDED
@@ -0,0 +1,425 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ FYECO:0000001
2
+ FYECO:0000002
3
+ FYECO:0000003
4
+ FYECO:0000004
5
+ FYECO:0000005
6
+ FYECO:0000006
7
+ FYECO:0000007
8
+ FYECO:0000008
9
+ FYECO:0000009
10
+ FYECO:0000010
11
+ FYECO:0000011
12
+ FYECO:0000013
13
+ FYECO:0000015
14
+ FYECO:0000016
15
+ FYECO:0000021
16
+ FYECO:0000022
17
+ FYECO:0000023
18
+ FYECO:0000024
19
+ FYECO:0000025
20
+ FYECO:0000026
21
+ FYECO:0000027
22
+ FYECO:0000028
23
+ FYECO:0000030
24
+ FYECO:0000031
25
+ FYECO:0000032
26
+ FYECO:0000033
27
+ FYECO:0000034
28
+ FYECO:0000035
29
+ FYECO:0000036
30
+ FYECO:0000037
31
+ FYECO:0000038
32
+ FYECO:0000039
33
+ FYECO:0000040
34
+ FYECO:0000041
35
+ FYECO:0000042
36
+ FYECO:0000043
37
+ FYECO:0000044
38
+ FYECO:0000045
39
+ FYECO:0000046
40
+ FYECO:0000047
41
+ FYECO:0000048
42
+ FYECO:0000049
43
+ FYECO:0000050
44
+ FYECO:0000051
45
+ FYECO:0000052
46
+ FYECO:0000053
47
+ FYECO:0000054
48
+ FYECO:0000055
49
+ FYECO:0000056
50
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51
+ FYECO:0000058
52
+ FYECO:0000059
53
+ FYECO:0000060
54
+ FYECO:0000061
55
+ FYECO:0000062
56
+ FYECO:0000063
57
+ FYECO:0000064
58
+ FYECO:0000065
59
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60
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61
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62
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63
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64
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65
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66
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67
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68
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69
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70
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71
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72
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73
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74
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75
+ FYECO:0000084
76
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77
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78
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79
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81
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82
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83
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84
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85
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86
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87
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88
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89
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90
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91
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92
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93
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94
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95
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96
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97
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98
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99
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100
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101
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102
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103
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104
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105
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106
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107
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108
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109
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110
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111
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112
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113
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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124
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125
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126
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127
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128
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129
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130
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131
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132
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133
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134
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135
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136
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137
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138
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139
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140
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141
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142
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143
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144
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145
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146
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147
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148
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149
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150
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151
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152
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153
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154
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155
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156
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157
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158
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159
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160
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161
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162
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163
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164
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165
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166
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167
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168
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169
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170
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171
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172
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173
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174
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175
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176
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177
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178
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179
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180
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181
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182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
+ FYECO:0000206
196
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197
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198
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199
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200
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201
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202
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203
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204
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205
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206
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207
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208
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209
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210
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211
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212
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213
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214
+ FYECO:0000225
215
+ FYECO:0000226
216
+ FYECO:0000227
217
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218
+ FYECO:0000229
219
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220
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221
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222
+ FYECO:0000233
223
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224
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225
+ FYECO:0000236
226
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227
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228
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229
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230
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231
+ FYECO:0000242
232
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233
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234
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235
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236
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237
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238
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239
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240
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241
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242
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243
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244
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245
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246
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247
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248
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249
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250
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251
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252
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253
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254
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255
+ FYECO:0000266
256
+ FYECO:0000267
257
+ FYECO:0000268
258
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259
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260
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261
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262
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263
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264
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265
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266
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267
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268
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269
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270
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271
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272
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273
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274
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275
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276
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277
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278
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279
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280
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281
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282
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283
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284
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285
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286
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287
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288
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289
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290
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291
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292
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293
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294
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295
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296
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297
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298
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299
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300
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301
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302
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303
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304
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305
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306
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307
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308
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309
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310
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311
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312
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313
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314
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315
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316
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317
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318
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319
+ FYECO:0000330
320
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321
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322
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323
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324
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325
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326
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327
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328
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329
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330
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331
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332
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333
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334
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335
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336
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337
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338
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339
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340
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341
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342
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343
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344
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345
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346
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347
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348
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349
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350
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351
+ FYECO:0000362
352
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353
+ FYECO:0000364
354
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355
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356
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357
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358
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359
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360
+ FYECO:0000371
361
+ FYECO:0000372
362
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363
+ FYECO:0000374
364
+ FYECO:0000375
365
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366
+ FYECO:0000377
367
+ FYECO:0000378
368
+ FYECO:0000379
369
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370
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371
+ FYECO:0000382
372
+ FYECO:0000383
373
+ FYECO:0000384
374
+ FYECO:0000385
375
+ FYECO:0000386
376
+ FYECO:0000387
377
+ FYECO:0000388
378
+ FYECO:0000389
379
+ FYECO:0000390
380
+ FYECO:0000391
381
+ FYECO:0000392
382
+ FYECO:0000393
383
+ FYECO:0000394
384
+ FYECO:0000395
385
+ FYECO:0000396
386
+ FYECO:0000397
387
+ FYECO:0000398
388
+ FYECO:0000399
389
+ FYECO:0000400
390
+ FYECO:0000401
391
+ FYECO:0000402
392
+ FYECO:0000404
393
+ FYECO:0000405
394
+ FYECO:0000406
395
+ FYECO:0000407
396
+ FYECO:0000408
397
+ FYECO:0000409
398
+ FYECO:0000410
399
+ FYECO:0000411
400
+ FYECO:0000412
401
+ FYECO:0000413
402
+ FYECO:0000414
403
+ FYECO:0000415
404
+ FYECO:0000416
405
+ FYECO:0000417
406
+ FYECO:0000418
407
+ FYECO:0000419
408
+ FYECO:0000420
409
+ FYECO:0000421
410
+ FYECO:0000422
411
+ FYECO:0000423
412
+ FYECO:0000424
413
+ FYECO:0000425
414
+ FYECO:0000426
415
+ FYECO:0000427
416
+ FYECO:0000428
417
+ FYECO:0000429
418
+ FYECO:0000430
419
+ FYECO:0000431
420
+ FYECO:0000432
421
+ FYECO:0000433
422
+ FYECO:0000434
423
+ FYECO:0000435
424
+ FYECO:0000436
425
+ HP:None
dict_new_fyeco/noabb_lemma.dic ADDED
@@ -0,0 +1,947 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ anaerobiosis
2
+ chemical
3
+ chemicals
4
+ cold
5
+ hypoxia
6
+ ice
7
+ knockdown
8
+ overexpression
9
+ ph
10
+ temperature
11
+ torin1
12
+ uv
13
+ yes
14
+ ypd
15
+ ypgala
16
+ + acetaldehyde
17
+ + ade
18
+ + adenine
19
+ + adriamycin
20
+ + agno3
21
+ + agnp
22
+ + aminopyrimidine
23
+ + amitrole
24
+ + amorolfine
25
+ + anidulafungin
26
+ + ap20187
27
+ + arginine
28
+ + arsenate
29
+ + arsenic
30
+ + asp
31
+ + asparagine
32
+ + aspartate
33
+ + auxin
34
+ + benzamidine
35
+ + bfa
36
+ + biotin
37
+ + bleomycin
38
+ + bortezomib
39
+ + cacl2
40
+ + caffeine
41
+ + camptothecin
42
+ + canavanin
43
+ + carbendazim
44
+ + caspofungin
45
+ + cccp
46
+ + cdcl2
47
+ + cdso4
48
+ + cerulenin
49
+ + choline
50
+ + cisplatin
51
+ + clomifene
52
+ + clomiphene
53
+ + clotrimazole
54
+ + cocl2
55
+ + compactin
56
+ + cpt
57
+ + cscl
58
+ + cucl2
59
+ + cuso4
60
+ + cycloheximide
61
+ + cysteine
62
+ + dethiobiotin
63
+ + diamide
64
+ + dihydroxyacetone
65
+ + dithiothreitol
66
+ + diuron
67
+ + dmso
68
+ + doxorubicin
69
+ + dtt
70
+ + echinocandin
71
+ + edta
72
+ + ethanol
73
+ + ethanolamine
74
+ + fccp
75
+ + fecl2
76
+ + fecl3
77
+ + ferrichrome
78
+ + feso4
79
+ + fluconazole
80
+ + foa
81
+ + formaldehyde
82
+ + formamide
83
+ + glucose
84
+ + glutamate
85
+ + glutamine
86
+ + glutathione
87
+ + glycerol
88
+ + gtp
89
+ + h2o2
90
+ + hemin
91
+ + hexestrol
92
+ + his
93
+ + hu
94
+ + ile
95
+ + inositol
96
+ + ion
97
+ + ions
98
+ + itraconazole
99
+ + kcl
100
+ + ketoconazole
101
+ + lata
102
+ + latb
103
+ + leu
104
+ + lmb
105
+ + lys
106
+ + mannose
107
+ + meet
108
+ + menadione
109
+ + met
110
+ + methylamine
111
+ + mevalonate
112
+ + mg132
113
+ + mgcl2
114
+ + micafungin
115
+ + mm
116
+ + mms
117
+ + mncl2
118
+ + mnso4
119
+ + mpa
120
+ + na2s
121
+ + na2so3
122
+ + na2so4
123
+ + naaso2
124
+ + nacl
125
+ + nad+
126
+ + nadp+
127
+ + nan3
128
+ + nh4cl
129
+ + nigericin
130
+ + nocodazole
131
+ + oleate
132
+ + ornithine
133
+ + pantothenate
134
+ + peptone
135
+ + phleomycin
136
+ + phosphate
137
+ + pro
138
+ + queuine
139
+ + queuosine
140
+ + rapamycin
141
+ + sam
142
+ + sd
143
+ + sds
144
+ + sirolimus
145
+ + snp
146
+ + sorbitol
147
+ + streptonigrin
148
+ + sugar
149
+ + sulfite
150
+ + tacrolimus
151
+ + tamoxifen
152
+ + tbc
153
+ + tbhp
154
+ + tebuconazole
155
+ + terbinafine
156
+ + terconazole
157
+ + tetrathiomolybdate
158
+ + thiabendazole
159
+ + thiamine
160
+ + thiazole
161
+ + thiolutin
162
+ + thiosulfate
163
+ + torin1
164
+ + tunicamycin
165
+ + ura
166
+ + urea
167
+ + val
168
+ + vanadate
169
+ + vanoxerine
170
+ + zncl2
171
+ + zymolyase
172
+ - oxygen
173
+ 2n cell
174
+ 2n cells
175
+ acetylcysteine add
176
+ acetylcysteine added
177
+ agar plate
178
+ agar plates
179
+ anaerobic environment
180
+ arginine absent
181
+ asn add
182
+ asn added
183
+ bca add
184
+ bca added
185
+ benzamidine add
186
+ benzamidine added
187
+ biotin absent
188
+ bisbenzimide add
189
+ bisbenzimide added
190
+ c add
191
+ c added
192
+ calcium absent
193
+ canavanin add
194
+ canavanin added
195
+ cbz add
196
+ cbz added
197
+ chemical add
198
+ chemical added
199
+ chemical produce
200
+ chemical produced
201
+ chill cell
202
+ chilled cells
203
+ competitive culture
204
+ complex medium
205
+ cys add
206
+ cys added
207
+ dapi add
208
+ dapi added
209
+ deoxynojirimycin add
210
+ deoxynojirimycin added
211
+ desthiobiotin add
212
+ desthiobiotin added
213
+ dha add
214
+ dha added
215
+ dihydroxyacetone mm
216
+ diploid cell
217
+ diploid cells
218
+ dnj add
219
+ dnj added
220
+ edta add
221
+ edta added
222
+ egta add
223
+ egta added
224
+ eta add
225
+ eta added
226
+ ethanol ye
227
+ expression level
228
+ fk506 add
229
+ fk506 added
230
+ fructose mm
231
+ fructose ye
232
+ galactose mm
233
+ galactose ye
234
+ gamma irradiation
235
+ gamma radiation
236
+ glucose mm
237
+ glycerol add
238
+ glycerol added
239
+ glycerol mm
240
+ glycerol ye
241
+ group absent
242
+ group excess
243
+ grouping absent
244
+ grouping excess
245
+ grouping limit
246
+ grouping limited
247
+ gsh add
248
+ gsh added
249
+ high ph
250
+ high temperature
251
+ histidine add
252
+ histidine added
253
+ hydroxyurea add
254
+ hydroxyurea added
255
+ hypoxic environment
256
+ in vitro
257
+ in vivo
258
+ ionize radiation
259
+ ionizing radiation
260
+ isoleucine add
261
+ isoleucine added
262
+ leucine absent
263
+ leucine add
264
+ leucine added
265
+ limited oxygen
266
+ liquid culture
267
+ low ph
268
+ low temperature
269
+ lysine add
270
+ lysine added
271
+ m add
272
+ m added
273
+ maltose mm
274
+ maltose ye
275
+ mannitol ye
276
+ mat medium
277
+ mating medium
278
+ mbc add
279
+ mbc added
280
+ mea add
281
+ mea added
282
+ mecarzole add
283
+ mecarzole added
284
+ medium texture
285
+ methionine add
286
+ methionine added
287
+ minus oxygen
288
+ mn2+ add
289
+ mn2+ added
290
+ monoethanolamine add
291
+ monoethanolamine added
292
+ nac add
293
+ nac added
294
+ nitrogen absent
295
+ nitrogen exclude
296
+ nitrogen excluded
297
+ nitrogen free
298
+ nitrogen starvation
299
+ nonpermissive temperature
300
+ normal temperature
301
+ overnight culture
302
+ oxygen level
303
+ pantothenate absent
304
+ permissive temperature
305
+ ph 6.8
306
+ phenotype condition
307
+ proline add
308
+ proline added
309
+ proteasome inhibitor
310
+ pyruvate mm
311
+ raffinose ye
312
+ restrictive temperature
313
+ rhodamine phalloidin
314
+ sd medium
315
+ self mating
316
+ semiaerobic environment
317
+ semianaerobic environment
318
+ semipermissive temperature
319
+ sorbitol absent
320
+ spa medium
321
+ sporulation medium
322
+ standard temperature
323
+ sucrose mm
324
+ sucrose ye
325
+ synchronous culture
326
+ tacrolimus add
327
+ tacrolimus added
328
+ tbz add
329
+ tbz added
330
+ thiamine absent
331
+ trehalose mm
332
+ tunicamycin add
333
+ tunicamycin added
334
+ ultraviolet light
335
+ uracil absent
336
+ uracil add
337
+ uracil added
338
+ urea add
339
+ urea added
340
+ uv irradiation
341
+ valine add
342
+ valine added
343
+ water medium
344
+ x ray
345
+ x rays
346
+ xylose add
347
+ xylose added
348
+ xylose ye
349
+ + aminolevulinic acid
350
+ + ammonium sulfate
351
+ + anidulafungin ld
352
+ + anidulafungin sld
353
+ + antimycin a
354
+ + arachidic acid
355
+ + bi ion
356
+ + bi ions
357
+ + biochanin a
358
+ + brefeldin a
359
+ + ca ion
360
+ + ca ions
361
+ + cadmium chloride
362
+ + cadmium sulfate
363
+ + calcium chloride
364
+ + calcofluor white
365
+ + caspofungin ld
366
+ + caspofungin sld
367
+ + cd ion
368
+ + cd ions
369
+ + ciclopirox olamine
370
+ + cl ion
371
+ + cl ions
372
+ + cobalt chloride
373
+ + copper chelator
374
+ + cu ion
375
+ + cu ions
376
+ + cyclosporin a
377
+ + diethyl maleate
378
+ + dimethyl sulfoxide
379
+ + egtazic acid
380
+ + ethyl methanesulfonate
381
+ + ethylene glycol
382
+ + fatty acid
383
+ + guanosine triphosphate
384
+ + iron chelator
385
+ + k ion
386
+ + k ions
387
+ + latrunculin a
388
+ + latrunculin b
389
+ + lauric acid
390
+ + leptomycin b
391
+ + li ion
392
+ + li ions
393
+ + limit glucose
394
+ + limit sulfur
395
+ + limited adenine
396
+ + limited ala
397
+ + limited ammonium
398
+ + limited biotin
399
+ + limited dethiobiotin
400
+ + limited ethanolamine
401
+ + limited glucose
402
+ + limited iron
403
+ + limited leucine
404
+ + limited nh4cl
405
+ + limited nickel
406
+ + limited nitrogen
407
+ + limited pantothenate
408
+ + limited phosphate
409
+ + limited sodium
410
+ + limited sulfur
411
+ + limited thiamine
412
+ + limited uracil
413
+ + limited zinc
414
+ + linoleic acid
415
+ + linolenic acid
416
+ + manganese sulfate
417
+ + manumycin a
418
+ + margaric acid
419
+ + mat pheromone
420
+ + mating pheromone
421
+ + melissic acid
422
+ + mg ion
423
+ + mg ions
424
+ + micafungin ld
425
+ + micafungin sld
426
+ + mn ion
427
+ + mn ions
428
+ + mycophenolic acid
429
+ + myristic acid
430
+ + na ion
431
+ + na ions
432
+ + na oleate
433
+ + naphthaleneacetic acid
434
+ + ni ion
435
+ + ni ions
436
+ + oleic acid
437
+ + palmitic acid
438
+ + pb ion
439
+ + pb ions
440
+ + pentadecanoic acid
441
+ + petroselinic acid
442
+ + phloxine b
443
+ + silver nanoparticles
444
+ + silver nitrate
445
+ + sodium azide
446
+ + sodium nitroprusside
447
+ + stearic acid
448
+ + tev protease
449
+ + trichostatin a
450
+ + ubiquinone q6
451
+ + vaccenic acid
452
+ + valproic acid
453
+ + xenobiotic substrate
454
+ + zinc sulfate
455
+ + zinc sulphate
456
+ + zn ion
457
+ + zn ions
458
+ 17 degree celsius
459
+ 17 degrees celsius
460
+ 18 degree celsius
461
+ 18 degrees celsius
462
+ 19 degree celsius
463
+ 19 degrees celsius
464
+ 20 degree celsius
465
+ 20 degrees celsius
466
+ 21 degree celsius
467
+ 21 degrees celsius
468
+ 22 degree celsius
469
+ 22 degrees celsius
470
+ 23 degree celsius
471
+ 23 degrees celsius
472
+ 24 degree celsius
473
+ 24 degrees celsius
474
+ 25 degree celsius
475
+ 25 degrees celsius
476
+ 26 degree celsius
477
+ 26 degrees celsius
478
+ 27 degree celsius
479
+ 27 degrees celsius
480
+ 28 degree celsius
481
+ 28 degrees celsius
482
+ 29 degree celsius
483
+ 29 degrees celsius
484
+ 30 degree celsius
485
+ 30 degrees celsius
486
+ 31 degree celsius
487
+ 31 degrees celsius
488
+ 32 degree celsius
489
+ 32 degrees celsius
490
+ 33 degree celsius
491
+ 33 degrees celsius
492
+ 34 degree celsius
493
+ 34 degrees celsius
494
+ 35 degree celsius
495
+ 35 degrees celsius
496
+ 36 degree celsius
497
+ 36 degrees celsius
498
+ 37 degree celsius
499
+ 37 degrees celsius
500
+ 38 degree celsius
501
+ 38 degrees celsius
502
+ 39 degree celsius
503
+ 39 degrees celsius
504
+ 40 degree celsius
505
+ 40 degrees celsius
506
+ 41 degree celsius
507
+ 41 degrees celsius
508
+ 42 degree celsius
509
+ 42 degrees celsius
510
+ 43 degree celsius
511
+ 43 degrees celsius
512
+ absence of adenine
513
+ absence of chemical
514
+ absence of inositol
515
+ absence of nitrogen
516
+ absence of uracil
517
+ acute hydroxyurea treatment
518
+ ammonium chloride add
519
+ ammonium chloride added
520
+ bismuth ion add
521
+ bismuth ions added
522
+ ca ion add
523
+ ca ions added
524
+ cadmium ion add
525
+ cadmium ions added
526
+ caesium chloride add
527
+ caesium chloride added
528
+ calcium ion add
529
+ calcium ions added
530
+ cesium chloride add
531
+ cesium chloride added
532
+ chloride ion add
533
+ chloride ions added
534
+ coenzyme q6 add
535
+ coenzyme q6 added
536
+ copper chloride add
537
+ copper chloride added
538
+ copper ion add
539
+ copper ions added
540
+ dha minimal medium
541
+ diethyl maleate add
542
+ diethyl maleate added
543
+ dihydroxyactone minimal medium
544
+ egtazic acid add
545
+ egtazic acid added
546
+ ethanol rich medium
547
+ ethylenediaminetetraacetic acid add
548
+ ethylenediaminetetraacetic acid added
549
+ fructose minimal medium
550
+ fructose rich medium
551
+ galactose rich medium
552
+ glucose minimal medium
553
+ glucose rich medium
554
+ glycerol minimal medium
555
+ glycerol rich medium
556
+ group condition combination
557
+ group define medium
558
+ group experimental environment
559
+ group growth medium
560
+ group growth timing
561
+ group heat shock
562
+ group rich medium
563
+ grouping condition combinations
564
+ grouping defined medium
565
+ grouping experimental environment
566
+ grouping growth medium
567
+ grouping growth timing
568
+ grouping heat shock
569
+ grouping rich medium
570
+ high glucose mm
571
+ high glucose yes
572
+ hoechst stain add
573
+ hoechst stain added
574
+ hydrogen peroxide add
575
+ hydrogen peroxide added
576
+ inorganic phosphate absent
577
+ iron chloride add
578
+ iron chloride added
579
+ iron dichloride add
580
+ iron dichloride added
581
+ iron sulfate add
582
+ iron sulfate added
583
+ iron sulphate add
584
+ iron sulphate added
585
+ iron trichloride add
586
+ iron trichloride added
587
+ lead ion add
588
+ lead ions added
589
+ limited desthiobiotin add
590
+ limited desthiobiotin added
591
+ limited inositol add
592
+ limited inositol added
593
+ limited o atom
594
+ limited o atoms
595
+ limited sulphur add
596
+ limited sulphur added
597
+ limited zn add
598
+ limited zn added
599
+ lithium ion add
600
+ lithium ions added
601
+ lnb glucose medium
602
+ low glucose mm
603
+ low glucose ye
604
+ low glucose yes
605
+ m factor add
606
+ m factor added
607
+ magnesium chloride add
608
+ magnesium chloride added
609
+ magnesium ion add
610
+ magnesium ions added
611
+ malt extract medium
612
+ maltose minimal medium
613
+ maltose rich medium
614
+ manganese chloride add
615
+ manganese chloride added
616
+ manganese ion add
617
+ manganese ions added
618
+ mannitol rich medium
619
+ mat with wt
620
+ mating with wt
621
+ methyl methanesulfonate add
622
+ methyl methanesulfonate added
623
+ multiple passage culture
624
+ nickel ion add
625
+ nickel ions added
626
+ nitrogen source shift
627
+ no glucose yes
628
+ normal glucose mm
629
+ p factor add
630
+ p factor added
631
+ potassium chloride add
632
+ potassium chloride added
633
+ potassium ion add
634
+ potassium ions added
635
+ pyruvate minimal medium
636
+ raffinose rich medium
637
+ reduce oxygen level
638
+ reduced oxygen level
639
+ respiratory chain inhibitor
640
+ semi aerobic environment
641
+ single passage culture
642
+ sodium arsenite add
643
+ sodium arsenite added
644
+ sodium chloride add
645
+ sodium chloride added
646
+ sodium ion add
647
+ sodium ions added
648
+ sodium oleate add
649
+ sodium oleate added
650
+ sodium orthovanadate add
651
+ sodium orthovanadate added
652
+ sodium sulfate add
653
+ sodium sulfate added
654
+ sodium sulfide add
655
+ sodium sulfide added
656
+ sodium sulfite add
657
+ sodium sulfite added
658
+ solid agar plate
659
+ solid agar plates
660
+ sucrose minimal medium
661
+ sucrose rich medium
662
+ sugar alcohol add
663
+ sugar alcohol added
664
+ transient hydroxyurea treatment
665
+ trehalose minimal medium
666
+ valproic acid add
667
+ valproic acid added
668
+ vitamin e add
669
+ vitamin e added
670
+ x - ray
671
+ x - rays
672
+ xylose rich medium
673
+ yes + galactose
674
+ zinc chloride add
675
+ zinc chloride added
676
+ zinc ion add
677
+ zinc ions added
678
+ + 1 - dnj
679
+ + 14 - hydroxydaunomycin
680
+ + 14 - hydroxydaunorubicine
681
+ + 2 - dg
682
+ + 2 - og
683
+ + 3,4 - dihydrocoumarin
684
+ + 3mb - pp1
685
+ + 4 - nqo
686
+ + 5 - fluorouracil
687
+ + 5 - fu
688
+ + alpha - tocopherol
689
+ + beta - estradiol
690
+ + beta - glucanase
691
+ + ck - 666
692
+ + cutin - 1
693
+ + icrf - 193
694
+ + limited aminolevulinic acid
695
+ + m - factor
696
+ + manu - a
697
+ + microtubule depolymerizing drug
698
+ + microtubule depolymerizing drugs
699
+ + p - factor
700
+ + r - limonene
701
+ + respiratory chain inhibitor
702
+ + s - adenosylmethionine
703
+ + tea tree oil
704
+ + top - 53
705
+ 1 - deoxynojirimycin add
706
+ 1 - deoxynojirimycin added
707
+ 2 - aminoethanol add
708
+ 2 - aminoethanol added
709
+ 2 - deoxyglucose add
710
+ 2 - deoxyglucose added
711
+ 2 - og present
712
+ 2 - oxoglutarate add
713
+ 2 - oxoglutarate added
714
+ 2 - oxoglutarate present
715
+ 3,4 - dihydrocoumarin add
716
+ 3,4 - dihydrocoumarin added
717
+ chemical add or exclude
718
+ chemical added or excluded
719
+ cpt block and release
720
+ fission yeast phenotype condition
721
+ glucose starvation and recovery
722
+ glycerol + ethanol ye
723
+ glycerol and ethanol ye
724
+ group sequential growth condition
725
+ group starvation and timing
726
+ grouping sequential growth conditions
727
+ grouping starvation and timing
728
+ growth < 24 hour
729
+ growth < 24 hours
730
+ growth < 24 hr
731
+ growth < 24 hrs
732
+ growth > 24 hour
733
+ growth > 24 hours
734
+ growth > 24 hr
735
+ growth > 24 hrs
736
+ growth > 48 hour
737
+ growth > 48 hours
738
+ growth > 48 hr
739
+ growth > 48 hrs
740
+ growth to exponential phase
741
+ growth to stationary phase
742
+ high glucose minimal medium
743
+ high glucose rich medium
744
+ hu block and release
745
+ low glucose minimal medium
746
+ low glucose rich medium
747
+ low nitrogen glucose mm
748
+ mbc block and release
749
+ mm with trace glucose
750
+ nitrogen starvation and recovery
751
+ non - permissive temperature
752
+ normal glucose minimal medium
753
+ normal glucose rich medium
754
+ presence of mat pheromone
755
+ presence of mating pheromone
756
+ presence of mating pheromones
757
+ recovery from nitrogen depletion
758
+ recovery from nitrogen starvation
759
+ rhodamine - phalloidin add
760
+ rhodamine - phalloidin added
761
+ semi - aerobic environment
762
+ semi - anaerobic environment
763
+ semi - permissive temperature
764
+ sodium dodecyl sulfate add
765
+ sodium dodecyl sulfate added
766
+ standard dextrose rich medium
767
+ standard glucose minimal medium
768
+ standard glucose rich medium
769
+ tea tree oil add
770
+ tea tree oil added
771
+ temperature block and release
772
+ tert - butyl hydroperoxide
773
+ very low glucose mm
774
+ very low glucose ye
775
+ ye with trace glucose
776
+ + ( nh4 ) 2so4
777
+ + 2,2 ' - dipyridyl
778
+ + 20 standard aa 's
779
+ + 3,5 - cyclic amp
780
+ + 5 - fluoroorotic acid
781
+ + electron transport chain inhibitor
782
+ + limited myo - inositol
783
+ + respiratory complex iii inhibitor
784
+ 2,2 ' - dipyridyl add
785
+ 2,2 ' - dipyridyl added
786
+ 22 standard amino acid add
787
+ 22 standard amino acids added
788
+ > 7 day nitrogen starvation
789
+ > 7 days nitrogen starvation
790
+ absence of p - factor
791
+ anti - tubulin antibodies added
792
+ anti - tubulin antibody add
793
+ anti - tubulin antibody added
794
+ fitc - conjugate lectin add
795
+ fitc - conjugated lectin added
796
+ glucose mm , no adenine
797
+ glucose mm , no glucose
798
+ glucose mm , no nitrogen
799
+ glycerol and ethanol rich medium
800
+ glycerol mm with trace ethanol
801
+ glycerol mm with trace glucose
802
+ glycerol sole carbon source ye
803
+ group growth to stationary phase
804
+ grouping growth to stationary phase
805
+ growth to late exponential phase
806
+ iron ( ii ) chloride
807
+ iron ( iii ) chloride
808
+ low nitrogen glucose minimal medium
809
+ m and p factor produce
810
+ m and p factor produced
811
+ minimal medium with trace glucose
812
+ rich medium with trace glucose
813
+ + ( 4r ) - limonene
814
+ + 1 - na - pp1
815
+ + 1 - nm - pp1
816
+ + 3 - brb - pp1
817
+ + copper ( ii ) sulfate
818
+ 1 - na - pp1 present
819
+ > 6 hour in nitrogen starvation
820
+ > 6 hours in nitrogen starvation
821
+ > 6 hr in nitrogen starvation
822
+ > 6 hrs in nitrogen starvation
823
+ carbonyl cyanide m - chlorophenyl hydrazone
824
+ galactose rich medium with trace glucose
825
+ glucose minimal medium , exclude nitrogen
826
+ glucose minimal medium , excluding nitrogen
827
+ glucose mm , adenine nitrogen source
828
+ glucose mm , ammonium nitrogen source
829
+ glucose mm , arginine nitrogen source
830
+ glucose mm , cysteine nitrogen source
831
+ glucose mm , glutamate nitrogen source
832
+ glucose mm , isoleucine nitrogen source
833
+ glucose mm , lysine nitrogen source
834
+ glucose mm , methionine nitrogen source
835
+ glucose mm , phenylalanine nitrogen source
836
+ glucose mm , proline nitrogen source
837
+ glucose mm , serine nitrogen source
838
+ glucose mm , sulfate sulfur source
839
+ glucose mm , sulphate sulphur source
840
+ glucose mm , uracil nitrogen source
841
+ glucose mm , urea nitrogen source
842
+ glucose mm , xanthine nitrogen source
843
+ glycerol minimal medium with trace glucose
844
+ glycerol sole carbon source rich medium
845
+ non - fermentable carbon source medium
846
+ non - fermentable carbon sources medium
847
+ nonfermentable glycerol and ethanol rich medium
848
+ rich medium with glucose and galactose
849
+ temperature shift , high to low
850
+ temperature shift , high to standard
851
+ temperature shift , low to high
852
+ temperature shift , low to standard
853
+ temperature shift , standard to high
854
+ zinc starvation follow by zinc shock
855
+ zinc starvation followed by zinc shock
856
+ + 4 - nitroquinoline n - oxide
857
+ + ammonium iron ( 2+ ) sulfate
858
+ + ferrous ammonium sulfate ( anhydrous )
859
+ + mitochondrial complex iii / iv inhibitor
860
+ cold shock and recovery at high temperature
861
+ cold shock and recovery at normal temperature
862
+ glucose minimal medium , arginine nitrogen source
863
+ glucose minimal medium , cysteine nitrogen source
864
+ glucose minimal medium , glutamate nitrogen source
865
+ glucose minimal medium , lysine nitrogen source
866
+ glucose minimal medium , methionine nitrogen source
867
+ glucose minimal medium , serine nitrogen source
868
+ glucose minimal medium , sulfate sulfur source
869
+ glucose minimal medium , sulphate sulphur source
870
+ glucose minimal medium , urea nitrogen source
871
+ heat shock and recovery at high temperature
872
+ heat shock and recovery at normal temperature
873
+ nitrogen source shift , glutamate to proline
874
+ nitrogen source shift , proline to glutamate
875
+ nonfermentable glycerol sole carbon source rich medium
876
+ presence of 3',5 ' - cyclic amp
877
+ transient amino acid starvation < 1 hour
878
+ + 3 - amino - 1,2,4 - triazole
879
+ + n - acetyl - l - cysteine
880
+ + s - adenosyl - l - methionine
881
+ 2 - deoxy - d - glucose add
882
+ 2 - deoxy - d - glucose added
883
+ 3 ' 5 ' - cyclic amp produce
884
+ 3 ' 5 ' - cyclic amp produced
885
+ 4',6 - diamidino - 2 - phenylindole add
886
+ 4',6 - diamidino - 2 - phenylindole added
887
+ non - fermentable glycerol and ethanol rich medium
888
+ nonfermentable galactose and very low glucose rich medium
889
+ standard glucose minimal medium , cysteine nitrogen source
890
+ standard glucose minimal medium , glutamate nitrogen source
891
+ standard glucose minimal medium , lysine nitrogen source
892
+ standard glucose minimal medium , methionine nitrogen source
893
+ standard glucose minimal medium , urea nitrogen source
894
+ absence of 3 ' 5 ' - cyclic amp
895
+ glucose rich medium , peptone / ye nitrogen source
896
+ glycerol main carbon source + very low glucose mm
897
+ isogenic cell of opposite mating type add to culture
898
+ isogenic cells of opposite mating type added to culture
899
+ non - fermentable glycerol sole carbon source rich medium
900
+ presence of m - factor and p - factor
901
+ glucose mm , organic nitrogen source , no inorganic nitrogen
902
+ growth at high temperature follow by growth at standard temperature
903
+ growth at high temperature followed by growth at standard temperature
904
+ growth at low temperature follow by growth at standard temperature
905
+ growth at low temperature followed by growth at standard temperature
906
+ l - gamma - glutamyl - l - cysteinylglycine add
907
+ l - gamma - glutamyl - l - cysteinylglycine added
908
+ non - fermentable galactose and very low glucose rich medium
909
+ wild type cell of opposite mating type add to culture
910
+ wild type cells of opposite mating type added to culture
911
+ nitrogen starvation follow by heat shock and recovery at normal temperature
912
+ nitrogen starvation follow by heat shock and recovery at permissive temperature
913
+ nitrogen starvation followed by heat shock and recovery at normal temperature
914
+ nitrogen starvation followed by heat shock and recovery at permissive temperature
915
+ + 3 - ( 3,4 - dichlorophenyl ) - 1,1 - dimethylurea
916
+ growth to stationary phase in rich medium follow by transfer to h2o
917
+ growth to stationary phase in rich medium followed by transfer to h2o
918
+ + ( 8e,10s ) - 10 - hydroxy - 8 - octadecenoic acid
919
+ growth to stationary phase in rich medium follow by transfer to minimal medium
920
+ growth to stationary phase in rich medium followed by transfer to minimal medium
921
+ nitrogen starvation at normal temperature and shift to high temperature in rich medium
922
+ two - step temperature shift , low to standard , standard to high
923
+ two - step temperature shift , standard to high , high to standard
924
+ two - step temperature shift , standard to low , low to high
925
+ 24 - 48h nitrogen starvation follow by 12 - 24h recovery in rich medium
926
+ 24 - 48h nitrogen starvation follow by 5 - 12h recovery in rich medium
927
+ 24 - 48h nitrogen starvation followed by 12 - 24h recovery in rich medium
928
+ 24 - 48h nitrogen starvation followed by 5 - 12h recovery in rich medium
929
+ 28 day nitrogen starvation follow by 10 - 50 hour recovery in minimal medium
930
+ 28 days nitrogen starvation followed by 10 - 50 hours recovery in minimal medium
931
+ 72h - 7days nitrogen starvation follow by 12 - 24h recovery in rich medium
932
+ 72h - 7days nitrogen starvation followed by 12 - 24h recovery in rich medium
933
+ + ( r , z ) - 10 - hydroxyoctadec - 8 - enoic acid
934
+ 24 - 48h nitrogen starvation follow by 4 - 7 day recovery in rich medium
935
+ 24 - 48h nitrogen starvation followed by 4 - 7 day recovery in rich medium
936
+ 72h - 7days nitrogen starvation follow by 4 - 7 day recovery in rich medium
937
+ 72h - 7days nitrogen starvation followed by 4 - 7 days recovery in rich medium
938
+ + n , n , n ' , n ' - tetramethyldiazene - 1,2 - dicarboxamide
939
+ heat shock for 20 - 30 min at 48 degree c , preceeded and follow by growth at high temperature
940
+ heat shock for 20 - 30 min at 48 degree c , preceeded and follow by growth at normal temperature
941
+ heat shock for 20 - 30 min at 48 degrees c , preceeded and followed by growth at high temperature
942
+ heat shock for 20 - 30 min at 48 degrees c , preceeded and followed by growth at normal temperature
943
+ 4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine add
944
+ 4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine added
945
+ 4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine present
946
+ an experimental condition in which carbonyl cyanide m - chlorophenyl hydrazone be add to the medium or assay buffer in excess compare to standard medium or assay buffer .
947
+ an experimental condition in which carbonyl cyanide m - chlorophenyl hydrazone was added to the medium or assay buffer in excess compared to standard medium or assay buffers .
dict_new_fyeco/obo.json ADDED
The diff for this file is too large to render. See raw diff
 
dict_new_fyeco/word_id_map.json ADDED
@@ -0,0 +1,2847 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "fission yeast phenotype condition": [
3
+ "FYECO:0000001"
4
+ ],
5
+ "phenotype condition": [
6
+ "FYECO:0000001"
7
+ ],
8
+ "temperature": [
9
+ "FYECO:0000002"
10
+ ],
11
+ "expression level": [
12
+ "FYECO:0000003"
13
+ ],
14
+ "high temperature": [
15
+ "FYECO:0000004"
16
+ ],
17
+ "33 degree celsius": [
18
+ "FYECO:0000004"
19
+ ],
20
+ "33 degrees celsius": [
21
+ "FYECO:0000004"
22
+ ],
23
+ "34 degree celsius": [
24
+ "FYECO:0000004"
25
+ ],
26
+ "34 degrees celsius": [
27
+ "FYECO:0000004"
28
+ ],
29
+ "35 degree celsius": [
30
+ "FYECO:0000004"
31
+ ],
32
+ "35 degrees celsius": [
33
+ "FYECO:0000004"
34
+ ],
35
+ "36 degree celsius": [
36
+ "FYECO:0000004"
37
+ ],
38
+ "36 degrees celsius": [
39
+ "FYECO:0000004"
40
+ ],
41
+ "37 degree celsius": [
42
+ "FYECO:0000004"
43
+ ],
44
+ "37 degrees celsius": [
45
+ "FYECO:0000004"
46
+ ],
47
+ "38 degree celsius": [
48
+ "FYECO:0000004"
49
+ ],
50
+ "38 degrees celsius": [
51
+ "FYECO:0000004"
52
+ ],
53
+ "39 degree celsius": [
54
+ "FYECO:0000004"
55
+ ],
56
+ "39 degrees celsius": [
57
+ "FYECO:0000004"
58
+ ],
59
+ "40 degree celsius": [
60
+ "FYECO:0000004"
61
+ ],
62
+ "40 degrees celsius": [
63
+ "FYECO:0000004"
64
+ ],
65
+ "41 degree celsius": [
66
+ "FYECO:0000004"
67
+ ],
68
+ "41 degrees celsius": [
69
+ "FYECO:0000004"
70
+ ],
71
+ "42 degree celsius": [
72
+ "FYECO:0000004"
73
+ ],
74
+ "42 degrees celsius": [
75
+ "FYECO:0000004"
76
+ ],
77
+ "43 degree celsius": [
78
+ "FYECO:0000004"
79
+ ],
80
+ "43 degrees celsius": [
81
+ "FYECO:0000004"
82
+ ],
83
+ "standard temperature": [
84
+ "FYECO:0000005"
85
+ ],
86
+ "25 degree celsius": [
87
+ "FYECO:0000005"
88
+ ],
89
+ "25 degrees celsius": [
90
+ "FYECO:0000005"
91
+ ],
92
+ "26 degree celsius": [
93
+ "FYECO:0000005"
94
+ ],
95
+ "26 degrees celsius": [
96
+ "FYECO:0000005"
97
+ ],
98
+ "27 degree celsius": [
99
+ "FYECO:0000005"
100
+ ],
101
+ "27 degrees celsius": [
102
+ "FYECO:0000005"
103
+ ],
104
+ "28 degree celsius": [
105
+ "FYECO:0000005"
106
+ ],
107
+ "28 degrees celsius": [
108
+ "FYECO:0000005"
109
+ ],
110
+ "29 degree celsius": [
111
+ "FYECO:0000005"
112
+ ],
113
+ "29 degrees celsius": [
114
+ "FYECO:0000005"
115
+ ],
116
+ "30 degree celsius": [
117
+ "FYECO:0000005"
118
+ ],
119
+ "30 degrees celsius": [
120
+ "FYECO:0000005"
121
+ ],
122
+ "31 degree celsius": [
123
+ "FYECO:0000005"
124
+ ],
125
+ "31 degrees celsius": [
126
+ "FYECO:0000005"
127
+ ],
128
+ "32 degree celsius": [
129
+ "FYECO:0000005"
130
+ ],
131
+ "32 degrees celsius": [
132
+ "FYECO:0000005"
133
+ ],
134
+ "normal temperature": [
135
+ "FYECO:0000005"
136
+ ],
137
+ "low temperature": [
138
+ "FYECO:0000006"
139
+ ],
140
+ "17 degree celsius": [
141
+ "FYECO:0000006"
142
+ ],
143
+ "17 degrees celsius": [
144
+ "FYECO:0000006"
145
+ ],
146
+ "18 degree celsius": [
147
+ "FYECO:0000006"
148
+ ],
149
+ "18 degrees celsius": [
150
+ "FYECO:0000006"
151
+ ],
152
+ "19 degree celsius": [
153
+ "FYECO:0000006"
154
+ ],
155
+ "19 degrees celsius": [
156
+ "FYECO:0000006"
157
+ ],
158
+ "20 degree celsius": [
159
+ "FYECO:0000006"
160
+ ],
161
+ "20 degrees celsius": [
162
+ "FYECO:0000006"
163
+ ],
164
+ "21 degree celsius": [
165
+ "FYECO:0000006"
166
+ ],
167
+ "21 degrees celsius": [
168
+ "FYECO:0000006"
169
+ ],
170
+ "22 degree celsius": [
171
+ "FYECO:0000006"
172
+ ],
173
+ "22 degrees celsius": [
174
+ "FYECO:0000006"
175
+ ],
176
+ "23 degree celsius": [
177
+ "FYECO:0000006"
178
+ ],
179
+ "23 degrees celsius": [
180
+ "FYECO:0000006"
181
+ ],
182
+ "24 degree celsius": [
183
+ "FYECO:0000006"
184
+ ],
185
+ "24 degrees celsius": [
186
+ "FYECO:0000006"
187
+ ],
188
+ "cold": [
189
+ "FYECO:0000006",
190
+ "FYECO:0000202"
191
+ ],
192
+ "overexpression": [
193
+ "FYECO:0000007"
194
+ ],
195
+ "knockdown": [
196
+ "FYECO:0000008"
197
+ ],
198
+ "group growth medium": [
199
+ "FYECO:0000009"
200
+ ],
201
+ "grouping growth medium": [
202
+ "FYECO:0000009"
203
+ ],
204
+ "absence of chemical": [
205
+ "FYECO:0000010"
206
+ ],
207
+ "grouping limit": [
208
+ "FYECO:0000011"
209
+ ],
210
+ "grouping limited": [
211
+ "FYECO:0000011"
212
+ ],
213
+ "group define medium": [
214
+ "FYECO:0000013"
215
+ ],
216
+ "grouping defined medium": [
217
+ "FYECO:0000013"
218
+ ],
219
+ "sporulation medium": [
220
+ "FYECO:0000015"
221
+ ],
222
+ "malt extract medium": [
223
+ "FYECO:0000015"
224
+ ],
225
+ "mat medium": [
226
+ "FYECO:0000015"
227
+ ],
228
+ "mating medium": [
229
+ "FYECO:0000015"
230
+ ],
231
+ "spa medium": [
232
+ "FYECO:0000015"
233
+ ],
234
+ "high glucose mm": [
235
+ "FYECO:0000016"
236
+ ],
237
+ "high glucose minimal medium": [
238
+ "FYECO:0000016"
239
+ ],
240
+ "+ limited adenine": [
241
+ "FYECO:0000021"
242
+ ],
243
+ "absence of p - factor": [
244
+ "FYECO:0000022"
245
+ ],
246
+ "presence of 3',5 ' - cyclic amp": [
247
+ "FYECO:0000023"
248
+ ],
249
+ "+ sugar": [
250
+ "FYECO:0000024"
251
+ ],
252
+ "+ sorbitol": [
253
+ "FYECO:0000025"
254
+ ],
255
+ "+ vanadate": [
256
+ "FYECO:0000026"
257
+ ],
258
+ "sodium orthovanadate add": [
259
+ "FYECO:0000026"
260
+ ],
261
+ "sodium orthovanadate added": [
262
+ "FYECO:0000026"
263
+ ],
264
+ "presence of mat pheromone": [
265
+ "FYECO:0000027"
266
+ ],
267
+ "presence of mating pheromone": [
268
+ "FYECO:0000027"
269
+ ],
270
+ "+ tbc": [
271
+ "FYECO:0000028"
272
+ ],
273
+ "+ ion": [
274
+ "FYECO:0000030"
275
+ ],
276
+ "+ ions": [
277
+ "FYECO:0000030"
278
+ ],
279
+ "+ k ion": [
280
+ "FYECO:0000031"
281
+ ],
282
+ "+ k ions": [
283
+ "FYECO:0000031"
284
+ ],
285
+ "potassium ion add": [
286
+ "FYECO:0000031"
287
+ ],
288
+ "potassium ions added": [
289
+ "FYECO:0000031"
290
+ ],
291
+ "+ cl ion": [
292
+ "FYECO:0000032"
293
+ ],
294
+ "+ cl ions": [
295
+ "FYECO:0000032"
296
+ ],
297
+ "chloride ion add": [
298
+ "FYECO:0000032"
299
+ ],
300
+ "chloride ions added": [
301
+ "FYECO:0000032"
302
+ ],
303
+ "+ cd ion": [
304
+ "FYECO:0000033"
305
+ ],
306
+ "+ cd ions": [
307
+ "FYECO:0000033"
308
+ ],
309
+ "cadmium ion add": [
310
+ "FYECO:0000033"
311
+ ],
312
+ "cadmium ions added": [
313
+ "FYECO:0000033"
314
+ ],
315
+ "+ ca ion": [
316
+ "FYECO:0000034"
317
+ ],
318
+ "+ ca ions": [
319
+ "FYECO:0000034"
320
+ ],
321
+ "ca ion add": [
322
+ "FYECO:0000034"
323
+ ],
324
+ "ca ions added": [
325
+ "FYECO:0000034"
326
+ ],
327
+ "calcium ion add": [
328
+ "FYECO:0000034"
329
+ ],
330
+ "calcium ions added": [
331
+ "FYECO:0000034"
332
+ ],
333
+ "+ cu ion": [
334
+ "FYECO:0000035"
335
+ ],
336
+ "+ cu ions": [
337
+ "FYECO:0000035"
338
+ ],
339
+ "copper ion add": [
340
+ "FYECO:0000035"
341
+ ],
342
+ "copper ions added": [
343
+ "FYECO:0000035"
344
+ ],
345
+ "+ pb ion": [
346
+ "FYECO:0000036"
347
+ ],
348
+ "+ pb ions": [
349
+ "FYECO:0000036"
350
+ ],
351
+ "lead ion add": [
352
+ "FYECO:0000036"
353
+ ],
354
+ "lead ions added": [
355
+ "FYECO:0000036"
356
+ ],
357
+ "+ bi ion": [
358
+ "FYECO:0000037"
359
+ ],
360
+ "+ bi ions": [
361
+ "FYECO:0000037"
362
+ ],
363
+ "bismuth ion add": [
364
+ "FYECO:0000037"
365
+ ],
366
+ "bismuth ions added": [
367
+ "FYECO:0000037"
368
+ ],
369
+ "+ mg ion": [
370
+ "FYECO:0000038"
371
+ ],
372
+ "+ mg ions": [
373
+ "FYECO:0000038"
374
+ ],
375
+ "magnesium ion add": [
376
+ "FYECO:0000038"
377
+ ],
378
+ "magnesium ions added": [
379
+ "FYECO:0000038"
380
+ ],
381
+ "+ p - factor": [
382
+ "FYECO:0000039"
383
+ ],
384
+ "p factor add": [
385
+ "FYECO:0000039"
386
+ ],
387
+ "p factor added": [
388
+ "FYECO:0000039"
389
+ ],
390
+ "+ m - factor": [
391
+ "FYECO:0000040"
392
+ ],
393
+ "m factor add": [
394
+ "FYECO:0000040"
395
+ ],
396
+ "m factor added": [
397
+ "FYECO:0000040"
398
+ ],
399
+ "sugar alcohol add": [
400
+ "FYECO:0000041"
401
+ ],
402
+ "sugar alcohol added": [
403
+ "FYECO:0000041"
404
+ ],
405
+ "+ fatty acid": [
406
+ "FYECO:0000042"
407
+ ],
408
+ "+ palmitic acid": [
409
+ "FYECO:0000043"
410
+ ],
411
+ "+ myristic acid": [
412
+ "FYECO:0000044"
413
+ ],
414
+ "+ pentadecanoic acid": [
415
+ "FYECO:0000045"
416
+ ],
417
+ "+ margaric acid": [
418
+ "FYECO:0000046"
419
+ ],
420
+ "+ stearic acid": [
421
+ "FYECO:0000047"
422
+ ],
423
+ "+ petroselinic acid": [
424
+ "FYECO:0000048"
425
+ ],
426
+ "+ oleic acid": [
427
+ "FYECO:0000049"
428
+ ],
429
+ "+ linoleic acid": [
430
+ "FYECO:0000050"
431
+ ],
432
+ "+ linolenic acid": [
433
+ "FYECO:0000051"
434
+ ],
435
+ "+ arachidic acid": [
436
+ "FYECO:0000052"
437
+ ],
438
+ "+ melissic acid": [
439
+ "FYECO:0000053"
440
+ ],
441
+ "glycerol mm": [
442
+ "FYECO:0000054"
443
+ ],
444
+ "glycerol minimal medium": [
445
+ "FYECO:0000054"
446
+ ],
447
+ "m and p factor produce": [
448
+ "FYECO:0000055"
449
+ ],
450
+ "m and p factor produced": [
451
+ "FYECO:0000055"
452
+ ],
453
+ "presence of m - factor and p - factor": [
454
+ "FYECO:0000055"
455
+ ],
456
+ "presence of mating pheromones": [
457
+ "FYECO:0000055"
458
+ ],
459
+ "+ 3,5 - cyclic amp": [
460
+ "FYECO:0000056"
461
+ ],
462
+ "3 ' 5 ' - cyclic amp produce": [
463
+ "FYECO:0000057"
464
+ ],
465
+ "3 ' 5 ' - cyclic amp produced": [
466
+ "FYECO:0000057"
467
+ ],
468
+ "+ mat pheromone": [
469
+ "FYECO:0000058"
470
+ ],
471
+ "+ mating pheromone": [
472
+ "FYECO:0000058"
473
+ ],
474
+ "chemical add or exclude": [
475
+ "FYECO:0000059"
476
+ ],
477
+ "chemical added or excluded": [
478
+ "FYECO:0000059"
479
+ ],
480
+ "chemical add": [
481
+ "FYECO:0000059"
482
+ ],
483
+ "chemical added": [
484
+ "FYECO:0000059"
485
+ ],
486
+ "chemical": [
487
+ "FYECO:0000059"
488
+ ],
489
+ "chemicals": [
490
+ "FYECO:0000059"
491
+ ],
492
+ "chemical produce": [
493
+ "FYECO:0000060"
494
+ ],
495
+ "chemical produced": [
496
+ "FYECO:0000060"
497
+ ],
498
+ "+ xenobiotic substrate": [
499
+ "FYECO:0000061"
500
+ ],
501
+ "absence of nitrogen": [
502
+ "FYECO:0000062"
503
+ ],
504
+ "absence of 3 ' 5 ' - cyclic amp": [
505
+ "FYECO:0000063"
506
+ ],
507
+ "+ inositol": [
508
+ "FYECO:0000064"
509
+ ],
510
+ "absence of adenine": [
511
+ "FYECO:0000065"
512
+ ],
513
+ "absence of inositol": [
514
+ "FYECO:0000066"
515
+ ],
516
+ "+ lauric acid": [
517
+ "FYECO:0000067"
518
+ ],
519
+ "+ vaccenic acid": [
520
+ "FYECO:0000068"
521
+ ],
522
+ "+ caffeine": [
523
+ "FYECO:0000069"
524
+ ],
525
+ "absence of uracil": [
526
+ "FYECO:0000070"
527
+ ],
528
+ "+ 1 - na - pp1": [
529
+ "FYECO:0000071"
530
+ ],
531
+ "1 - na - pp1 present": [
532
+ "FYECO:0000071"
533
+ ],
534
+ "4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine add": [
535
+ "FYECO:0000071"
536
+ ],
537
+ "4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine added": [
538
+ "FYECO:0000071"
539
+ ],
540
+ "4 - amino - 1 - tert - butyl - 3 - ( 1 ' - naphthyl ) pyrazolo [ 3,4 - d ] pyrimidine present": [
541
+ "FYECO:0000071"
542
+ ],
543
+ "glycerol mm with trace glucose": [
544
+ "FYECO:0000072"
545
+ ],
546
+ "glycerol main carbon source + very low glucose mm": [
547
+ "FYECO:0000072"
548
+ ],
549
+ "glycerol minimal medium with trace glucose": [
550
+ "FYECO:0000072"
551
+ ],
552
+ "dha minimal medium": [
553
+ "FYECO:0000073"
554
+ ],
555
+ "dihydroxyacetone mm": [
556
+ "FYECO:0000073"
557
+ ],
558
+ "dihydroxyactone minimal medium": [
559
+ "FYECO:0000073"
560
+ ],
561
+ "+ nad+": [
562
+ "FYECO:0000074"
563
+ ],
564
+ "+ nadp+": [
565
+ "FYECO:0000075"
566
+ ],
567
+ "+ dihydroxyacetone": [
568
+ "FYECO:0000076"
569
+ ],
570
+ "dha add": [
571
+ "FYECO:0000076"
572
+ ],
573
+ "dha added": [
574
+ "FYECO:0000076"
575
+ ],
576
+ "+ h2o2": [
577
+ "FYECO:0000078"
578
+ ],
579
+ "hydrogen peroxide add": [
580
+ "FYECO:0000078"
581
+ ],
582
+ "hydrogen peroxide added": [
583
+ "FYECO:0000078"
584
+ ],
585
+ "+ thiabendazole": [
586
+ "FYECO:0000079"
587
+ ],
588
+ "tbz add": [
589
+ "FYECO:0000079"
590
+ ],
591
+ "tbz added": [
592
+ "FYECO:0000079"
593
+ ],
594
+ "group rich medium": [
595
+ "FYECO:0000080"
596
+ ],
597
+ "grouping rich medium": [
598
+ "FYECO:0000080"
599
+ ],
600
+ "low glucose yes": [
601
+ "FYECO:0000081"
602
+ ],
603
+ "low glucose rich medium": [
604
+ "FYECO:0000081"
605
+ ],
606
+ "low glucose ye": [
607
+ "FYECO:0000081"
608
+ ],
609
+ "+ arginine": [
610
+ "FYECO:0000082"
611
+ ],
612
+ "+ glutamate": [
613
+ "FYECO:0000084"
614
+ ],
615
+ "+ glutamine": [
616
+ "FYECO:0000085"
617
+ ],
618
+ "+ ornithine": [
619
+ "FYECO:0000086"
620
+ ],
621
+ "+ pro": [
622
+ "FYECO:0000087"
623
+ ],
624
+ "proline add": [
625
+ "FYECO:0000087"
626
+ ],
627
+ "proline added": [
628
+ "FYECO:0000087"
629
+ ],
630
+ "+ 2 - og": [
631
+ "FYECO:0000088"
632
+ ],
633
+ "2 - og present": [
634
+ "FYECO:0000088"
635
+ ],
636
+ "2 - oxoglutarate add": [
637
+ "FYECO:0000088"
638
+ ],
639
+ "2 - oxoglutarate added": [
640
+ "FYECO:0000088"
641
+ ],
642
+ "2 - oxoglutarate present": [
643
+ "FYECO:0000088"
644
+ ],
645
+ "+ na oleate": [
646
+ "FYECO:0000089"
647
+ ],
648
+ "sodium oleate add": [
649
+ "FYECO:0000089"
650
+ ],
651
+ "sodium oleate added": [
652
+ "FYECO:0000089"
653
+ ],
654
+ "+ limited nitrogen": [
655
+ "FYECO:0000090"
656
+ ],
657
+ "nitrogen starvation": [
658
+ "FYECO:0000090",
659
+ "FYECO:0000127"
660
+ ],
661
+ "+ cisplatin": [
662
+ "FYECO:0000091"
663
+ ],
664
+ "+ na ion": [
665
+ "FYECO:0000092"
666
+ ],
667
+ "+ na ions": [
668
+ "FYECO:0000092"
669
+ ],
670
+ "sodium ion add": [
671
+ "FYECO:0000092"
672
+ ],
673
+ "sodium ions added": [
674
+ "FYECO:0000092"
675
+ ],
676
+ "+ li ion": [
677
+ "FYECO:0000093"
678
+ ],
679
+ "+ li ions": [
680
+ "FYECO:0000093"
681
+ ],
682
+ "lithium ion add": [
683
+ "FYECO:0000093"
684
+ ],
685
+ "lithium ions added": [
686
+ "FYECO:0000093"
687
+ ],
688
+ "group sequential growth condition": [
689
+ "FYECO:0000094"
690
+ ],
691
+ "grouping sequential growth conditions": [
692
+ "FYECO:0000094"
693
+ ],
694
+ "24 - 48h nitrogen starvation follow by 4 - 7 day recovery in rich medium": [
695
+ "FYECO:0000095"
696
+ ],
697
+ "24 - 48h nitrogen starvation followed by 4 - 7 day recovery in rich medium": [
698
+ "FYECO:0000095"
699
+ ],
700
+ "24 - 48h nitrogen starvation follow by 5 - 12h recovery in rich medium": [
701
+ "FYECO:0000096"
702
+ ],
703
+ "24 - 48h nitrogen starvation followed by 5 - 12h recovery in rich medium": [
704
+ "FYECO:0000096"
705
+ ],
706
+ "24 - 48h nitrogen starvation follow by 12 - 24h recovery in rich medium": [
707
+ "FYECO:0000097"
708
+ ],
709
+ "24 - 48h nitrogen starvation followed by 12 - 24h recovery in rich medium": [
710
+ "FYECO:0000097"
711
+ ],
712
+ "72h - 7days nitrogen starvation follow by 12 - 24h recovery in rich medium": [
713
+ "FYECO:0000098"
714
+ ],
715
+ "72h - 7days nitrogen starvation followed by 12 - 24h recovery in rich medium": [
716
+ "FYECO:0000098"
717
+ ],
718
+ "72h - 7days nitrogen starvation follow by 4 - 7 day recovery in rich medium": [
719
+ "FYECO:0000099"
720
+ ],
721
+ "72h - 7days nitrogen starvation followed by 4 - 7 days recovery in rich medium": [
722
+ "FYECO:0000099"
723
+ ],
724
+ "water medium": [
725
+ "FYECO:0000100"
726
+ ],
727
+ "medium texture": [
728
+ "FYECO:0000101"
729
+ ],
730
+ "agar plate": [
731
+ "FYECO:0000102"
732
+ ],
733
+ "agar plates": [
734
+ "FYECO:0000102"
735
+ ],
736
+ "solid agar plate": [
737
+ "FYECO:0000102"
738
+ ],
739
+ "solid agar plates": [
740
+ "FYECO:0000102"
741
+ ],
742
+ "liquid culture": [
743
+ "FYECO:0000103"
744
+ ],
745
+ "low glucose mm": [
746
+ "FYECO:0000104"
747
+ ],
748
+ "low glucose minimal medium": [
749
+ "FYECO:0000104"
750
+ ],
751
+ "+ limited thiamine": [
752
+ "FYECO:0000105"
753
+ ],
754
+ "+ thiamine": [
755
+ "FYECO:0000106"
756
+ ],
757
+ "+ aminopyrimidine": [
758
+ "FYECO:0000107"
759
+ ],
760
+ "+ thiazole": [
761
+ "FYECO:0000108"
762
+ ],
763
+ "group excess": [
764
+ "FYECO:0000109"
765
+ ],
766
+ "grouping excess": [
767
+ "FYECO:0000109"
768
+ ],
769
+ "nitrogen starvation and recovery": [
770
+ "FYECO:0000110"
771
+ ],
772
+ "recovery from nitrogen depletion": [
773
+ "FYECO:0000110"
774
+ ],
775
+ "recovery from nitrogen starvation": [
776
+ "FYECO:0000110"
777
+ ],
778
+ "+ limited myo - inositol": [
779
+ "FYECO:0000111"
780
+ ],
781
+ "limited inositol add": [
782
+ "FYECO:0000111"
783
+ ],
784
+ "limited inositol added": [
785
+ "FYECO:0000111"
786
+ ],
787
+ "+ limited phosphate": [
788
+ "FYECO:0000112"
789
+ ],
790
+ "+ calcofluor white": [
791
+ "FYECO:0000113"
792
+ ],
793
+ "+ cyclosporin a": [
794
+ "FYECO:0000114"
795
+ ],
796
+ "+ gtp": [
797
+ "FYECO:0000115"
798
+ ],
799
+ "+ guanosine triphosphate": [
800
+ "FYECO:0000115"
801
+ ],
802
+ "group heat shock": [
803
+ "FYECO:0000116"
804
+ ],
805
+ "grouping heat shock": [
806
+ "FYECO:0000116"
807
+ ],
808
+ "heat shock and recovery at normal temperature": [
809
+ "FYECO:0000117"
810
+ ],
811
+ "heat shock for 20 - 30 min at 48 degree c , preceeded and follow by growth at normal temperature": [
812
+ "FYECO:0000117"
813
+ ],
814
+ "heat shock for 20 - 30 min at 48 degrees c , preceeded and followed by growth at normal temperature": [
815
+ "FYECO:0000117"
816
+ ],
817
+ "+ glutathione": [
818
+ "FYECO:0000118"
819
+ ],
820
+ "gsh add": [
821
+ "FYECO:0000118"
822
+ ],
823
+ "gsh added": [
824
+ "FYECO:0000118"
825
+ ],
826
+ "l - gamma - glutamyl - l - cysteinylglycine add": [
827
+ "FYECO:0000118"
828
+ ],
829
+ "l - gamma - glutamyl - l - cysteinylglycine added": [
830
+ "FYECO:0000118"
831
+ ],
832
+ "+ n - acetyl - l - cysteine": [
833
+ "FYECO:0000119"
834
+ ],
835
+ "acetylcysteine add": [
836
+ "FYECO:0000119"
837
+ ],
838
+ "acetylcysteine added": [
839
+ "FYECO:0000119"
840
+ ],
841
+ "nac add": [
842
+ "FYECO:0000119"
843
+ ],
844
+ "nac added": [
845
+ "FYECO:0000119"
846
+ ],
847
+ "group absent": [
848
+ "FYECO:0000120"
849
+ ],
850
+ "grouping absent": [
851
+ "FYECO:0000120"
852
+ ],
853
+ "+ methylamine": [
854
+ "FYECO:0000121"
855
+ ],
856
+ "group growth timing": [
857
+ "FYECO:0000122"
858
+ ],
859
+ "grouping growth timing": [
860
+ "FYECO:0000122"
861
+ ],
862
+ "growth to stationary phase": [
863
+ "FYECO:0000123"
864
+ ],
865
+ "growth to late exponential phase": [
866
+ "FYECO:0000124"
867
+ ],
868
+ "growth to exponential phase": [
869
+ "FYECO:0000125"
870
+ ],
871
+ "glucose mm": [
872
+ "FYECO:0000126"
873
+ ],
874
+ "glucose minimal medium": [
875
+ "FYECO:0000126"
876
+ ],
877
+ "normal glucose minimal medium": [
878
+ "FYECO:0000126"
879
+ ],
880
+ "normal glucose mm": [
881
+ "FYECO:0000126"
882
+ ],
883
+ "sd medium": [
884
+ "FYECO:0000126"
885
+ ],
886
+ "standard glucose minimal medium": [
887
+ "FYECO:0000126"
888
+ ],
889
+ "nitrogen absent": [
890
+ "FYECO:0000127"
891
+ ],
892
+ "nitrogen exclude": [
893
+ "FYECO:0000127"
894
+ ],
895
+ "nitrogen excluded": [
896
+ "FYECO:0000127"
897
+ ],
898
+ "nitrogen free": [
899
+ "FYECO:0000127"
900
+ ],
901
+ "ph": [
902
+ "FYECO:0000128"
903
+ ],
904
+ "high ph": [
905
+ "FYECO:0000129"
906
+ ],
907
+ "ph 6.8": [
908
+ "FYECO:0000129"
909
+ ],
910
+ "+ ubiquinone q6": [
911
+ "FYECO:0000131"
912
+ ],
913
+ "coenzyme q6 add": [
914
+ "FYECO:0000131"
915
+ ],
916
+ "coenzyme q6 added": [
917
+ "FYECO:0000131"
918
+ ],
919
+ "group experimental environment": [
920
+ "FYECO:0000132"
921
+ ],
922
+ "grouping experimental environment": [
923
+ "FYECO:0000132"
924
+ ],
925
+ "oxygen level": [
926
+ "FYECO:0000133"
927
+ ],
928
+ "anaerobic environment": [
929
+ "FYECO:0000134"
930
+ ],
931
+ "- oxygen": [
932
+ "FYECO:0000134"
933
+ ],
934
+ "anaerobiosis": [
935
+ "FYECO:0000134"
936
+ ],
937
+ "minus oxygen": [
938
+ "FYECO:0000134"
939
+ ],
940
+ "semi - aerobic environment": [
941
+ "FYECO:0000135"
942
+ ],
943
+ "hypoxia": [
944
+ "FYECO:0000135"
945
+ ],
946
+ "hypoxic environment": [
947
+ "FYECO:0000135"
948
+ ],
949
+ "limited o atom": [
950
+ "FYECO:0000135"
951
+ ],
952
+ "limited o atoms": [
953
+ "FYECO:0000135"
954
+ ],
955
+ "limited oxygen": [
956
+ "FYECO:0000135"
957
+ ],
958
+ "reduce oxygen level": [
959
+ "FYECO:0000135"
960
+ ],
961
+ "reduced oxygen level": [
962
+ "FYECO:0000135"
963
+ ],
964
+ "semi aerobic environment": [
965
+ "FYECO:0000135"
966
+ ],
967
+ "semi - anaerobic environment": [
968
+ "FYECO:0000135"
969
+ ],
970
+ "semiaerobic environment": [
971
+ "FYECO:0000135"
972
+ ],
973
+ "semianaerobic environment": [
974
+ "FYECO:0000135"
975
+ ],
976
+ "raffinose ye": [
977
+ "FYECO:0000136"
978
+ ],
979
+ "raffinose rich medium": [
980
+ "FYECO:0000136"
981
+ ],
982
+ "yes": [
983
+ "FYECO:0000137"
984
+ ],
985
+ "complex medium": [
986
+ "FYECO:0000137"
987
+ ],
988
+ "glucose rich medium": [
989
+ "FYECO:0000137"
990
+ ],
991
+ "normal glucose rich medium": [
992
+ "FYECO:0000137"
993
+ ],
994
+ "standard dextrose rich medium": [
995
+ "FYECO:0000137"
996
+ ],
997
+ "standard glucose rich medium": [
998
+ "FYECO:0000137"
999
+ ],
1000
+ "glycerol ye": [
1001
+ "FYECO:0000138"
1002
+ ],
1003
+ "glycerol rich medium": [
1004
+ "FYECO:0000138"
1005
+ ],
1006
+ "glycerol sole carbon source rich medium": [
1007
+ "FYECO:0000138"
1008
+ ],
1009
+ "glycerol sole carbon source ye": [
1010
+ "FYECO:0000138"
1011
+ ],
1012
+ "non - fermentable glycerol sole carbon source rich medium": [
1013
+ "FYECO:0000138"
1014
+ ],
1015
+ "nonfermentable glycerol sole carbon source rich medium": [
1016
+ "FYECO:0000138"
1017
+ ],
1018
+ "glycerol and ethanol rich medium": [
1019
+ "FYECO:0000139"
1020
+ ],
1021
+ "glycerol + ethanol ye": [
1022
+ "FYECO:0000139"
1023
+ ],
1024
+ "glycerol and ethanol ye": [
1025
+ "FYECO:0000139"
1026
+ ],
1027
+ "non - fermentable glycerol and ethanol rich medium": [
1028
+ "FYECO:0000139"
1029
+ ],
1030
+ "nonfermentable glycerol and ethanol rich medium": [
1031
+ "FYECO:0000139"
1032
+ ],
1033
+ "in vitro": [
1034
+ "FYECO:0000140"
1035
+ ],
1036
+ "in vivo": [
1037
+ "FYECO:0000141"
1038
+ ],
1039
+ "+ ade": [
1040
+ "FYECO:0000142"
1041
+ ],
1042
+ "+ adenine": [
1043
+ "FYECO:0000142"
1044
+ ],
1045
+ "+ antimycin a": [
1046
+ "FYECO:0000143"
1047
+ ],
1048
+ "respiratory chain inhibitor": [
1049
+ "FYECO:0000143"
1050
+ ],
1051
+ "sucrose ye": [
1052
+ "FYECO:0000144"
1053
+ ],
1054
+ "sucrose rich medium": [
1055
+ "FYECO:0000144"
1056
+ ],
1057
+ "maltose mm": [
1058
+ "FYECO:0000145"
1059
+ ],
1060
+ "maltose minimal medium": [
1061
+ "FYECO:0000145"
1062
+ ],
1063
+ "trehalose mm": [
1064
+ "FYECO:0000146"
1065
+ ],
1066
+ "trehalose minimal medium": [
1067
+ "FYECO:0000146"
1068
+ ],
1069
+ "sucrose mm": [
1070
+ "FYECO:0000147"
1071
+ ],
1072
+ "sucrose minimal medium": [
1073
+ "FYECO:0000147"
1074
+ ],
1075
+ "galactose rich medium with trace glucose": [
1076
+ "FYECO:0000148"
1077
+ ],
1078
+ "non - fermentable galactose and very low glucose rich medium": [
1079
+ "FYECO:0000148"
1080
+ ],
1081
+ "nonfermentable galactose and very low glucose rich medium": [
1082
+ "FYECO:0000148"
1083
+ ],
1084
+ "ypgala": [
1085
+ "FYECO:0000148"
1086
+ ],
1087
+ "+ 1 - dnj": [
1088
+ "FYECO:0000149"
1089
+ ],
1090
+ "1 - deoxynojirimycin add": [
1091
+ "FYECO:0000149"
1092
+ ],
1093
+ "1 - deoxynojirimycin added": [
1094
+ "FYECO:0000149"
1095
+ ],
1096
+ "deoxynojirimycin add": [
1097
+ "FYECO:0000149"
1098
+ ],
1099
+ "deoxynojirimycin added": [
1100
+ "FYECO:0000149"
1101
+ ],
1102
+ "dnj add": [
1103
+ "FYECO:0000149"
1104
+ ],
1105
+ "dnj added": [
1106
+ "FYECO:0000149"
1107
+ ],
1108
+ "calcium absent": [
1109
+ "FYECO:0000150"
1110
+ ],
1111
+ "+ mn ion": [
1112
+ "FYECO:0000151"
1113
+ ],
1114
+ "+ mn ions": [
1115
+ "FYECO:0000151"
1116
+ ],
1117
+ "manganese ion add": [
1118
+ "FYECO:0000151"
1119
+ ],
1120
+ "manganese ions added": [
1121
+ "FYECO:0000151"
1122
+ ],
1123
+ "mn2+ add": [
1124
+ "FYECO:0000151"
1125
+ ],
1126
+ "mn2+ added": [
1127
+ "FYECO:0000151"
1128
+ ],
1129
+ "+ mannose": [
1130
+ "FYECO:0000152"
1131
+ ],
1132
+ "+ diethyl maleate": [
1133
+ "FYECO:0000153"
1134
+ ],
1135
+ "diethyl maleate add": [
1136
+ "FYECO:0000153"
1137
+ ],
1138
+ "diethyl maleate added": [
1139
+ "FYECO:0000153"
1140
+ ],
1141
+ "+ ethanolamine": [
1142
+ "FYECO:0000154"
1143
+ ],
1144
+ "2 - aminoethanol add": [
1145
+ "FYECO:0000154"
1146
+ ],
1147
+ "2 - aminoethanol added": [
1148
+ "FYECO:0000154"
1149
+ ],
1150
+ "eta add": [
1151
+ "FYECO:0000154"
1152
+ ],
1153
+ "eta added": [
1154
+ "FYECO:0000154"
1155
+ ],
1156
+ "mea add": [
1157
+ "FYECO:0000154"
1158
+ ],
1159
+ "mea added": [
1160
+ "FYECO:0000154"
1161
+ ],
1162
+ "monoethanolamine add": [
1163
+ "FYECO:0000154"
1164
+ ],
1165
+ "monoethanolamine added": [
1166
+ "FYECO:0000154"
1167
+ ],
1168
+ "+ choline": [
1169
+ "FYECO:0000155"
1170
+ ],
1171
+ "rhodamine - phalloidin add": [
1172
+ "FYECO:0000156"
1173
+ ],
1174
+ "rhodamine - phalloidin added": [
1175
+ "FYECO:0000156"
1176
+ ],
1177
+ "rhodamine phalloidin": [
1178
+ "FYECO:0000156"
1179
+ ],
1180
+ "growth to stationary phase in rich medium follow by transfer to h2o": [
1181
+ "FYECO:0000157"
1182
+ ],
1183
+ "growth to stationary phase in rich medium followed by transfer to h2o": [
1184
+ "FYECO:0000157"
1185
+ ],
1186
+ "group growth to stationary phase": [
1187
+ "FYECO:0000158"
1188
+ ],
1189
+ "grouping growth to stationary phase": [
1190
+ "FYECO:0000158"
1191
+ ],
1192
+ "growth to stationary phase in rich medium follow by transfer to minimal medium": [
1193
+ "FYECO:0000159"
1194
+ ],
1195
+ "growth to stationary phase in rich medium followed by transfer to minimal medium": [
1196
+ "FYECO:0000159"
1197
+ ],
1198
+ "+ tacrolimus": [
1199
+ "FYECO:0000160"
1200
+ ],
1201
+ "fk506 add": [
1202
+ "FYECO:0000160"
1203
+ ],
1204
+ "fk506 added": [
1205
+ "FYECO:0000160"
1206
+ ],
1207
+ "tacrolimus add": [
1208
+ "FYECO:0000160"
1209
+ ],
1210
+ "tacrolimus added": [
1211
+ "FYECO:0000160"
1212
+ ],
1213
+ "hoechst stain add": [
1214
+ "FYECO:0000161"
1215
+ ],
1216
+ "hoechst stain added": [
1217
+ "FYECO:0000161"
1218
+ ],
1219
+ "bisbenzimide add": [
1220
+ "FYECO:0000161"
1221
+ ],
1222
+ "bisbenzimide added": [
1223
+ "FYECO:0000161"
1224
+ ],
1225
+ "high glucose yes": [
1226
+ "FYECO:0000162"
1227
+ ],
1228
+ "high glucose rich medium": [
1229
+ "FYECO:0000162"
1230
+ ],
1231
+ "fitc - conjugate lectin add": [
1232
+ "FYECO:0000163"
1233
+ ],
1234
+ "fitc - conjugated lectin added": [
1235
+ "FYECO:0000163"
1236
+ ],
1237
+ "anti - tubulin antibody add": [
1238
+ "FYECO:0000164"
1239
+ ],
1240
+ "anti - tubulin antibodies added": [
1241
+ "FYECO:0000164"
1242
+ ],
1243
+ "anti - tubulin antibody added": [
1244
+ "FYECO:0000164"
1245
+ ],
1246
+ "+ na2s": [
1247
+ "FYECO:0000165"
1248
+ ],
1249
+ "sodium sulfide add": [
1250
+ "FYECO:0000165"
1251
+ ],
1252
+ "sodium sulfide added": [
1253
+ "FYECO:0000165"
1254
+ ],
1255
+ "+ nacl": [
1256
+ "FYECO:0000166"
1257
+ ],
1258
+ "sodium chloride add": [
1259
+ "FYECO:0000166"
1260
+ ],
1261
+ "sodium chloride added": [
1262
+ "FYECO:0000166"
1263
+ ],
1264
+ "+ sd": [
1265
+ "FYECO:0000167"
1266
+ ],
1267
+ "+ sds": [
1268
+ "FYECO:0000167"
1269
+ ],
1270
+ "sodium dodecyl sulfate add": [
1271
+ "FYECO:0000167"
1272
+ ],
1273
+ "sodium dodecyl sulfate added": [
1274
+ "FYECO:0000167"
1275
+ ],
1276
+ "heat shock and recovery at high temperature": [
1277
+ "FYECO:0000168"
1278
+ ],
1279
+ "heat shock for 20 - 30 min at 48 degree c , preceeded and follow by growth at high temperature": [
1280
+ "FYECO:0000168"
1281
+ ],
1282
+ "heat shock for 20 - 30 min at 48 degrees c , preceeded and followed by growth at high temperature": [
1283
+ "FYECO:0000168"
1284
+ ],
1285
+ "+ limited ethanolamine": [
1286
+ "FYECO:0000169"
1287
+ ],
1288
+ "+ hu": [
1289
+ "FYECO:0000170"
1290
+ ],
1291
+ "hydroxyurea add": [
1292
+ "FYECO:0000170"
1293
+ ],
1294
+ "hydroxyurea added": [
1295
+ "FYECO:0000170"
1296
+ ],
1297
+ "sorbitol absent": [
1298
+ "FYECO:0000171"
1299
+ ],
1300
+ "+ zn ion": [
1301
+ "FYECO:0000172"
1302
+ ],
1303
+ "+ zn ions": [
1304
+ "FYECO:0000172"
1305
+ ],
1306
+ "zinc ion add": [
1307
+ "FYECO:0000172"
1308
+ ],
1309
+ "zinc ions added": [
1310
+ "FYECO:0000172"
1311
+ ],
1312
+ "+ zncl2": [
1313
+ "FYECO:0000173"
1314
+ ],
1315
+ "zinc chloride add": [
1316
+ "FYECO:0000173"
1317
+ ],
1318
+ "zinc chloride added": [
1319
+ "FYECO:0000173"
1320
+ ],
1321
+ "+ fecl2": [
1322
+ "FYECO:0000174"
1323
+ ],
1324
+ "iron chloride add": [
1325
+ "FYECO:0000174",
1326
+ "FYECO:0000281"
1327
+ ],
1328
+ "iron chloride added": [
1329
+ "FYECO:0000174",
1330
+ "FYECO:0000281"
1331
+ ],
1332
+ "iron dichloride add": [
1333
+ "FYECO:0000174"
1334
+ ],
1335
+ "iron dichloride added": [
1336
+ "FYECO:0000174"
1337
+ ],
1338
+ "iron ( ii ) chloride": [
1339
+ "FYECO:0000174"
1340
+ ],
1341
+ "+ cdcl2": [
1342
+ "FYECO:0000175"
1343
+ ],
1344
+ "+ cadmium chloride": [
1345
+ "FYECO:0000175"
1346
+ ],
1347
+ "+ edta": [
1348
+ "FYECO:0000176"
1349
+ ],
1350
+ "edta add": [
1351
+ "FYECO:0000176"
1352
+ ],
1353
+ "edta added": [
1354
+ "FYECO:0000176"
1355
+ ],
1356
+ "ethylenediaminetetraacetic acid add": [
1357
+ "FYECO:0000176"
1358
+ ],
1359
+ "ethylenediaminetetraacetic acid added": [
1360
+ "FYECO:0000176"
1361
+ ],
1362
+ "+ limited zinc": [
1363
+ "FYECO:0000177"
1364
+ ],
1365
+ "limited zn add": [
1366
+ "FYECO:0000177"
1367
+ ],
1368
+ "limited zn added": [
1369
+ "FYECO:0000177"
1370
+ ],
1371
+ "+ meet": [
1372
+ "FYECO:0000178"
1373
+ ],
1374
+ "+ met": [
1375
+ "FYECO:0000178"
1376
+ ],
1377
+ "m add": [
1378
+ "FYECO:0000178"
1379
+ ],
1380
+ "m added": [
1381
+ "FYECO:0000178"
1382
+ ],
1383
+ "methionine add": [
1384
+ "FYECO:0000178"
1385
+ ],
1386
+ "methionine added": [
1387
+ "FYECO:0000178"
1388
+ ],
1389
+ "+ cysteine": [
1390
+ "FYECO:0000179"
1391
+ ],
1392
+ "c add": [
1393
+ "FYECO:0000179"
1394
+ ],
1395
+ "c added": [
1396
+ "FYECO:0000179"
1397
+ ],
1398
+ "cys add": [
1399
+ "FYECO:0000179"
1400
+ ],
1401
+ "cys added": [
1402
+ "FYECO:0000179"
1403
+ ],
1404
+ "+ limit sulfur": [
1405
+ "FYECO:0000180"
1406
+ ],
1407
+ "+ limited sulfur": [
1408
+ "FYECO:0000180"
1409
+ ],
1410
+ "limited sulphur add": [
1411
+ "FYECO:0000180"
1412
+ ],
1413
+ "limited sulphur added": [
1414
+ "FYECO:0000180"
1415
+ ],
1416
+ "+ glucose": [
1417
+ "FYECO:0000181"
1418
+ ],
1419
+ "+ asparagine": [
1420
+ "FYECO:0000182"
1421
+ ],
1422
+ "asn add": [
1423
+ "FYECO:0000182"
1424
+ ],
1425
+ "asn added": [
1426
+ "FYECO:0000182"
1427
+ ],
1428
+ "+ alpha - tocopherol": [
1429
+ "FYECO:0000183"
1430
+ ],
1431
+ "vitamin e add": [
1432
+ "FYECO:0000183"
1433
+ ],
1434
+ "vitamin e added": [
1435
+ "FYECO:0000183"
1436
+ ],
1437
+ "+ cucl2": [
1438
+ "FYECO:0000184"
1439
+ ],
1440
+ "copper chloride add": [
1441
+ "FYECO:0000184"
1442
+ ],
1443
+ "copper chloride added": [
1444
+ "FYECO:0000184"
1445
+ ],
1446
+ "+ limited sodium": [
1447
+ "FYECO:0000185"
1448
+ ],
1449
+ "+ feso4": [
1450
+ "FYECO:0000186"
1451
+ ],
1452
+ "iron sulfate add": [
1453
+ "FYECO:0000186"
1454
+ ],
1455
+ "iron sulfate added": [
1456
+ "FYECO:0000186"
1457
+ ],
1458
+ "iron sulphate add": [
1459
+ "FYECO:0000186"
1460
+ ],
1461
+ "iron sulphate added": [
1462
+ "FYECO:0000186"
1463
+ ],
1464
+ "pantothenate absent": [
1465
+ "FYECO:0000187"
1466
+ ],
1467
+ "+ pantothenate": [
1468
+ "FYECO:0000188"
1469
+ ],
1470
+ "+ limited pantothenate": [
1471
+ "FYECO:0000189"
1472
+ ],
1473
+ "dapi add": [
1474
+ "FYECO:0000190"
1475
+ ],
1476
+ "dapi added": [
1477
+ "FYECO:0000190"
1478
+ ],
1479
+ "4',6 - diamidino - 2 - phenylindole add": [
1480
+ "FYECO:0000190"
1481
+ ],
1482
+ "4',6 - diamidino - 2 - phenylindole added": [
1483
+ "FYECO:0000190"
1484
+ ],
1485
+ "+ biotin": [
1486
+ "FYECO:0000191"
1487
+ ],
1488
+ "biotin absent": [
1489
+ "FYECO:0000192"
1490
+ ],
1491
+ "+ dethiobiotin": [
1492
+ "FYECO:0000193"
1493
+ ],
1494
+ "desthiobiotin add": [
1495
+ "FYECO:0000193"
1496
+ ],
1497
+ "desthiobiotin added": [
1498
+ "FYECO:0000193"
1499
+ ],
1500
+ "+ limited biotin": [
1501
+ "FYECO:0000194"
1502
+ ],
1503
+ "+ limited dethiobiotin": [
1504
+ "FYECO:0000195"
1505
+ ],
1506
+ "limited desthiobiotin add": [
1507
+ "FYECO:0000195"
1508
+ ],
1509
+ "limited desthiobiotin added": [
1510
+ "FYECO:0000195"
1511
+ ],
1512
+ "glucose mm , urea nitrogen source": [
1513
+ "FYECO:0000196"
1514
+ ],
1515
+ "glucose minimal medium , urea nitrogen source": [
1516
+ "FYECO:0000196"
1517
+ ],
1518
+ "standard glucose minimal medium , urea nitrogen source": [
1519
+ "FYECO:0000196"
1520
+ ],
1521
+ "+ limited nickel": [
1522
+ "FYECO:0000197"
1523
+ ],
1524
+ "+ ni ion": [
1525
+ "FYECO:0000198"
1526
+ ],
1527
+ "+ ni ions": [
1528
+ "FYECO:0000198"
1529
+ ],
1530
+ "nickel ion add": [
1531
+ "FYECO:0000198"
1532
+ ],
1533
+ "nickel ions added": [
1534
+ "FYECO:0000198"
1535
+ ],
1536
+ "+ lys": [
1537
+ "FYECO:0000199"
1538
+ ],
1539
+ "lysine add": [
1540
+ "FYECO:0000199"
1541
+ ],
1542
+ "lysine added": [
1543
+ "FYECO:0000199"
1544
+ ],
1545
+ "+ peptone": [
1546
+ "FYECO:0000200"
1547
+ ],
1548
+ "ypd": [
1549
+ "FYECO:0000201"
1550
+ ],
1551
+ "glucose rich medium , peptone / ye nitrogen source": [
1552
+ "FYECO:0000201"
1553
+ ],
1554
+ "chill cell": [
1555
+ "FYECO:0000202"
1556
+ ],
1557
+ "chilled cells": [
1558
+ "FYECO:0000202"
1559
+ ],
1560
+ "ice": [
1561
+ "FYECO:0000202"
1562
+ ],
1563
+ "diploid cell": [
1564
+ "FYECO:0000203"
1565
+ ],
1566
+ "diploid cells": [
1567
+ "FYECO:0000203"
1568
+ ],
1569
+ "2n cell": [
1570
+ "FYECO:0000203"
1571
+ ],
1572
+ "2n cells": [
1573
+ "FYECO:0000203"
1574
+ ],
1575
+ "+ na2so4": [
1576
+ "FYECO:0000205"
1577
+ ],
1578
+ "sodium sulfate add": [
1579
+ "FYECO:0000205"
1580
+ ],
1581
+ "sodium sulfate added": [
1582
+ "FYECO:0000205"
1583
+ ],
1584
+ "+ cscl": [
1585
+ "FYECO:0000206"
1586
+ ],
1587
+ "caesium chloride add": [
1588
+ "FYECO:0000206"
1589
+ ],
1590
+ "caesium chloride added": [
1591
+ "FYECO:0000206"
1592
+ ],
1593
+ "cesium chloride add": [
1594
+ "FYECO:0000206"
1595
+ ],
1596
+ "cesium chloride added": [
1597
+ "FYECO:0000206"
1598
+ ],
1599
+ "+ kcl": [
1600
+ "FYECO:0000207"
1601
+ ],
1602
+ "potassium chloride add": [
1603
+ "FYECO:0000207"
1604
+ ],
1605
+ "potassium chloride added": [
1606
+ "FYECO:0000207"
1607
+ ],
1608
+ "+ nh4cl": [
1609
+ "FYECO:0000208"
1610
+ ],
1611
+ "ammonium chloride add": [
1612
+ "FYECO:0000208"
1613
+ ],
1614
+ "ammonium chloride added": [
1615
+ "FYECO:0000208"
1616
+ ],
1617
+ "+ biochanin a": [
1618
+ "FYECO:0000209"
1619
+ ],
1620
+ "bca add": [
1621
+ "FYECO:0000209"
1622
+ ],
1623
+ "bca added": [
1624
+ "FYECO:0000209"
1625
+ ],
1626
+ "+ limit glucose": [
1627
+ "FYECO:0000210"
1628
+ ],
1629
+ "+ limited glucose": [
1630
+ "FYECO:0000210"
1631
+ ],
1632
+ "+ mm": [
1633
+ "FYECO:0000211"
1634
+ ],
1635
+ "+ mms": [
1636
+ "FYECO:0000211"
1637
+ ],
1638
+ "methyl methanesulfonate add": [
1639
+ "FYECO:0000211"
1640
+ ],
1641
+ "methyl methanesulfonate added": [
1642
+ "FYECO:0000211"
1643
+ ],
1644
+ "+ ethanol": [
1645
+ "FYECO:0000212"
1646
+ ],
1647
+ "non - fermentable carbon source medium": [
1648
+ "FYECO:0000213"
1649
+ ],
1650
+ "non - fermentable carbon sources medium": [
1651
+ "FYECO:0000213"
1652
+ ],
1653
+ "+ mgcl2": [
1654
+ "FYECO:0000214"
1655
+ ],
1656
+ "magnesium chloride add": [
1657
+ "FYECO:0000214"
1658
+ ],
1659
+ "magnesium chloride added": [
1660
+ "FYECO:0000214"
1661
+ ],
1662
+ "low ph": [
1663
+ "FYECO:0000215"
1664
+ ],
1665
+ "growth < 24 hr": [
1666
+ "FYECO:0000216"
1667
+ ],
1668
+ "growth < 24 hrs": [
1669
+ "FYECO:0000216"
1670
+ ],
1671
+ "growth < 24 hour": [
1672
+ "FYECO:0000216"
1673
+ ],
1674
+ "growth < 24 hours": [
1675
+ "FYECO:0000216"
1676
+ ],
1677
+ "overnight culture": [
1678
+ "FYECO:0000216"
1679
+ ],
1680
+ "growth > 24 hr": [
1681
+ "FYECO:0000217"
1682
+ ],
1683
+ "growth > 24 hrs": [
1684
+ "FYECO:0000217"
1685
+ ],
1686
+ "growth > 24 hour": [
1687
+ "FYECO:0000217"
1688
+ ],
1689
+ "growth > 24 hours": [
1690
+ "FYECO:0000217"
1691
+ ],
1692
+ "+ beta - estradiol": [
1693
+ "FYECO:0000218"
1694
+ ],
1695
+ "nitrogen source shift , proline to glutamate": [
1696
+ "FYECO:0000219"
1697
+ ],
1698
+ "nitrogen source shift , glutamate to proline": [
1699
+ "FYECO:0000220"
1700
+ ],
1701
+ "nitrogen source shift": [
1702
+ "FYECO:0000221"
1703
+ ],
1704
+ "+ nocodazole": [
1705
+ "FYECO:0000222"
1706
+ ],
1707
+ "+ 1 - nm - pp1": [
1708
+ "FYECO:0000223"
1709
+ ],
1710
+ "+ his": [
1711
+ "FYECO:0000224"
1712
+ ],
1713
+ "histidine add": [
1714
+ "FYECO:0000224"
1715
+ ],
1716
+ "histidine added": [
1717
+ "FYECO:0000224"
1718
+ ],
1719
+ "+ ura": [
1720
+ "FYECO:0000225"
1721
+ ],
1722
+ "uracil add": [
1723
+ "FYECO:0000225"
1724
+ ],
1725
+ "uracil added": [
1726
+ "FYECO:0000225"
1727
+ ],
1728
+ "+ leu": [
1729
+ "FYECO:0000226"
1730
+ ],
1731
+ "leucine add": [
1732
+ "FYECO:0000226"
1733
+ ],
1734
+ "leucine added": [
1735
+ "FYECO:0000226"
1736
+ ],
1737
+ "permissive temperature": [
1738
+ "FYECO:0000227"
1739
+ ],
1740
+ "semi - permissive temperature": [
1741
+ "FYECO:0000228"
1742
+ ],
1743
+ "semipermissive temperature": [
1744
+ "FYECO:0000228"
1745
+ ],
1746
+ "restrictive temperature": [
1747
+ "FYECO:0000229"
1748
+ ],
1749
+ "non - permissive temperature": [
1750
+ "FYECO:0000229"
1751
+ ],
1752
+ "nonpermissive temperature": [
1753
+ "FYECO:0000229"
1754
+ ],
1755
+ "low nitrogen glucose mm": [
1756
+ "FYECO:0000230"
1757
+ ],
1758
+ "low nitrogen glucose minimal medium": [
1759
+ "FYECO:0000230"
1760
+ ],
1761
+ "+ na2so3": [
1762
+ "FYECO:0000231"
1763
+ ],
1764
+ "sodium sulfite add": [
1765
+ "FYECO:0000231"
1766
+ ],
1767
+ "sodium sulfite added": [
1768
+ "FYECO:0000231"
1769
+ ],
1770
+ "temperature shift , low to standard": [
1771
+ "FYECO:0000232"
1772
+ ],
1773
+ "growth at low temperature follow by growth at standard temperature": [
1774
+ "FYECO:0000232"
1775
+ ],
1776
+ "growth at low temperature followed by growth at standard temperature": [
1777
+ "FYECO:0000232"
1778
+ ],
1779
+ "uracil absent": [
1780
+ "FYECO:0000233"
1781
+ ],
1782
+ "+ sulfite": [
1783
+ "FYECO:0000234"
1784
+ ],
1785
+ "+ microtubule depolymerizing drug": [
1786
+ "FYECO:0000235"
1787
+ ],
1788
+ "+ microtubule depolymerizing drugs": [
1789
+ "FYECO:0000235"
1790
+ ],
1791
+ "maltose ye": [
1792
+ "FYECO:0000236"
1793
+ ],
1794
+ "maltose rich medium": [
1795
+ "FYECO:0000236"
1796
+ ],
1797
+ "growth > 48 hr": [
1798
+ "FYECO:0000237"
1799
+ ],
1800
+ "growth > 48 hrs": [
1801
+ "FYECO:0000237"
1802
+ ],
1803
+ "growth > 48 hour": [
1804
+ "FYECO:0000237"
1805
+ ],
1806
+ "growth > 48 hours": [
1807
+ "FYECO:0000237"
1808
+ ],
1809
+ "group condition combination": [
1810
+ "FYECO:0000238"
1811
+ ],
1812
+ "grouping condition combinations": [
1813
+ "FYECO:0000238"
1814
+ ],
1815
+ "group starvation and timing": [
1816
+ "FYECO:0000239"
1817
+ ],
1818
+ "grouping starvation and timing": [
1819
+ "FYECO:0000239"
1820
+ ],
1821
+ "> 7 day nitrogen starvation": [
1822
+ "FYECO:0000240"
1823
+ ],
1824
+ "> 7 days nitrogen starvation": [
1825
+ "FYECO:0000240"
1826
+ ],
1827
+ "28 day nitrogen starvation follow by 10 - 50 hour recovery in minimal medium": [
1828
+ "FYECO:0000241"
1829
+ ],
1830
+ "28 days nitrogen starvation followed by 10 - 50 hours recovery in minimal medium": [
1831
+ "FYECO:0000241"
1832
+ ],
1833
+ "+ rapamycin": [
1834
+ "FYECO:0000242"
1835
+ ],
1836
+ "+ sirolimus": [
1837
+ "FYECO:0000242"
1838
+ ],
1839
+ "+ lmb": [
1840
+ "FYECO:0000243"
1841
+ ],
1842
+ "+ leptomycin b": [
1843
+ "FYECO:0000243"
1844
+ ],
1845
+ "+ 3mb - pp1": [
1846
+ "FYECO:0000244"
1847
+ ],
1848
+ "+ phosphate": [
1849
+ "FYECO:0000245"
1850
+ ],
1851
+ "glucose mm , proline nitrogen source": [
1852
+ "FYECO:0000246"
1853
+ ],
1854
+ "+ cdso4": [
1855
+ "FYECO:0000247"
1856
+ ],
1857
+ "+ cadmium sulfate": [
1858
+ "FYECO:0000247"
1859
+ ],
1860
+ "+ lata": [
1861
+ "FYECO:0000248"
1862
+ ],
1863
+ "+ latrunculin a": [
1864
+ "FYECO:0000248"
1865
+ ],
1866
+ "+ cuso4": [
1867
+ "FYECO:0000249"
1868
+ ],
1869
+ "+ copper ( ii ) sulfate": [
1870
+ "FYECO:0000249"
1871
+ ],
1872
+ "+ agno3": [
1873
+ "FYECO:0000250"
1874
+ ],
1875
+ "+ silver nitrate": [
1876
+ "FYECO:0000250"
1877
+ ],
1878
+ "+ amitrole": [
1879
+ "FYECO:0000251"
1880
+ ],
1881
+ "+ 3 - amino - 1,2,4 - triazole": [
1882
+ "FYECO:0000251"
1883
+ ],
1884
+ "+ glycerol": [
1885
+ "FYECO:0000252"
1886
+ ],
1887
+ "glycerol add": [
1888
+ "FYECO:0000252"
1889
+ ],
1890
+ "glycerol added": [
1891
+ "FYECO:0000252"
1892
+ ],
1893
+ "+ limited ammonium": [
1894
+ "FYECO:0000253"
1895
+ ],
1896
+ "+ limited nh4cl": [
1897
+ "FYECO:0000253"
1898
+ ],
1899
+ "glucose mm , ammonium nitrogen source": [
1900
+ "FYECO:0000254"
1901
+ ],
1902
+ "arginine absent": [
1903
+ "FYECO:0000255"
1904
+ ],
1905
+ "glycerol mm with trace ethanol": [
1906
+ "FYECO:0000256"
1907
+ ],
1908
+ "+ cycloheximide": [
1909
+ "FYECO:0000257"
1910
+ ],
1911
+ "+ arsenate": [
1912
+ "FYECO:0000258"
1913
+ ],
1914
+ "+ arsenic": [
1915
+ "FYECO:0000259"
1916
+ ],
1917
+ "hu block and release": [
1918
+ "FYECO:0000260"
1919
+ ],
1920
+ "+ cacl2": [
1921
+ "FYECO:0000261"
1922
+ ],
1923
+ "+ calcium chloride": [
1924
+ "FYECO:0000261"
1925
+ ],
1926
+ "glucose minimal medium , exclude nitrogen": [
1927
+ "FYECO:0000262"
1928
+ ],
1929
+ "glucose minimal medium , excluding nitrogen": [
1930
+ "FYECO:0000262"
1931
+ ],
1932
+ "glucose mm , glutamate nitrogen source": [
1933
+ "FYECO:0000263"
1934
+ ],
1935
+ "glucose minimal medium , glutamate nitrogen source": [
1936
+ "FYECO:0000263"
1937
+ ],
1938
+ "standard glucose minimal medium , glutamate nitrogen source": [
1939
+ "FYECO:0000263"
1940
+ ],
1941
+ "glucose mm , organic nitrogen source , no inorganic nitrogen": [
1942
+ "FYECO:0000264"
1943
+ ],
1944
+ "> 6 hr in nitrogen starvation": [
1945
+ "FYECO:0000265"
1946
+ ],
1947
+ "> 6 hrs in nitrogen starvation": [
1948
+ "FYECO:0000265"
1949
+ ],
1950
+ "> 6 hour in nitrogen starvation": [
1951
+ "FYECO:0000265"
1952
+ ],
1953
+ "> 6 hours in nitrogen starvation": [
1954
+ "FYECO:0000265"
1955
+ ],
1956
+ "glucose mm , xanthine nitrogen source": [
1957
+ "FYECO:0000266"
1958
+ ],
1959
+ "+ naphthaleneacetic acid": [
1960
+ "FYECO:0000267"
1961
+ ],
1962
+ "+ trichostatin a": [
1963
+ "FYECO:0000268"
1964
+ ],
1965
+ "+ mevalonate": [
1966
+ "FYECO:0000269"
1967
+ ],
1968
+ "+ tev protease": [
1969
+ "FYECO:0000270"
1970
+ ],
1971
+ "+ snp": [
1972
+ "FYECO:0000271"
1973
+ ],
1974
+ "+ sodium nitroprusside": [
1975
+ "FYECO:0000271"
1976
+ ],
1977
+ "glucose mm , no nitrogen": [
1978
+ "FYECO:0000272"
1979
+ ],
1980
+ "glucose mm , no glucose": [
1981
+ "FYECO:0000273"
1982
+ ],
1983
+ "glucose mm , adenine nitrogen source": [
1984
+ "FYECO:0000274"
1985
+ ],
1986
+ "competitive culture": [
1987
+ "FYECO:0000275"
1988
+ ],
1989
+ "glucose mm , uracil nitrogen source": [
1990
+ "FYECO:0000276"
1991
+ ],
1992
+ "+ bleomycin": [
1993
+ "FYECO:0000277"
1994
+ ],
1995
+ "glucose mm , isoleucine nitrogen source": [
1996
+ "FYECO:0000278"
1997
+ ],
1998
+ "+ mncl2": [
1999
+ "FYECO:0000279"
2000
+ ],
2001
+ "manganese chloride add": [
2002
+ "FYECO:0000279"
2003
+ ],
2004
+ "manganese chloride added": [
2005
+ "FYECO:0000279"
2006
+ ],
2007
+ "+ limited leucine": [
2008
+ "FYECO:0000280"
2009
+ ],
2010
+ "+ fecl3": [
2011
+ "FYECO:0000281"
2012
+ ],
2013
+ "iron trichloride add": [
2014
+ "FYECO:0000281"
2015
+ ],
2016
+ "iron trichloride added": [
2017
+ "FYECO:0000281"
2018
+ ],
2019
+ "iron ( iii ) chloride": [
2020
+ "FYECO:0000281"
2021
+ ],
2022
+ "+ limited aminolevulinic acid": [
2023
+ "FYECO:0000282"
2024
+ ],
2025
+ "+ limited ala": [
2026
+ "FYECO:0000282"
2027
+ ],
2028
+ "+ hemin": [
2029
+ "FYECO:0000283"
2030
+ ],
2031
+ "+ thiosulfate": [
2032
+ "FYECO:0000284"
2033
+ ],
2034
+ "cold shock and recovery at normal temperature": [
2035
+ "FYECO:0000285"
2036
+ ],
2037
+ "glucose mm , no adenine": [
2038
+ "FYECO:0000286"
2039
+ ],
2040
+ "+ nigericin": [
2041
+ "FYECO:0000287"
2042
+ ],
2043
+ "temperature shift , high to standard": [
2044
+ "FYECO:0000288"
2045
+ ],
2046
+ "growth at high temperature follow by growth at standard temperature": [
2047
+ "FYECO:0000288"
2048
+ ],
2049
+ "growth at high temperature followed by growth at standard temperature": [
2050
+ "FYECO:0000288"
2051
+ ],
2052
+ "galactose mm": [
2053
+ "FYECO:0000289"
2054
+ ],
2055
+ "+ carbendazim": [
2056
+ "FYECO:0000290"
2057
+ ],
2058
+ "cbz add": [
2059
+ "FYECO:0000290"
2060
+ ],
2061
+ "cbz added": [
2062
+ "FYECO:0000290"
2063
+ ],
2064
+ "mbc add": [
2065
+ "FYECO:0000290"
2066
+ ],
2067
+ "mbc added": [
2068
+ "FYECO:0000290"
2069
+ ],
2070
+ "mecarzole add": [
2071
+ "FYECO:0000290"
2072
+ ],
2073
+ "mecarzole added": [
2074
+ "FYECO:0000290"
2075
+ ],
2076
+ "temperature block and release": [
2077
+ "FYECO:0000291"
2078
+ ],
2079
+ "nitrogen starvation at normal temperature and shift to high temperature in rich medium": [
2080
+ "FYECO:0000292"
2081
+ ],
2082
+ "temperature shift , low to high": [
2083
+ "FYECO:0000293"
2084
+ ],
2085
+ "temperature shift , high to low": [
2086
+ "FYECO:0000294"
2087
+ ],
2088
+ "two - step temperature shift , low to standard , standard to high": [
2089
+ "FYECO:0000295"
2090
+ ],
2091
+ "glucose mm , phenylalanine nitrogen source": [
2092
+ "FYECO:0000296"
2093
+ ],
2094
+ "+ naaso2": [
2095
+ "FYECO:0000297"
2096
+ ],
2097
+ "sodium arsenite add": [
2098
+ "FYECO:0000297"
2099
+ ],
2100
+ "sodium arsenite added": [
2101
+ "FYECO:0000297"
2102
+ ],
2103
+ "+ zymolyase": [
2104
+ "FYECO:0000298"
2105
+ ],
2106
+ "+ queuosine": [
2107
+ "FYECO:0000299"
2108
+ ],
2109
+ "temperature shift , standard to high": [
2110
+ "FYECO:0000300"
2111
+ ],
2112
+ "+ queuine": [
2113
+ "FYECO:0000301"
2114
+ ],
2115
+ "+ ammonium iron ( 2+ ) sulfate": [
2116
+ "FYECO:0000302"
2117
+ ],
2118
+ "+ ferrous ammonium sulfate ( anhydrous )": [
2119
+ "FYECO:0000302"
2120
+ ],
2121
+ "+ menadione": [
2122
+ "FYECO:0000303"
2123
+ ],
2124
+ "+ tbhp": [
2125
+ "FYECO:0000304"
2126
+ ],
2127
+ "tert - butyl hydroperoxide": [
2128
+ "FYECO:0000304"
2129
+ ],
2130
+ "ionize radiation": [
2131
+ "FYECO:0000305"
2132
+ ],
2133
+ "ionizing radiation": [
2134
+ "FYECO:0000305"
2135
+ ],
2136
+ "gamma irradiation": [
2137
+ "FYECO:0000305"
2138
+ ],
2139
+ "gamma radiation": [
2140
+ "FYECO:0000305"
2141
+ ],
2142
+ "two - step temperature shift , standard to low , low to high": [
2143
+ "FYECO:0000306"
2144
+ ],
2145
+ "+ cutin - 1": [
2146
+ "FYECO:0000307"
2147
+ ],
2148
+ "+ doxorubicin": [
2149
+ "FYECO:0000308"
2150
+ ],
2151
+ "+ 14 - hydroxydaunomycin": [
2152
+ "FYECO:0000308"
2153
+ ],
2154
+ "+ 14 - hydroxydaunorubicine": [
2155
+ "FYECO:0000308"
2156
+ ],
2157
+ "+ adriamycin": [
2158
+ "FYECO:0000308"
2159
+ ],
2160
+ "nitrogen starvation follow by heat shock and recovery at normal temperature": [
2161
+ "FYECO:0000309"
2162
+ ],
2163
+ "nitrogen starvation followed by heat shock and recovery at normal temperature": [
2164
+ "FYECO:0000309"
2165
+ ],
2166
+ "nitrogen starvation follow by heat shock and recovery at permissive temperature": [
2167
+ "FYECO:0000309"
2168
+ ],
2169
+ "nitrogen starvation followed by heat shock and recovery at permissive temperature": [
2170
+ "FYECO:0000309"
2171
+ ],
2172
+ "glucose starvation and recovery": [
2173
+ "FYECO:0000310"
2174
+ ],
2175
+ "+ cocl2": [
2176
+ "FYECO:0000311"
2177
+ ],
2178
+ "+ cobalt chloride": [
2179
+ "FYECO:0000311"
2180
+ ],
2181
+ "+ sam": [
2182
+ "FYECO:0000312"
2183
+ ],
2184
+ "+ s - adenosyl - l - methionine": [
2185
+ "FYECO:0000312"
2186
+ ],
2187
+ "+ s - adenosylmethionine": [
2188
+ "FYECO:0000312"
2189
+ ],
2190
+ "+ top - 53": [
2191
+ "FYECO:0000313"
2192
+ ],
2193
+ "+ cpt": [
2194
+ "FYECO:0000314"
2195
+ ],
2196
+ "+ camptothecin": [
2197
+ "FYECO:0000314"
2198
+ ],
2199
+ "uv": [
2200
+ "FYECO:0000315"
2201
+ ],
2202
+ "ultraviolet light": [
2203
+ "FYECO:0000315"
2204
+ ],
2205
+ "uv irradiation": [
2206
+ "FYECO:0000315"
2207
+ ],
2208
+ "+ limited uracil": [
2209
+ "FYECO:0000316"
2210
+ ],
2211
+ "+ urea": [
2212
+ "FYECO:0000317"
2213
+ ],
2214
+ "urea add": [
2215
+ "FYECO:0000317"
2216
+ ],
2217
+ "urea added": [
2218
+ "FYECO:0000317"
2219
+ ],
2220
+ "+ compactin": [
2221
+ "FYECO:0000318"
2222
+ ],
2223
+ "+ bfa": [
2224
+ "FYECO:0000319"
2225
+ ],
2226
+ "+ brefeldin a": [
2227
+ "FYECO:0000319"
2228
+ ],
2229
+ "+ oleate": [
2230
+ "FYECO:0000320"
2231
+ ],
2232
+ "+ copper chelator": [
2233
+ "FYECO:0000321"
2234
+ ],
2235
+ "+ tetrathiomolybdate": [
2236
+ "FYECO:0000321"
2237
+ ],
2238
+ "+ bortezomib": [
2239
+ "FYECO:0000322"
2240
+ ],
2241
+ "cold shock and recovery at high temperature": [
2242
+ "FYECO:0000323"
2243
+ ],
2244
+ "+ latb": [
2245
+ "FYECO:0000324"
2246
+ ],
2247
+ "+ latrunculin b": [
2248
+ "FYECO:0000324"
2249
+ ],
2250
+ "+ ethylene glycol": [
2251
+ "FYECO:0000325"
2252
+ ],
2253
+ "+ 4 - nqo": [
2254
+ "FYECO:0000326"
2255
+ ],
2256
+ "+ 4 - nitroquinoline n - oxide": [
2257
+ "FYECO:0000326"
2258
+ ],
2259
+ "+ mg132": [
2260
+ "FYECO:0000327"
2261
+ ],
2262
+ "proteasome inhibitor": [
2263
+ "FYECO:0000327"
2264
+ ],
2265
+ "lnb glucose medium": [
2266
+ "FYECO:0000328"
2267
+ ],
2268
+ "+ formamide": [
2269
+ "FYECO:0000329"
2270
+ ],
2271
+ "+ limited iron": [
2272
+ "FYECO:0000330"
2273
+ ],
2274
+ "glucose mm , arginine nitrogen source": [
2275
+ "FYECO:0000331"
2276
+ ],
2277
+ "glucose minimal medium , arginine nitrogen source": [
2278
+ "FYECO:0000331"
2279
+ ],
2280
+ "+ 2 - dg": [
2281
+ "FYECO:0000332"
2282
+ ],
2283
+ "2 - deoxy - d - glucose add": [
2284
+ "FYECO:0000332"
2285
+ ],
2286
+ "2 - deoxy - d - glucose added": [
2287
+ "FYECO:0000332"
2288
+ ],
2289
+ "2 - deoxyglucose add": [
2290
+ "FYECO:0000332"
2291
+ ],
2292
+ "2 - deoxyglucose added": [
2293
+ "FYECO:0000332"
2294
+ ],
2295
+ "+ 20 standard aa 's": [
2296
+ "FYECO:0000333"
2297
+ ],
2298
+ "22 standard amino acid add": [
2299
+ "FYECO:0000333"
2300
+ ],
2301
+ "22 standard amino acids added": [
2302
+ "FYECO:0000333"
2303
+ ],
2304
+ "+ phloxine b": [
2305
+ "FYECO:0000334"
2306
+ ],
2307
+ "+ ap20187": [
2308
+ "FYECO:0000335"
2309
+ ],
2310
+ "+ cerulenin": [
2311
+ "FYECO:0000336"
2312
+ ],
2313
+ "inorganic phosphate absent": [
2314
+ "FYECO:0000337"
2315
+ ],
2316
+ "+ 3 - brb - pp1": [
2317
+ "FYECO:0000338"
2318
+ ],
2319
+ "+ auxin": [
2320
+ "FYECO:0000339"
2321
+ ],
2322
+ "+ iron chelator": [
2323
+ "FYECO:0000340"
2324
+ ],
2325
+ "+ dtt": [
2326
+ "FYECO:0000341"
2327
+ ],
2328
+ "+ dithiothreitol": [
2329
+ "FYECO:0000341"
2330
+ ],
2331
+ "+ icrf - 193": [
2332
+ "FYECO:0000342"
2333
+ ],
2334
+ "+ ( nh4 ) 2so4": [
2335
+ "FYECO:0000343"
2336
+ ],
2337
+ "+ ammonium sulfate": [
2338
+ "FYECO:0000343"
2339
+ ],
2340
+ "+ mnso4": [
2341
+ "FYECO:0000344"
2342
+ ],
2343
+ "+ manganese sulfate": [
2344
+ "FYECO:0000344"
2345
+ ],
2346
+ "zinc starvation follow by zinc shock": [
2347
+ "FYECO:0000345"
2348
+ ],
2349
+ "zinc starvation followed by zinc shock": [
2350
+ "FYECO:0000345"
2351
+ ],
2352
+ "synchronous culture": [
2353
+ "FYECO:0000346"
2354
+ ],
2355
+ "+ vanoxerine": [
2356
+ "FYECO:0000347"
2357
+ ],
2358
+ "+ hexestrol": [
2359
+ "FYECO:0000348"
2360
+ ],
2361
+ "+ clomifene": [
2362
+ "FYECO:0000349"
2363
+ ],
2364
+ "+ clomiphene": [
2365
+ "FYECO:0000349"
2366
+ ],
2367
+ "+ ketoconazole": [
2368
+ "FYECO:0000350"
2369
+ ],
2370
+ "+ terconazole": [
2371
+ "FYECO:0000351"
2372
+ ],
2373
+ "+ aminolevulinic acid": [
2374
+ "FYECO:0000352"
2375
+ ],
2376
+ "+ agnp": [
2377
+ "FYECO:0000353"
2378
+ ],
2379
+ "+ silver nanoparticles": [
2380
+ "FYECO:0000353"
2381
+ ],
2382
+ "+ phleomycin": [
2383
+ "FYECO:0000354"
2384
+ ],
2385
+ "+ r - limonene": [
2386
+ "FYECO:0000355"
2387
+ ],
2388
+ "+ ( 4r ) - limonene": [
2389
+ "FYECO:0000355"
2390
+ ],
2391
+ "+ ck - 666": [
2392
+ "FYECO:0000356"
2393
+ ],
2394
+ "+ aspartate": [
2395
+ "FYECO:0000357"
2396
+ ],
2397
+ "+ asp": [
2398
+ "FYECO:0000357"
2399
+ ],
2400
+ "yes + galactose": [
2401
+ "FYECO:0000358"
2402
+ ],
2403
+ "rich medium with glucose and galactose": [
2404
+ "FYECO:0000358"
2405
+ ],
2406
+ "+ clotrimazole": [
2407
+ "FYECO:0000359"
2408
+ ],
2409
+ "+ terbinafine": [
2410
+ "FYECO:0000360"
2411
+ ],
2412
+ "+ acetaldehyde": [
2413
+ "FYECO:0000361"
2414
+ ],
2415
+ "+ formaldehyde": [
2416
+ "FYECO:0000362"
2417
+ ],
2418
+ "two - step temperature shift , standard to high , high to standard": [
2419
+ "FYECO:0000363"
2420
+ ],
2421
+ "+ diamide": [
2422
+ "FYECO:0000364"
2423
+ ],
2424
+ "+ n , n , n ' , n ' - tetramethyldiazene - 1,2 - dicarboxamide": [
2425
+ "FYECO:0000364"
2426
+ ],
2427
+ "mbc block and release": [
2428
+ "FYECO:0000365"
2429
+ ],
2430
+ "single passage culture": [
2431
+ "FYECO:0000366"
2432
+ ],
2433
+ "multiple passage culture": [
2434
+ "FYECO:0000367"
2435
+ ],
2436
+ "+ tamoxifen": [
2437
+ "FYECO:0000368"
2438
+ ],
2439
+ "+ beta - glucanase": [
2440
+ "FYECO:0000369"
2441
+ ],
2442
+ "+ foa": [
2443
+ "FYECO:0000370"
2444
+ ],
2445
+ "+ 5 - fluoroorotic acid": [
2446
+ "FYECO:0000370"
2447
+ ],
2448
+ "+ dmso": [
2449
+ "FYECO:0000371"
2450
+ ],
2451
+ "+ dimethyl sulfoxide": [
2452
+ "FYECO:0000371"
2453
+ ],
2454
+ "+ manumycin a": [
2455
+ "FYECO:0000372"
2456
+ ],
2457
+ "+ manu - a": [
2458
+ "FYECO:0000372"
2459
+ ],
2460
+ "+ thiolutin": [
2461
+ "FYECO:0000373"
2462
+ ],
2463
+ "glucose mm , serine nitrogen source": [
2464
+ "FYECO:0000374"
2465
+ ],
2466
+ "glucose minimal medium , serine nitrogen source": [
2467
+ "FYECO:0000374"
2468
+ ],
2469
+ "+ streptonigrin": [
2470
+ "FYECO:0000375"
2471
+ ],
2472
+ "pyruvate mm": [
2473
+ "FYECO:0000376"
2474
+ ],
2475
+ "pyruvate minimal medium": [
2476
+ "FYECO:0000376"
2477
+ ],
2478
+ "+ 5 - fu": [
2479
+ "FYECO:0000377"
2480
+ ],
2481
+ "+ 5 - fluorouracil": [
2482
+ "FYECO:0000377"
2483
+ ],
2484
+ "+ respiratory chain inhibitor": [
2485
+ "FYECO:0000378"
2486
+ ],
2487
+ "+ electron transport chain inhibitor": [
2488
+ "FYECO:0000378"
2489
+ ],
2490
+ "+ mitochondrial complex iii / iv inhibitor": [
2491
+ "FYECO:0000378"
2492
+ ],
2493
+ "+ respiratory complex iii inhibitor": [
2494
+ "FYECO:0000378"
2495
+ ],
2496
+ "+ diuron": [
2497
+ "FYECO:0000379"
2498
+ ],
2499
+ "+ 3 - ( 3,4 - dichlorophenyl ) - 1,1 - dimethylurea": [
2500
+ "FYECO:0000379"
2501
+ ],
2502
+ "+ nan3": [
2503
+ "FYECO:0000380"
2504
+ ],
2505
+ "+ sodium azide": [
2506
+ "FYECO:0000380"
2507
+ ],
2508
+ "thiamine absent": [
2509
+ "FYECO:0000381"
2510
+ ],
2511
+ "fructose mm": [
2512
+ "FYECO:0000382"
2513
+ ],
2514
+ "fructose minimal medium": [
2515
+ "FYECO:0000382"
2516
+ ],
2517
+ "wild type cell of opposite mating type add to culture": [
2518
+ "FYECO:0000383"
2519
+ ],
2520
+ "wild type cells of opposite mating type added to culture": [
2521
+ "FYECO:0000383"
2522
+ ],
2523
+ "mat with wt": [
2524
+ "FYECO:0000383"
2525
+ ],
2526
+ "mating with wt": [
2527
+ "FYECO:0000383"
2528
+ ],
2529
+ "isogenic cell of opposite mating type add to culture": [
2530
+ "FYECO:0000384"
2531
+ ],
2532
+ "isogenic cells of opposite mating type added to culture": [
2533
+ "FYECO:0000384"
2534
+ ],
2535
+ "self mating": [
2536
+ "FYECO:0000384"
2537
+ ],
2538
+ "+ fluconazole": [
2539
+ "FYECO:0000385"
2540
+ ],
2541
+ "cpt block and release": [
2542
+ "FYECO:0000386"
2543
+ ],
2544
+ "+ tebuconazole": [
2545
+ "FYECO:0000387"
2546
+ ],
2547
+ "+ mpa": [
2548
+ "FYECO:0000388"
2549
+ ],
2550
+ "+ mycophenolic acid": [
2551
+ "FYECO:0000388"
2552
+ ],
2553
+ "glucose mm , sulfate sulfur source": [
2554
+ "FYECO:0000389"
2555
+ ],
2556
+ "glucose minimal medium , sulfate sulfur source": [
2557
+ "FYECO:0000389"
2558
+ ],
2559
+ "glucose minimal medium , sulphate sulphur source": [
2560
+ "FYECO:0000389"
2561
+ ],
2562
+ "glucose mm , sulphate sulphur source": [
2563
+ "FYECO:0000389"
2564
+ ],
2565
+ "+ torin1": [
2566
+ "FYECO:0000390"
2567
+ ],
2568
+ "torin1": [
2569
+ "FYECO:0000390"
2570
+ ],
2571
+ "+ echinocandin": [
2572
+ "FYECO:0000391"
2573
+ ],
2574
+ "+ caspofungin": [
2575
+ "FYECO:0000392"
2576
+ ],
2577
+ "+ caspofungin sld": [
2578
+ "FYECO:0000393"
2579
+ ],
2580
+ "+ caspofungin ld": [
2581
+ "FYECO:0000394"
2582
+ ],
2583
+ "+ micafungin": [
2584
+ "FYECO:0000395"
2585
+ ],
2586
+ "+ micafungin sld": [
2587
+ "FYECO:0000396"
2588
+ ],
2589
+ "+ micafungin ld": [
2590
+ "FYECO:0000397"
2591
+ ],
2592
+ "+ anidulafungin": [
2593
+ "FYECO:0000398"
2594
+ ],
2595
+ "+ anidulafungin sld": [
2596
+ "FYECO:0000399"
2597
+ ],
2598
+ "+ anidulafungin ld": [
2599
+ "FYECO:0000400"
2600
+ ],
2601
+ "transient amino acid starvation < 1 hour": [
2602
+ "FYECO:0000401"
2603
+ ],
2604
+ "xylose add": [
2605
+ "FYECO:0000402"
2606
+ ],
2607
+ "xylose added": [
2608
+ "FYECO:0000402"
2609
+ ],
2610
+ "+ zinc sulfate": [
2611
+ "FYECO:0000404"
2612
+ ],
2613
+ "+ zinc sulphate": [
2614
+ "FYECO:0000404"
2615
+ ],
2616
+ "+ ile": [
2617
+ "FYECO:0000405"
2618
+ ],
2619
+ "isoleucine add": [
2620
+ "FYECO:0000405"
2621
+ ],
2622
+ "isoleucine added": [
2623
+ "FYECO:0000405"
2624
+ ],
2625
+ "+ val": [
2626
+ "FYECO:0000406"
2627
+ ],
2628
+ "valine add": [
2629
+ "FYECO:0000406"
2630
+ ],
2631
+ "valine added": [
2632
+ "FYECO:0000406"
2633
+ ],
2634
+ "+ benzamidine": [
2635
+ "FYECO:0000407"
2636
+ ],
2637
+ "benzamidine add": [
2638
+ "FYECO:0000407"
2639
+ ],
2640
+ "benzamidine added": [
2641
+ "FYECO:0000407"
2642
+ ],
2643
+ "+ canavanin": [
2644
+ "FYECO:0000408"
2645
+ ],
2646
+ "canavanin add": [
2647
+ "FYECO:0000408"
2648
+ ],
2649
+ "canavanin added": [
2650
+ "FYECO:0000408"
2651
+ ],
2652
+ "+ 2,2 ' - dipyridyl": [
2653
+ "FYECO:0000409"
2654
+ ],
2655
+ "2,2 ' - dipyridyl add": [
2656
+ "FYECO:0000409"
2657
+ ],
2658
+ "2,2 ' - dipyridyl added": [
2659
+ "FYECO:0000409"
2660
+ ],
2661
+ "+ 3,4 - dihydrocoumarin": [
2662
+ "FYECO:0000410"
2663
+ ],
2664
+ "3,4 - dihydrocoumarin add": [
2665
+ "FYECO:0000410"
2666
+ ],
2667
+ "3,4 - dihydrocoumarin added": [
2668
+ "FYECO:0000410"
2669
+ ],
2670
+ "+ egtazic acid": [
2671
+ "FYECO:0000411"
2672
+ ],
2673
+ "egtazic acid add": [
2674
+ "FYECO:0000411"
2675
+ ],
2676
+ "egtazic acid added": [
2677
+ "FYECO:0000411"
2678
+ ],
2679
+ "egta add": [
2680
+ "FYECO:0000411"
2681
+ ],
2682
+ "egta added": [
2683
+ "FYECO:0000411"
2684
+ ],
2685
+ "+ tunicamycin": [
2686
+ "FYECO:0000412"
2687
+ ],
2688
+ "tunicamycin add": [
2689
+ "FYECO:0000412"
2690
+ ],
2691
+ "tunicamycin added": [
2692
+ "FYECO:0000412"
2693
+ ],
2694
+ "+ valproic acid": [
2695
+ "FYECO:0000413"
2696
+ ],
2697
+ "valproic acid add": [
2698
+ "FYECO:0000413"
2699
+ ],
2700
+ "valproic acid added": [
2701
+ "FYECO:0000413"
2702
+ ],
2703
+ "xylose ye": [
2704
+ "FYECO:0000414"
2705
+ ],
2706
+ "xylose rich medium": [
2707
+ "FYECO:0000414"
2708
+ ],
2709
+ "+ tea tree oil": [
2710
+ "FYECO:0000415"
2711
+ ],
2712
+ "tea tree oil add": [
2713
+ "FYECO:0000415"
2714
+ ],
2715
+ "tea tree oil added": [
2716
+ "FYECO:0000415"
2717
+ ],
2718
+ "glucose mm , cysteine nitrogen source": [
2719
+ "FYECO:0000416"
2720
+ ],
2721
+ "glucose minimal medium , cysteine nitrogen source": [
2722
+ "FYECO:0000416"
2723
+ ],
2724
+ "standard glucose minimal medium , cysteine nitrogen source": [
2725
+ "FYECO:0000416"
2726
+ ],
2727
+ "glucose mm , methionine nitrogen source": [
2728
+ "FYECO:0000417"
2729
+ ],
2730
+ "glucose minimal medium , methionine nitrogen source": [
2731
+ "FYECO:0000417"
2732
+ ],
2733
+ "standard glucose minimal medium , methionine nitrogen source": [
2734
+ "FYECO:0000417"
2735
+ ],
2736
+ "leucine absent": [
2737
+ "FYECO:0000418"
2738
+ ],
2739
+ "+ ethyl methanesulfonate": [
2740
+ "FYECO:0000419"
2741
+ ],
2742
+ "+ ferrichrome": [
2743
+ "FYECO:0000420"
2744
+ ],
2745
+ "+ ( 8e,10s ) - 10 - hydroxy - 8 - octadecenoic acid": [
2746
+ "FYECO:0000421"
2747
+ ],
2748
+ "+ ( r , z ) - 10 - hydroxyoctadec - 8 - enoic acid": [
2749
+ "FYECO:0000421"
2750
+ ],
2751
+ "no glucose yes": [
2752
+ "FYECO:0000422"
2753
+ ],
2754
+ "+ ciclopirox olamine": [
2755
+ "FYECO:0000423"
2756
+ ],
2757
+ "+ amorolfine": [
2758
+ "FYECO:0000424"
2759
+ ],
2760
+ "x - ray": [
2761
+ "FYECO:0000425"
2762
+ ],
2763
+ "x - rays": [
2764
+ "FYECO:0000425"
2765
+ ],
2766
+ "x ray": [
2767
+ "FYECO:0000425"
2768
+ ],
2769
+ "x rays": [
2770
+ "FYECO:0000425"
2771
+ ],
2772
+ "glucose mm , lysine nitrogen source": [
2773
+ "FYECO:0000426"
2774
+ ],
2775
+ "glucose minimal medium , lysine nitrogen source": [
2776
+ "FYECO:0000426"
2777
+ ],
2778
+ "standard glucose minimal medium , lysine nitrogen source": [
2779
+ "FYECO:0000426"
2780
+ ],
2781
+ "fructose ye": [
2782
+ "FYECO:0000427"
2783
+ ],
2784
+ "fructose rich medium": [
2785
+ "FYECO:0000427"
2786
+ ],
2787
+ "ethanol ye": [
2788
+ "FYECO:0000428"
2789
+ ],
2790
+ "ethanol rich medium": [
2791
+ "FYECO:0000428"
2792
+ ],
2793
+ "ye with trace glucose": [
2794
+ "FYECO:0000429"
2795
+ ],
2796
+ "very low glucose ye": [
2797
+ "FYECO:0000429"
2798
+ ],
2799
+ "rich medium with trace glucose": [
2800
+ "FYECO:0000429"
2801
+ ],
2802
+ "mm with trace glucose": [
2803
+ "FYECO:0000430"
2804
+ ],
2805
+ "very low glucose mm": [
2806
+ "FYECO:0000430"
2807
+ ],
2808
+ "minimal medium with trace glucose": [
2809
+ "FYECO:0000430"
2810
+ ],
2811
+ "+ itraconazole": [
2812
+ "FYECO:0000431"
2813
+ ],
2814
+ "galactose ye": [
2815
+ "FYECO:0000432"
2816
+ ],
2817
+ "galactose rich medium": [
2818
+ "FYECO:0000432"
2819
+ ],
2820
+ "mannitol ye": [
2821
+ "FYECO:0000433"
2822
+ ],
2823
+ "mannitol rich medium": [
2824
+ "FYECO:0000433"
2825
+ ],
2826
+ "transient hydroxyurea treatment": [
2827
+ "FYECO:0000434"
2828
+ ],
2829
+ "acute hydroxyurea treatment": [
2830
+ "FYECO:0000434"
2831
+ ],
2832
+ "+ cccp": [
2833
+ "FYECO:0000435"
2834
+ ],
2835
+ "an experimental condition in which carbonyl cyanide m - chlorophenyl hydrazone be add to the medium or assay buffer in excess compare to standard medium or assay buffer .": [
2836
+ "FYECO:0000435"
2837
+ ],
2838
+ "an experimental condition in which carbonyl cyanide m - chlorophenyl hydrazone was added to the medium or assay buffer in excess compared to standard medium or assay buffers .": [
2839
+ "FYECO:0000435"
2840
+ ],
2841
+ "+ fccp": [
2842
+ "FYECO:0000436"
2843
+ ],
2844
+ "carbonyl cyanide m - chlorophenyl hydrazone": [
2845
+ "FYECO:0000436"
2846
+ ]
2847
+ }
dict_new_hpo/alt_hpoid.json ADDED
The diff for this file is too large to render. See raw diff
 
dict_new_hpo/id_word_map.json ADDED
The diff for this file is too large to render. See raw diff
 
dict_new_hpo/lable.vocab ADDED
The diff for this file is too large to render. See raw diff
 
dict_new_hpo/noabb_lemma.dic ADDED
The diff for this file is too large to render. See raw diff
 
dict_new_hpo/obo.json ADDED
The diff for this file is too large to render. See raw diff
 
dict_new_hpo/word_id_map.json ADDED
The diff for this file is too large to render. See raw diff
 
src/__pycache__/Transformer_keras.cpython-37.pyc ADDED
Binary file (3.77 kB). View file
 
src/__pycache__/abbre_resolution.cpython-37.pyc ADDED
Binary file (9.35 kB). View file
 
src/__pycache__/combine_result.cpython-37.pyc ADDED
Binary file (2.26 kB). View file
 
src/__pycache__/dic_ner.cpython-37.pyc ADDED
Binary file (5.29 kB). View file
 
src/__pycache__/ml_ner.cpython-37.pyc ADDED
Binary file (11.7 kB). View file
 
src/__pycache__/nn_model.cpython-37.pyc ADDED
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src/__pycache__/nn_represent.cpython-37.pyc ADDED
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src/__pycache__/post_processing.cpython-37.pyc ADDED
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src/__pycache__/restore_index.cpython-37.pyc ADDED
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src/__pycache__/ssplit_tokenzier.cpython-37.pyc ADDED
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src/__pycache__/tagging_text.cpython-37.pyc ADDED
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src/abbre_resolution.py ADDED
@@ -0,0 +1,434 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Tue Aug 11 16:52:40 2020
4
+
5
+ @author: luol2
6
+ """
7
+
8
+ import logging
9
+ import regex
10
+ import sys
11
+ import io
12
+
13
+ """
14
+ A Python 3 refactoring of Vincent Van Asch's Python 2 code at
15
+
16
+ http://www.cnts.ua.ac.be/~vincent/scripts/abbreviations.py
17
+
18
+ Based on
19
+
20
+ A Simple Algorithm for Identifying Abbreviations Definitions in Biomedical Text
21
+ A. Schwartz and M. Hearst
22
+ Biocomputing, 2003, pp 451-462.
23
+
24
+ """
25
+
26
+ logging.basicConfig(format='%(asctime)s : %(levelname)s : %(message)s', level=logging.INFO)
27
+ log = logging.getLogger('Abbre')
28
+
29
+
30
+ class Candidate(str):
31
+ def __init__(self, value):
32
+ super().__init__()
33
+ self.start = 0
34
+ self.stop = 0
35
+
36
+ def set_position(self, start, stop):
37
+ self.start = start
38
+ self.stop = stop
39
+
40
+
41
+ def yield_lines_from_file(file_path):
42
+ with open(file_path, 'rb') as f:
43
+ for line in f:
44
+ try:
45
+ line = line.decode('utf-8')
46
+ except UnicodeDecodeError:
47
+ line = line.decode('latin-1').encode('utf-8').decode('utf-8')
48
+ line = line.strip()
49
+ yield line
50
+ f.close()
51
+
52
+
53
+ def yield_lines_from_doc(doc_text):
54
+ for line in doc_text.split("\n"):
55
+ yield line.strip()
56
+
57
+
58
+ def best_candidates(sentence):
59
+ """
60
+ :param sentence: line read from input file
61
+ :return: a Candidate iterator
62
+ """
63
+
64
+ if '(' in sentence:
65
+ # Check some things first
66
+ if sentence.count('(') != sentence.count(')'):
67
+ raise ValueError("Unbalanced parentheses: {}".format(sentence))
68
+
69
+ if sentence.find('(') > sentence.find(')'):
70
+ raise ValueError("First parentheses is right: {}".format(sentence))
71
+
72
+ closeindex = -1
73
+ while 1:
74
+ # Look for open parenthesis
75
+ openindex = sentence.find('(', closeindex + 1)
76
+
77
+ if openindex == -1: break
78
+
79
+ # Look for closing parentheses
80
+ closeindex = openindex + 1
81
+ open = 1
82
+ skip = False
83
+ while open:
84
+ try:
85
+ char = sentence[closeindex]
86
+ except IndexError:
87
+ # We found an opening bracket but no associated closing bracket
88
+ # Skip the opening bracket
89
+ skip = True
90
+ break
91
+ if char == '(':
92
+ open += 1
93
+ elif char in [')', ';', ':']:
94
+ open -= 1
95
+ closeindex += 1
96
+
97
+ if skip:
98
+ closeindex = openindex + 1
99
+ continue
100
+
101
+ # Output if conditions are met
102
+ start = openindex + 1
103
+ stop = closeindex - 1
104
+ candidate = sentence[start:stop]
105
+
106
+ # Take into account whitespace that should be removed
107
+ start = start + len(candidate) - len(candidate.lstrip())
108
+ stop = stop - len(candidate) + len(candidate.rstrip())
109
+ candidate = sentence[start:stop]
110
+
111
+ if conditions(candidate):
112
+ new_candidate = Candidate(candidate)
113
+ new_candidate.set_position(start, stop)
114
+ yield new_candidate
115
+
116
+
117
+ def conditions(candidate):
118
+ """
119
+ Based on Schwartz&Hearst
120
+
121
+ 2 <= len(str) <= 10
122
+ len(tokens) <= 2
123
+ re.search('\p{L}', str)
124
+ str[0].isalnum()
125
+
126
+ and extra:
127
+ if it matches (\p{L}\.?\s?){2,}
128
+ it is a good candidate.
129
+
130
+ :param candidate: candidate abbreviation
131
+ :return: True if this is a good candidate
132
+ """
133
+ viable = True
134
+ if regex.match('(\p{L}\.?\s?){2,}', candidate.lstrip()):
135
+ viable = True
136
+ if len(candidate) < 2 or len(candidate) > 10:
137
+ viable = False
138
+ if len(candidate.split()) > 2:
139
+ viable = False
140
+ if not regex.search('\p{L}', candidate):
141
+ viable = False
142
+ if not candidate[0].isalnum():
143
+ viable = False
144
+
145
+ return viable
146
+
147
+
148
+ def get_definition(candidate, sentence):
149
+ """
150
+ Takes a candidate and a sentence and returns the definition candidate.
151
+
152
+ The definintion candidate is the set of tokens (in front of the candidate)
153
+ that starts with a token starting with the first character of the candidate
154
+
155
+ :param candidate: candidate abbreviation
156
+ :param sentence: current sentence (single line from input file)
157
+ :return: candidate definition for this abbreviation
158
+ """
159
+ # Take the tokens in front of the candidate
160
+ tokens = regex.split(r'[\s\-]+', sentence[:candidate.start - 2].lower())
161
+ #print(tokens)
162
+ # the char that we are looking for
163
+ key = candidate[0].lower()
164
+
165
+ # Count the number of tokens that start with the same character as the candidate
166
+ # print(tokens)
167
+ firstchars = [t[0] for t in tokens]
168
+ # print(firstchars)
169
+ definition_freq = firstchars.count(key)
170
+ candidate_freq = candidate.lower().count(key)
171
+
172
+ # Look for the list of tokens in front of candidate that
173
+ # have a sufficient number of tokens starting with key
174
+ if candidate_freq <= definition_freq:
175
+ # we should at least have a good number of starts
176
+ count = 0
177
+ start = 0
178
+ startindex = len(firstchars) - 1
179
+
180
+ while count < candidate_freq:
181
+ if abs(start) > len(firstchars):
182
+ raise ValueError("candiate {} not found".format(candidate))
183
+ start -= 1
184
+ # Look up key in the definition
185
+ try:
186
+ startindex = firstchars.index(key, len(firstchars) + start)
187
+ except ValueError:
188
+ pass
189
+
190
+ # Count the number of keys in definition
191
+ count = firstchars[startindex:].count(key)
192
+
193
+ # We found enough keys in the definition so return the definition as a definition candidate
194
+ start = len(' '.join(tokens[:startindex]))
195
+ stop = candidate.start - 1
196
+ candidate = sentence[start:stop]
197
+
198
+ # Remove whitespace
199
+ start = start + len(candidate) - len(candidate.lstrip())
200
+ stop = stop - len(candidate) + len(candidate.rstrip())
201
+ candidate = sentence[start:stop]
202
+
203
+ new_candidate = Candidate(candidate)
204
+ new_candidate.set_position(start, stop)
205
+ #print('new_candidate:')
206
+ #print(new_candidate,start,stop)
207
+ return new_candidate
208
+
209
+ else:
210
+ raise ValueError('There are less keys in the tokens in front of candidate than there are in the candidate')
211
+
212
+
213
+ def select_definition(definition, abbrev):
214
+ """
215
+ Takes a definition candidate and an abbreviation candidate
216
+ and returns True if the chars in the abbreviation occur in the definition
217
+
218
+ Based on
219
+ A simple algorithm for identifying abbreviation definitions in biomedical texts, Schwartz & Hearst
220
+ :param definition: candidate definition
221
+ :param abbrev: candidate abbreviation
222
+ :return:
223
+ """
224
+
225
+
226
+ if len(definition) < len(abbrev):
227
+ raise ValueError('Abbreviation is longer than definition')
228
+
229
+ if abbrev in definition.split():
230
+ raise ValueError('Abbreviation is full word of definition')
231
+
232
+ sindex = -1
233
+ lindex = -1
234
+
235
+ while 1:
236
+ try:
237
+ longchar = definition[lindex].lower()
238
+ except IndexError:
239
+ raise
240
+
241
+ shortchar = abbrev[sindex].lower()
242
+
243
+ if not shortchar.isalnum():
244
+ sindex -= 1
245
+
246
+ if sindex == -1 * len(abbrev):
247
+ if shortchar == longchar:
248
+ if lindex == -1 * len(definition) or not definition[lindex - 1].isalnum():
249
+ break
250
+ else:
251
+ lindex -= 1
252
+ else:
253
+ lindex -= 1
254
+ if lindex == -1 * (len(definition) + 1):
255
+ raise ValueError("definition {} was not found in {}".format(abbrev, definition))
256
+
257
+ else:
258
+ if shortchar == longchar:
259
+ sindex -= 1
260
+ lindex -= 1
261
+ else:
262
+ lindex -= 1
263
+ # print('lindex:',lindex,len(definition),definition[lindex:len(definition)])
264
+ new_candidate = Candidate(definition[lindex:len(definition)])
265
+ new_candidate.set_position(definition.start+lindex+len(definition), definition.stop)
266
+ definition = new_candidate
267
+
268
+ tokens = len(definition.split())
269
+ length = len(abbrev)
270
+
271
+ if tokens > min([length + 5, length * 2]):
272
+ raise ValueError("did not meet min(|A|+5, |A|*2) constraint")
273
+
274
+ # Do not return definitions that contain unbalanced parentheses
275
+ if definition.count('(') != definition.count(')'):
276
+ raise ValueError("Unbalanced parentheses not allowed in a definition")
277
+ # print('select:')
278
+ # print(definition,definition.start, definition.stop)
279
+ new_definition_dict={'definition':definition,'start':definition.start,'stop':definition.stop}
280
+ return new_definition_dict
281
+
282
+
283
+ def extract_abbreviation_definition_pairs(file_path=None, doc_text=None):
284
+ abbrev_map = []
285
+ omit = 0
286
+ written = 0
287
+ if file_path:
288
+ sentence_iterator = enumerate(yield_lines_from_file(file_path))
289
+ elif doc_text:
290
+ sentence_iterator = enumerate(yield_lines_from_doc(doc_text))
291
+ else:
292
+ return abbrev_map
293
+
294
+ for i, sentence in sentence_iterator:
295
+ #print(sentence)
296
+ try:
297
+ for candidate in best_candidates(sentence):
298
+ #print(candidate)
299
+ try:
300
+ #print('begin get definition')
301
+ definition = get_definition(candidate, sentence)
302
+ #print('get_definition:')
303
+ #print(definition)
304
+
305
+ except (ValueError, IndexError) as e:
306
+ #log.debug("{} Omitting candidate {}. Reason: {}".format(i, candidate, e.args[0]))
307
+ omit += 1
308
+ else:
309
+ try:
310
+ definition_dict = select_definition(definition, candidate)
311
+ except (ValueError, IndexError) as e:
312
+ #log.debug("{} Omitting definition {} for candidate {}. Reason: {}".format(i, definition_dict, candidate, e.args[0]))
313
+ omit += 1
314
+ else:
315
+ definition_dict['abbre']=candidate
316
+ abbrev_map.append(definition_dict)
317
+ written += 1
318
+ except (ValueError, IndexError) as e:
319
+ log.debug("{} Error processing sentence {}: {}".format(i, sentence, e.args[0]))
320
+ log.debug("{} abbreviations detected and kept ({} omitted)".format(written, omit))
321
+ return abbrev_map
322
+
323
+ def postprocess_abbr(ner_result,ori_text):
324
+
325
+ final_result={}
326
+ if len(ner_result)==0:
327
+ return []
328
+ # abbr recognition
329
+ abbr_result=extract_abbreviation_definition_pairs(doc_text=ori_text)
330
+
331
+ # read ner results
332
+ nor_loc_list={} #{entity_name_location:entity_information}
333
+
334
+ for ele in ner_result:
335
+ nor_loc_list[str(ele[0])+' '+str(ele[1])]=ele
336
+ final_result['\t'.join(ele)]=[int(ele[0]),int(ele[1])]
337
+
338
+ #abbr matching
339
+ for abbr in abbr_result:
340
+ abbr_index=str(abbr['start'])+' '+str(abbr['stop'])
341
+ if abbr_index in nor_loc_list.keys():
342
+
343
+ line=ori_text
344
+ abbr_text=abbr['abbre']
345
+ abbr_eid=0
346
+ while line.find(abbr_text)>=0:
347
+ abbr_sid=line.find(abbr_text)+abbr_eid
348
+ abbr_eid=abbr_sid+len(abbr_text)
349
+ # print(abbr_sid,abbr_eid)
350
+ if abbr_sid>0 and abbr_eid<len(ori_text):
351
+ if ori_text[abbr_sid-1].isalnum()==False and ori_text[abbr_eid].isalnum()==False:
352
+ final_result[str(abbr_sid)+'\t'+str(abbr_eid)+'\t'+nor_loc_list[abbr_index][2]+'\t'+nor_loc_list[abbr_index][3]]=[abbr_sid,abbr_eid]
353
+ elif abbr_sid==0 and abbr_eid<len(ori_text):
354
+ if ori_text[abbr_eid].isalnum()==False:
355
+ final_result[str(abbr_sid)+'\t'+str(abbr_eid)+'\t'+nor_loc_list[abbr_index][2]+'\t'+nor_loc_list[abbr_index][3]]=[abbr_sid,abbr_eid]
356
+ elif abbr_sid>0 and abbr_eid==len(ori_text):
357
+ if ori_text[abbr_sid-1].isalnum()==False :
358
+ final_result[str(abbr_sid)+'\t'+str(abbr_eid)+'\t'+nor_loc_list[abbr_index][2]+'\t'+nor_loc_list[abbr_index][3]]=[abbr_sid,abbr_eid]
359
+ line=ori_text[abbr_eid:]
360
+ # print(final_result)
361
+ sorted_final_result=sorted(final_result.items(), key=lambda kv:(kv[1]), reverse=False)
362
+ final_result=[]
363
+ for ele in sorted_final_result:
364
+ final_result.append(ele[0].split('\t'))
365
+ return final_result
366
+
367
+ def ner_abbr(ner_result,abbr_result,ori_text):
368
+ # read ner results
369
+ nor_name_list={} #{entity_name:entity_information}
370
+ nor_loc_list={} #{entity_name_location:entity_information}
371
+ final_result={} #{entity_information:location} use to sort
372
+ for ele in ner_result:
373
+ temp_seg=ele.split('\t')
374
+ nor_loc_list[temp_seg[0]+' '+temp_seg[1]]=temp_seg
375
+ nor_name_list[temp_seg[2].lower()]=temp_seg
376
+ final_result['\t'.join(temp_seg[0:4])]=[int(temp_seg[0]),int(temp_seg[1])]
377
+
378
+ #abbr matching
379
+ for abbr in abbr_result:
380
+ abbr_index=str(abbr['start'])+' '+str(abbr['stop'])
381
+ if abbr_index in nor_loc_list.keys():
382
+
383
+ line=ori_text
384
+ abbr_text=abbr['abbre']
385
+ abbr_eid=0
386
+ while line.find(abbr_text)>=0:
387
+ abbr_sid=line.find(abbr_text)+abbr_eid
388
+ abbr_eid=abbr_sid+len(abbr_text)
389
+ # print(abbr_sid,abbr_eid)
390
+ if abbr_sid>0 and abbr_eid<len(ori_text):
391
+ if ori_text[abbr_sid-1].isalnum()==False and ori_text[abbr_eid].isalnum()==False:
392
+ final_result[str(abbr_sid)+'\t'+str(abbr_eid)+'\t'+abbr_text+'\t'+nor_loc_list[abbr_index][3]]=[abbr_sid,abbr_eid]
393
+ elif abbr_sid==0 and abbr_eid<len(ori_text):
394
+ if ori_text[abbr_eid].isalnum()==False:
395
+ final_result[str(abbr_sid)+'\t'+str(abbr_eid)+'\t'+abbr_text+'\t'+nor_loc_list[abbr_index][3]]=[abbr_sid,abbr_eid]
396
+ elif abbr_sid>0 and abbr_eid==len(ori_text):
397
+ if ori_text[abbr_sid-1].isalnum()==False :
398
+ final_result[str(abbr_sid)+'\t'+str(abbr_eid)+'\t'+abbr_text+'\t'+nor_loc_list[abbr_index][3]]=[abbr_sid,abbr_eid]
399
+ line=ori_text[abbr_eid:]
400
+ # print(final_result)
401
+ final_result=sorted(final_result.items(), key=lambda kv:(kv[1]), reverse=False)
402
+
403
+ return final_result
404
+
405
+
406
+
407
+
408
+ if __name__ == '__main__':
409
+ path='//panfs/pan1/bionlp/lulab/luoling/HPO_project/diseaseTag/data/test/results/'
410
+ fin=open(path+'NCBI_test_phecr_95.tsv','r',encoding='utf-8')
411
+ context=fin.read().strip().split('\n\n')
412
+ fin.close()
413
+ fout=open(path+'NCBI_test_phecr_abbre_95.tsv','w',encoding='utf-8')
414
+ for doc in context:
415
+ lines=doc.split('\n')
416
+ ori_text=lines[1]
417
+ # print(ori_text)
418
+ fout.write(lines[0]+'\n'+lines[1]+'\n')
419
+ if len(lines)>2:
420
+ abbr_result=extract_abbreviation_definition_pairs(doc_text=ori_text)
421
+ print(abbr_result)
422
+ abbr_out=ner_abbr(lines[2:],abbr_result,ori_text)
423
+ else:
424
+ abbr_out=[]
425
+ # print('final:',abbr_out)
426
+ for ele in abbr_out:
427
+ fout.write(ele[0]+'\n')
428
+ fout.write('\n')
429
+ # sys.exit()
430
+ fout.close()
431
+ #last_out=combine_ml_dict_fn(abbr_out,infile)
432
+ #print(last_out)
433
+
434
+
src/combine_result.py ADDED
@@ -0,0 +1,102 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Mon Jun 15 11:24:45 2020
4
+
5
+ @author: luol2
6
+ """
7
+
8
+ import io
9
+ def nest_overlap_entity(nest_list):
10
+ temp_result_list={}
11
+ for i in range(0, len(nest_list)):
12
+ hpoid=nest_list[i][3]
13
+ if hpoid not in temp_result_list.keys():
14
+ temp_result_list[hpoid]=nest_list[i]
15
+ else:
16
+ score=float(nest_list[i][4])
17
+ old_score=float(temp_result_list[hpoid][4])
18
+ if score>old_score: # retain higer score concept
19
+ temp_result_list[hpoid]=nest_list[i]
20
+ new_list=[]
21
+ for hpoid in temp_result_list.keys():
22
+ new_list.append(temp_result_list[hpoid])
23
+
24
+ temp_result_list={} #same index, different ids
25
+ for i in range(0, len(new_list)):
26
+ ids=new_list[i][0]+' '+new_list[i][1]
27
+ if ids not in temp_result_list.keys():
28
+ temp_result_list[ids]=new_list[i]
29
+ else:
30
+ score=float(nest_list[i][4])
31
+ old_score=float(temp_result_list[ids][4])
32
+ if score>old_score:
33
+ temp_result_list[ids]=new_list[i]
34
+ final_list=[]
35
+ for ids in temp_result_list.keys():
36
+ final_list.append(temp_result_list[ids])
37
+ return final_list
38
+ def combine_ml_dict(dict_tsv,ml_tsv,nest=True):
39
+ fin_dic=io.StringIO(dict_tsv)
40
+ fin_ml=io.StringIO(ml_tsv)
41
+ fout=io.StringIO()
42
+ all_dic=fin_dic.read().strip().split('\n\n')
43
+ all_ml=fin_ml.read().strip().split('\n\n')
44
+ fin_dic.close()
45
+ fin_ml.close()
46
+
47
+ for i in range(0,len(all_dic)):
48
+ lines_dic=all_dic[i].split('\n')
49
+ lines_ml=all_ml[i].split('\n')
50
+ entity_list={}
51
+ for j in range(1,len(lines_dic)):
52
+ seg=lines_dic[j].split('\t')
53
+ entity_list[lines_dic[j]]=[int(seg[0]),int(seg[1])] #dict results score 1.00
54
+ for j in range(1,len(lines_ml)):
55
+ seg=lines_ml[j].split('\t')
56
+ entity_list[lines_ml[j]]=[int(seg[0]),int(seg[1])]
57
+
58
+ entity_list=sorted(entity_list.items(), key=lambda kv:(kv[1]), reverse=False)
59
+ entity_list_sort=[]
60
+ for ele in entity_list:
61
+ entity_list_sort.append(ele[0])
62
+
63
+ final_entity=[]
64
+ if len(entity_list_sort)!=0:
65
+ first_entity=entity_list_sort[0].split('\t')
66
+ nest_list=[first_entity]
67
+ max_eid=int(first_entity[1])
68
+
69
+ for i in range(1,len(entity_list_sort)):
70
+ segs=entity_list_sort[i].split('\t')
71
+ if int(segs[0])> max_eid:
72
+ if len(nest_list)==1:
73
+ final_entity.append(nest_list[0])
74
+ nest_list=[]
75
+ nest_list.append(segs)
76
+ if int(segs[1])>max_eid:
77
+ max_eid=int(segs[1])
78
+ else:
79
+ tem=nest_overlap_entity(nest_list)
80
+ final_entity.extend(tem)
81
+ nest_list=[]
82
+ nest_list.append(segs)
83
+ if int(segs[1])>max_eid:
84
+ max_eid=int(segs[1])
85
+ else:
86
+ nest_list.append(segs)
87
+ if int(segs[1])>max_eid:
88
+ max_eid=int(segs[1])
89
+ if nest_list!=[]:
90
+ if len(nest_list)==1:
91
+ final_entity.append(nest_list[0])
92
+
93
+ else:
94
+ tem=nest_overlap_entity(nest_list)#find max entity
95
+ final_entity.extend(tem)
96
+
97
+ fout.write(lines_ml[0]+'\n')
98
+ for ele in final_entity:
99
+ fout.write('\t'.join(ele)+'\n')
100
+ fout.write('\n')
101
+ return fout.getvalue()
102
+
src/dic_ner.py ADDED
@@ -0,0 +1,164 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Fri Jun 12 15:05:00 2020
4
+
5
+ @author: luol2
6
+ """
7
+ import sys
8
+ import json
9
+ import io
10
+ from src.ssplit_tokenzier import ssplit_token_pos_lemma
11
+ class Trie(object):
12
+ class Node(object):
13
+ def __init__(self):
14
+ self.term = None
15
+ self.next = {}
16
+
17
+ def __init__(self, terms=[]):
18
+ self.root = Trie.Node()
19
+ for term in terms:
20
+ self.add(term)
21
+
22
+ def add(self, term):
23
+ node = self.root
24
+ for char in term:
25
+ if not char in node.next:
26
+ node.next[char] = Trie.Node()
27
+ node = node.next[char]
28
+ node.term = term
29
+
30
+ def match(self, query):
31
+ results = []
32
+ for i in range(len(query)):
33
+ node = self.root
34
+ for j in range(i, len(query)):
35
+ node = node.next.get(query[j])
36
+ if not node:
37
+ break
38
+ if node.term:
39
+ results.append((i, len(node.term)))
40
+ return results
41
+
42
+ def __repr__(self):
43
+ output = []
44
+ def _debug(output, char, node, depth=0):
45
+ output.append('%s[%s][%s]' % (' '*depth, char, node.term))
46
+ for (key, n) in node.next.items():
47
+ _debug(output, key, n, depth+1)
48
+ _debug(output, '', self.root)
49
+ return '\n'.join(output)
50
+
51
+ class dic_ont():
52
+
53
+ def __init__(self, ont_files):
54
+
55
+ dicin=open(ont_files['dic_file'],'r',encoding='utf-8')
56
+ win_size=50000
57
+ Dic=[]
58
+ print("loading dict!")
59
+ for line in dicin:
60
+ line=line.strip()
61
+ if len(line.split())<=win_size:
62
+ words=line.split()
63
+ for i in range(len(words)):
64
+ if len(words[i])>3 and (not words[i].isupper()):
65
+ words[i]=words[i].lower()
66
+ line=' '.join(words[0:])
67
+ Dic.append(line.strip())
68
+ print("Dic_len:",len(Dic))
69
+ dicin.close()
70
+
71
+ self.dic_trie = Trie(Dic)
72
+ print("load dic done!")
73
+
74
+ #load word hpo mapping
75
+ fin_map=open(ont_files['word_hpo_file'],'r',encoding='utf-8')
76
+ self.word_hpo=json.load(fin_map)
77
+ fin_map.close()
78
+
79
+ #load hpo word mapping
80
+ fin_map=open(ont_files['hpo_word_file'],'r',encoding='utf-8')
81
+ self.hpo_word=json.load(fin_map)
82
+ fin_map.close()
83
+
84
+ def matching(self, source):
85
+
86
+ fin=io.StringIO(source)
87
+ fout=io.StringIO()
88
+
89
+ sent_list=[]
90
+ sent = []
91
+ sent_ori_list=[]
92
+ sent_ori=[]
93
+
94
+ for line in fin:
95
+ line=line.strip()
96
+ if line=="":
97
+ sent_list.append(sent)
98
+ sent_ori_list.append(sent_ori)
99
+ sent=[]
100
+ sent_ori=[]
101
+ else:
102
+ words=line.split('\t')
103
+ words[1]=words[1].lower()
104
+ sent.append(words[1]) # word lemma
105
+ sent_ori.append(words[0])
106
+ sent=[]
107
+ fin.close()
108
+
109
+ for k in range(len(sent_list)):
110
+ sent = sent_list[k]
111
+ sentence=' '.join(sent[0:])+" "
112
+ sentence_ori=' '.join(sent_ori_list[k])
113
+ # print('sentence:',sentence)
114
+ result=self.dic_trie.match(sentence)
115
+ # print('result:',result)
116
+ new_result=[]
117
+ for i in range(0,len(result)):
118
+ if result[i][0]==0 and sentence[result[i][1]]==" ":
119
+ new_result.append([result[i][0],result[i][0]+result[i][1]])
120
+ elif result[i][0]>0 and sentence[result[i][0]-1]==' ' and sentence[result[i][0]+result[i][1]]==' ':
121
+ new_result.append([result[i][0],result[i][0]+result[i][1]])
122
+ # print('new result:',new_result)
123
+
124
+
125
+
126
+ if len(new_result)==0:
127
+ fout.write(sentence_ori+'\n\n')
128
+
129
+ else:
130
+ fout.write(sentence_ori+'\n')
131
+ for ele in new_result:
132
+ entity_text=sentence[ele[0]:ele[1]]
133
+ if entity_text in self.word_hpo.keys():
134
+ hpoid=self.word_hpo[entity_text]
135
+ else:
136
+ print('no id:', entity_text)
137
+ hpoid=['None']
138
+ if ele[0]==0:
139
+ sid="0"
140
+ else:
141
+ temp_sent=sentence[0:ele[0]]
142
+ sid=str(len(temp_sent.rstrip().split(' ')))
143
+ temp_sent=sentence[0:ele[1]]
144
+ eid=str(len(temp_sent.rstrip().split(' '))-1)
145
+ # print(sid,eid,entity_text,hpoid[0])
146
+ fout.write(sid+'\t'+eid+'\t'+entity_text+'\t'+";".join(hpoid)+'\t1.00\n')
147
+ fout.write('\n')
148
+
149
+ return fout.getvalue()
150
+
151
+
152
+ if __name__=='__main__':
153
+
154
+ ontfiles={'dic_file':'//panfs/pan1/bionlp/lulab/luoling/HPO_project/bioTag/dict/hpo_noabb_lemma.dic',
155
+ 'word_hpo_file':'//panfs/pan1/bionlp/lulab/luoling/HPO_project/bioTag/dict/word_hpoid_map.json',
156
+ 'hpo_word_file':'//panfs/pan1/bionlp/lulab/luoling/HPO_project/bioTag/dict/hpoid_word_map.json'}
157
+ biotag_dic=dic_ont(ontfiles)
158
+ text='Nevoid basal cell carcinoma syndrome (NBCCS) is a hereditary condition transmitted as an autosomal dominant trait with complete penetrance and variable expressivity. The syndrome is characterised by numerous basal cell carcinomas (BCCs), odontogenic keratocysts of the jaws, palmar and/or plantar pits, skeletal abnormalities and intracranial calcifications. In this paper, the clinical features of 37 Italian patients are reviewed. Jaw cysts and calcification of falx cerebri were the most frequently observed anomalies, followed by BCCs and palmar/plantar pits. Similar to the case of African Americans, the relatively low frequency of BCCs in the Italian population is probably due to protective skin pigmentation. A future search based on mutation screening might establish a possible genotype phenotype correlation in Italian patients.'
159
+ ssplit_token=ssplit_token_pos_lemma(text)
160
+ # print(ssplit_token)
161
+ dic_result=biotag_dic.matching(ssplit_token)
162
+ print(dic_result)
163
+
164
+
src/ml_ner.py ADDED
@@ -0,0 +1,578 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Fri Jun 12 16:41:54 2020
4
+
5
+ @author: luol2
6
+ """
7
+
8
+ import io
9
+ import time
10
+ import numpy as np
11
+
12
+ def ml_intext(infile):
13
+ fin=open(infile,'r',encoding='utf-8')
14
+ alltexts=fin.read().strip().split('\n\n')
15
+ fin.close()
16
+ data_list=[]
17
+ label_list=[]
18
+ for sents in alltexts:
19
+ lines=sents.split('\n')
20
+ temp_sentece=[]
21
+ label=lines[0].split('\t')[0]
22
+ label_list.append(label)
23
+ for i in range(1,len(lines)):
24
+ seg=lines[i].split('\t')
25
+ temp_sentece.append(seg)
26
+ data_list.append(temp_sentece)
27
+ return data_list,label_list
28
+ def ml_intext_fn(ml_input):
29
+ fin=io.StringIO(ml_input)
30
+ alltexts=fin.read().strip().split('\n\n')
31
+ fin.close()
32
+ data_list=[]
33
+ label_list=[]
34
+ for sents in alltexts:
35
+ lines=sents.split('\n')
36
+ temp_sentece=[]
37
+ label=lines[0].split('\t')[0]
38
+ label_list.append(label)
39
+ for i in range(1,len(lines)):
40
+ seg=lines[i].split('\t')
41
+ temp_sentece.append(seg)
42
+ data_list.append(temp_sentece)
43
+ return data_list,label_list
44
+ def pun_filter(temp_entity):
45
+ pun_list=[',','.','!',';',':','?','(',')','[',']','{','}']
46
+ filter_flag=0
47
+ for ele in temp_entity:
48
+ if ele in pun_list:
49
+ filter_flag=1
50
+ break
51
+ return filter_flag
52
+ def pos_filter(temp_pos,temp_entity):
53
+ pos_list_l=['PRP']
54
+ pos_list=['IN','DT','CC','O','MD','EX','POS','WDT','WP','WP$','WRB','TO','PRP$']
55
+ verb_word=['is','are','was','were','had','have','has','be','been','also']
56
+ filter_flag=0
57
+
58
+ if (temp_entity[0] in verb_word) or (temp_entity[-1] in verb_word):
59
+ filter_flag=1
60
+ if (temp_pos[0] in pos_list) or (temp_pos[-1] in pos_list) or (temp_pos[0] in pos_list_l):
61
+ filter_flag=1
62
+ return filter_flag
63
+
64
+ def build_ngram_testset_filted(conll_input,Ngram=8):
65
+
66
+ fin_genia=io.StringIO(conll_input)
67
+ fout_context=io.StringIO()
68
+ fout_txt=io.StringIO()
69
+
70
+ index_dict={}
71
+ allentity=[]
72
+ alltext=fin_genia.read().strip().split('\n\n')
73
+ fin_genia.close()
74
+ num_total=0
75
+ for i in range(0,len(alltext)):
76
+
77
+ lines=alltext[i].split('\n')
78
+ ori_txt=[]
79
+ for ele in lines:
80
+ seg=ele.split('\t')
81
+ ori_txt.append(seg[0])
82
+ fout_txt.write(' '.join(ori_txt)+'\n')
83
+
84
+ if Ngram>len(lines):
85
+ Ngram=len(lines)
86
+
87
+ fout_context_list=[]
88
+ temp_entity=[]
89
+ temp_pos=[]
90
+ for ngram in range(2,Ngram+1):
91
+ if ngram==1:
92
+ for j in range(0, len(lines)):
93
+ sid=0
94
+ eid=0
95
+ for m in range(0,len(lines)):
96
+ if m==j:
97
+ sid=m
98
+ eid=m
99
+ fout_context_list.append(lines[m]+'\tO\tB')
100
+ temp_seg=lines[m].split('\t')
101
+ temp_entity.append(temp_seg[0])
102
+ temp_pos.append(temp_seg[3])
103
+ else:
104
+ pass
105
+ # print(sentence[m])
106
+ # fout_context_list.append(lines[m]+'\tO\tO')
107
+ if pun_filter(temp_entity)==0 and pos_filter(temp_pos,temp_entity)==0:
108
+ num_total+=1
109
+ if ' '.join(temp_entity) not in allentity:
110
+ allentity.append(' '.join(temp_entity))
111
+ fout_context.write('HP:None\t'+' '.join(temp_entity)+'\n')
112
+ fout_context.write('\n'.join(fout_context_list)+'\n\n')
113
+ index_dict[str(num_total)]=[i,sid,eid]
114
+ temp_entity=[]
115
+ temp_pos=[]
116
+ fout_context_list=[]
117
+ elif ngram==2:
118
+ for j in range(0, len(lines)-1):
119
+ sid=0
120
+ eid=0
121
+ for m in range(0,len(lines)):
122
+ if m==j:
123
+ fout_context_list.append(lines[m]+'\tO\tB')
124
+ sid=m
125
+ temp_seg=lines[m].split('\t')
126
+ temp_entity.append(temp_seg[0])
127
+ temp_pos.append(temp_seg[3])
128
+ elif m==j+1:
129
+ fout_context_list.append(lines[m]+'\tO\tB')
130
+ eid=m
131
+ temp_seg=lines[m].split('\t')
132
+ temp_entity.append(temp_seg[0])
133
+ temp_pos.append(temp_seg[3])
134
+ else:
135
+ pass
136
+ # fout_context_list.append(lines[m]+'\tO\tO')
137
+
138
+ if pun_filter(temp_entity)==0 and pos_filter(temp_pos,temp_entity)==0:
139
+ num_total+=1
140
+ if ' '.join(temp_entity) not in allentity:
141
+ allentity.append(' '.join(temp_entity))
142
+ fout_context.write('HP:None\t'+' '.join(temp_entity)+'\n')
143
+ fout_context.write('\n'.join(fout_context_list)+'\n\n')
144
+ index_dict[str(num_total)]=[i,sid,eid]
145
+ temp_entity=[]
146
+ temp_pos=[]
147
+ fout_context_list=[]
148
+ else :
149
+ for j in range(0, len(lines)-ngram+1):
150
+ sid=0
151
+ eid=0
152
+ for m in range(0,len(lines)):
153
+ if m==j:
154
+ fout_context_list.append(lines[m]+'\tO\tB')
155
+ sid=m
156
+ temp_seg=lines[m].split('\t')
157
+ temp_entity.append(temp_seg[0])
158
+ temp_pos.append(temp_seg[3])
159
+ elif m>j and m<j+ngram-1:
160
+ fout_context_list.append(lines[m]+'\tO\tB')
161
+ temp_seg=lines[m].split('\t')
162
+ temp_entity.append(temp_seg[0])
163
+ temp_pos.append(temp_seg[2])
164
+ elif m==j+ngram-1:
165
+ fout_context_list.append(lines[m]+'\tO\tB')
166
+ eid=m
167
+ temp_seg=lines[m].split('\t')
168
+ temp_entity.append(temp_seg[0])
169
+ temp_pos.append(temp_seg[3])
170
+ else:
171
+ pass
172
+ # fout_context_list.append(lines[m]+'\tO\tO')
173
+
174
+ if pun_filter(temp_entity)==0 and pos_filter(temp_pos,temp_entity)==0:
175
+ num_total+=1
176
+ if ' '.join(temp_entity) not in allentity:
177
+ allentity.append(' '.join(temp_entity))
178
+ fout_context.write('HP:None\t'+' '.join(temp_entity)+'\n')
179
+ fout_context.write('\n'.join(fout_context_list)+'\n\n')
180
+ index_dict[str(num_total)]=[i,sid,eid]
181
+
182
+ temp_entity=[]
183
+ temp_pos=[]
184
+ fout_context_list=[]
185
+
186
+ return fout_context.getvalue(),fout_txt.getvalue(),index_dict
187
+
188
+ def build_all_ngram_testset_filted(conll_input,Ngram=8):
189
+
190
+ fin_genia=io.StringIO(conll_input)
191
+ fout_context=io.StringIO()
192
+ fout_txt=io.StringIO()
193
+
194
+ index_dict={}
195
+ allentity=[]
196
+ alltext=fin_genia.read().strip().split('\n\n')
197
+ fin_genia.close()
198
+ num_total=0
199
+ for i in range(0,len(alltext)):
200
+
201
+ lines=alltext[i].split('\n')
202
+ ori_txt=[]
203
+ for ele in lines:
204
+ seg=ele.split('\t')
205
+ ori_txt.append(seg[0])
206
+ fout_txt.write(' '.join(ori_txt)+'\n')
207
+
208
+ if Ngram>len(lines):
209
+ Ngram=len(lines)
210
+
211
+ fout_context_list=[]
212
+ temp_entity=[]
213
+ temp_pos=[]
214
+ for ngram in range(1,Ngram+1):
215
+ if ngram==1:
216
+ for j in range(0, len(lines)):
217
+ sid=0
218
+ eid=0
219
+ for m in range(0,len(lines)):
220
+ if m==j:
221
+ sid=m
222
+ eid=m
223
+ fout_context_list.append(lines[m]+'\tO\tB')
224
+ temp_seg=lines[m].split('\t')
225
+ temp_entity.append(temp_seg[0])
226
+ temp_pos.append(temp_seg[3])
227
+ else:
228
+ pass
229
+ # print(sentence[m])
230
+ # fout_context_list.append(lines[m]+'\tO\tO')
231
+ if pun_filter(temp_entity)==0 and pos_filter(temp_pos,temp_entity)==0:
232
+ num_total+=1
233
+ if ' '.join(temp_entity) not in allentity:
234
+ allentity.append(' '.join(temp_entity))
235
+ fout_context.write('HP:None\t'+' '.join(temp_entity)+'\n')
236
+ fout_context.write('\n'.join(fout_context_list)+'\n\n')
237
+ index_dict[str(num_total)]=[i,sid,eid]
238
+ temp_entity=[]
239
+ temp_pos=[]
240
+ fout_context_list=[]
241
+ elif ngram==2:
242
+ for j in range(0, len(lines)-1):
243
+ sid=0
244
+ eid=0
245
+ for m in range(0,len(lines)):
246
+ if m==j:
247
+ fout_context_list.append(lines[m]+'\tO\tB')
248
+ sid=m
249
+ temp_seg=lines[m].split('\t')
250
+ temp_entity.append(temp_seg[0])
251
+ temp_pos.append(temp_seg[3])
252
+ elif m==j+1:
253
+ fout_context_list.append(lines[m]+'\tO\tB')
254
+ eid=m
255
+ temp_seg=lines[m].split('\t')
256
+ temp_entity.append(temp_seg[0])
257
+ temp_pos.append(temp_seg[3])
258
+ else:
259
+ pass
260
+ # fout_context_list.append(lines[m]+'\tO\tO')
261
+
262
+ if pun_filter(temp_entity)==0 and pos_filter(temp_pos,temp_entity)==0:
263
+ num_total+=1
264
+ if ' '.join(temp_entity) not in allentity:
265
+ allentity.append(' '.join(temp_entity))
266
+ fout_context.write('HP:None\t'+' '.join(temp_entity)+'\n')
267
+ fout_context.write('\n'.join(fout_context_list)+'\n\n')
268
+ index_dict[str(num_total)]=[i,sid,eid]
269
+ temp_entity=[]
270
+ temp_pos=[]
271
+ fout_context_list=[]
272
+ else :
273
+ for j in range(0, len(lines)-ngram+1):
274
+ sid=0
275
+ eid=0
276
+ for m in range(0,len(lines)):
277
+ if m==j:
278
+ fout_context_list.append(lines[m]+'\tO\tB')
279
+ sid=m
280
+ temp_seg=lines[m].split('\t')
281
+ temp_entity.append(temp_seg[0])
282
+ temp_pos.append(temp_seg[3])
283
+ elif m>j and m<j+ngram-1:
284
+ fout_context_list.append(lines[m]+'\tO\tB')
285
+ temp_seg=lines[m].split('\t')
286
+ temp_entity.append(temp_seg[0])
287
+ temp_pos.append(temp_seg[2])
288
+ elif m==j+ngram-1:
289
+ fout_context_list.append(lines[m]+'\tO\tB')
290
+ eid=m
291
+ temp_seg=lines[m].split('\t')
292
+ temp_entity.append(temp_seg[0])
293
+ temp_pos.append(temp_seg[3])
294
+ else:
295
+ pass
296
+ # fout_context_list.append(lines[m]+'\tO\tO')
297
+
298
+ if pun_filter(temp_entity)==0 and pos_filter(temp_pos,temp_entity)==0:
299
+ num_total+=1
300
+ if ' '.join(temp_entity) not in allentity:
301
+ allentity.append(' '.join(temp_entity))
302
+ fout_context.write('HP:None\t'+' '.join(temp_entity)+'\n')
303
+ fout_context.write('\n'.join(fout_context_list)+'\n\n')
304
+ index_dict[str(num_total)]=[i,sid,eid]
305
+
306
+ temp_entity=[]
307
+ temp_pos=[]
308
+ fout_context_list=[]
309
+
310
+ return fout_context.getvalue(),fout_txt.getvalue(),index_dict
311
+
312
+ def output_result(result,label_2_index,Top_N=5):
313
+
314
+ fout=io.StringIO()
315
+ hpo_label={}
316
+
317
+ for key in label_2_index.keys():
318
+ hpo_label[label_2_index[key]]=key
319
+
320
+
321
+ for line in result:
322
+ #Top_index=line.argsort()[-1*Top_N:][::-1]
323
+ index_top_unsort=np.argpartition(line,-Top_N)[-Top_N:]
324
+ values_top=line[index_top_unsort]
325
+ Top_index=index_top_unsort[np.argsort(-values_top)]
326
+ temp_list=[]
327
+ for max_index in Top_index:
328
+ hpo_id=hpo_label[max_index]
329
+ hpo_id_value=round(line[max_index],5)
330
+ temp_list.append(str(hpo_id)+'|'+str(hpo_id_value))
331
+ fout.write('\t'.join(temp_list)+'\n')
332
+
333
+ return fout.getvalue()
334
+
335
+ def decode_tsv(test_score, ml_input_index, ml_input_txt, T=0.8):
336
+
337
+ fin_predict=io.StringIO(test_score)
338
+ fin_text=io.StringIO(ml_input_txt)
339
+ fout=io.StringIO()
340
+
341
+ test_txt=fin_text.read().strip().split('\n')
342
+ test_index=ml_input_index
343
+ test_pre=fin_predict.read().strip().split('\n')
344
+
345
+ fin_text.close()
346
+ fin_predict.close()
347
+
348
+ sent_result={}
349
+ for i in range(0,len(test_pre)):
350
+ seg_pre=test_pre[i].split('\t')[0].split('|')
351
+ #print(seg_pre,T)
352
+ if float(seg_pre[1])>T and seg_pre[0]!='HP:None':
353
+ term_id=str(i+1)
354
+ pre_result=[test_index[term_id][1],test_index[term_id][2],seg_pre[0],seg_pre[1]]
355
+ sent_id=str(test_index[term_id][0])
356
+ if sent_id not in sent_result.keys():
357
+ sent_result[sent_id]=[pre_result]
358
+ else:
359
+ sent_result[sent_id].append(pre_result)
360
+
361
+ for i in range(0,len(test_txt)):
362
+ fout.write(test_txt[i]+'\n')
363
+ if str(i) in sent_result.keys():
364
+ temp_result={}
365
+ for ele in sent_result[str(i)]:
366
+ temp_line=str(ele[0])+'\t'+str(ele[1])+'\t'+' '.join(test_txt[i].split()[ele[0]:ele[1]+1])+'\t'+ele[2]+'\t'+ele[3]
367
+ temp_result[temp_line]=[ele[0],ele[1]]
368
+ if len(temp_result)>=1:
369
+ temp_result=sorted(temp_result.items(), key=lambda d: (d[1][0],d[1][1]), reverse=False)
370
+ for ent in temp_result:
371
+ fout.write(ent[0]+'\n')
372
+ fout.write('\n')
373
+
374
+ return fout.getvalue()
375
+
376
+ def score_filter(temp_entity, T=0.1):
377
+
378
+ result_list=[]
379
+ for i in range(0,len(temp_entity)):
380
+ if float (temp_entity[i][-1])>=T:
381
+ result_list.append(temp_entity[i])
382
+ return(result_list)
383
+ def find_max_entity_nest(nest_list):
384
+ temp_result_list={}
385
+ for i in range(0, len(nest_list)):
386
+ hpoid=nest_list[i][-2]
387
+ score=float(nest_list[i][-1])
388
+ if hpoid not in temp_result_list.keys():
389
+ temp_result_list[hpoid]=nest_list[i]
390
+ else:
391
+ if score>float(temp_result_list[hpoid][-1]):
392
+ temp_result_list[hpoid]=nest_list[i]
393
+ new_list=[]
394
+ for hpoid in temp_result_list.keys():
395
+ new_list.append(temp_result_list[hpoid])
396
+ return new_list
397
+ def duplicate_filter(temp_entity):
398
+ result_list=[]
399
+ if len(temp_entity)>1:
400
+ first_entity=temp_entity[0]
401
+ nest_list=[first_entity]
402
+ max_eid=int(first_entity[1])
403
+
404
+ for i in range(1,len(temp_entity)):
405
+ segs=temp_entity[i]
406
+ if int(segs[0])> max_eid:
407
+ if len(nest_list)==1:
408
+ result_list.append(nest_list[0])
409
+ nest_list=[segs]
410
+ if int(segs[1])>max_eid:
411
+ max_eid=int(segs[1])
412
+ else:
413
+ result_list.extend(find_max_entity_nest(nest_list))
414
+ nest_list=[segs]
415
+
416
+ if int(segs[1])>max_eid:
417
+ max_eid=int(segs[1])
418
+
419
+ else:
420
+ nest_list.append(segs)
421
+ if int(segs[1])>max_eid:
422
+ max_eid=int(segs[1])
423
+ if nest_list!=[]:
424
+ if len(nest_list)==1:
425
+ result_list.append(nest_list[0])
426
+
427
+ else:
428
+ result_list.extend(find_max_entity_nest(nest_list))
429
+ else:
430
+ result_list=temp_entity
431
+ return result_list
432
+ def combine_strategy(test_decode_temp, T=0.8):
433
+ fin=io.StringIO(test_decode_temp)
434
+ fout=io.StringIO()
435
+
436
+ documents=fin.read().strip().split('\n\n')
437
+ fin.close()
438
+
439
+ for doc in documents:
440
+ lines=doc.split('\n')
441
+ context=lines[0]
442
+ final_entity_list=[]
443
+ if len(lines)>1:
444
+ # all entity candidates
445
+ temp_entity=[]
446
+ for i in range(1,len(lines)):
447
+ temp_entity.append(lines[i].split('\t'))
448
+ #print('all entity condidates: ',len(temp_entity))
449
+
450
+ # 将阈值低于T的候选过滤
451
+ filter1=score_filter(temp_entity,T)
452
+ # print('filter1:', len(filter1))
453
+ filter2=duplicate_filter(filter1)
454
+ #print('filter2:', filter2)
455
+ final_entity_list=filter2
456
+
457
+ fout.write(context+'\n')
458
+ for ele in final_entity_list:
459
+ fout.write('\t'.join(ele)+'\n')
460
+ fout.write('\n')
461
+
462
+ return fout.getvalue()
463
+
464
+
465
+ def model_predict(ml_input,nn_model,ml_input_txt,ml_input_index,Threshold):
466
+ if nn_model.model_type=='cnn':
467
+ #startTime=time.time()
468
+ test_set,test_label = ml_intext_fn(ml_input)
469
+ test_x, test_y = nn_model.rep.represent_instances_all_feas(test_set,test_label,word_max_len=nn_model.hyper['sen_max'],char_max_len=nn_model.hyper['word_max'])
470
+ input_test = []
471
+
472
+ if nn_model.fea_dict['word'] == 1:
473
+ input_test.append(test_x[0])
474
+
475
+ if nn_model.fea_dict['char'] == 1:
476
+ input_test.append(test_x[1])
477
+
478
+ if nn_model.fea_dict['lemma'] == 1:
479
+ input_test.append(test_x[2])
480
+
481
+ if nn_model.fea_dict['pos'] == 1:
482
+ input_test.append(test_x[3])
483
+ # print('ml-model-represent:',time.time()-startTime)
484
+ # startTime=time.time()
485
+ test_pre = nn_model.model.predict(input_test)
486
+ # print('ml-model-predict:',time.time()-startTime)
487
+
488
+ elif nn_model.model_type=='bert' or nn_model.model_type=='bioformer':
489
+ #startTime=time.time()
490
+ test_set,test_label = ml_intext_fn(ml_input)
491
+ test_x,test_y=nn_model.rep.load_data(test_set,test_label,word_max_len=nn_model.maxlen)
492
+ #print('ml-model-represent:',time.time()-startTime)
493
+ #startTime=time.time()
494
+ test_pre = nn_model.model.predict(test_x)
495
+ #print('ml-model-modedpred:',time.time()-startTime)
496
+ # startTime=time.time()
497
+ test_score=output_result(test_pre, nn_model.rep.label_2_index,Top_N=3)
498
+ # print('ml-model-output:',time.time()-startTime)
499
+ #print('test_score:',test_score)
500
+ # startTime=time.time()
501
+ test_decode_temp=decode_tsv(test_score, ml_input_index, ml_input_txt, T=Threshold)
502
+ # print('ml-model-decode:',time.time()-startTime)
503
+ #print('decode_temp:\n',test_decode_temp)
504
+ # test_pre_tsv=combine_strategy(test_decode_temp,T=Threshold)
505
+ return test_decode_temp
506
+
507
+ def model_predict_old(ml_input,nn_model,ml_input_txt,ml_input_index,Threshold):
508
+ if nn_model.model_type=='cnn':
509
+
510
+ test_set,test_label = ml_intext_fn(ml_input)
511
+ test_x, test_y = nn_model.rep.represent_instances_all_feas(test_set,test_label,word_max_len=nn_model.hyper['sen_max'],char_max_len=nn_model.hyper['word_max'])
512
+ input_test = []
513
+
514
+ if nn_model.fea_dict['word'] == 1:
515
+ input_test.append(test_x[0])
516
+
517
+ if nn_model.fea_dict['char'] == 1:
518
+ input_test.append(test_x[1])
519
+
520
+ if nn_model.fea_dict['lemma'] == 1:
521
+ input_test.append(test_x[2])
522
+
523
+ if nn_model.fea_dict['pos'] == 1:
524
+ input_test.append(test_x[3])
525
+
526
+ test_pre = nn_model.model.predict(input_test,batch_size=256)
527
+
528
+ elif nn_model.model_type=='bert' or nn_model.model_type=='bioformer':
529
+
530
+ test_set,test_label = ml_intext_fn(ml_input)
531
+ test_x,test_y=nn_model.rep.load_data(test_set,test_label,word_max_len=nn_model.maxlen)
532
+
533
+ test_pre = nn_model.model.predict(test_x,batch_size=128)
534
+
535
+ test_score=output_result(test_pre, nn_model.rep.label_2_index,Top_N=3)
536
+ #print('test_score:',test_score)
537
+ test_decode_temp=decode_tsv(test_score, ml_input_index, ml_input_txt, T=0.0)
538
+ #print('decode_temp:\n',test_decode_temp)
539
+ test_pre_tsv=combine_strategy(test_decode_temp,T=Threshold)
540
+ return test_pre_tsv
541
+
542
+ def output_txt(ml_input_txt):
543
+ fin_text=io.StringIO(ml_input_txt)
544
+ fout=io.StringIO()
545
+
546
+ test_txt=fin_text.read().strip().split('\n')
547
+
548
+ fin_text.close()
549
+
550
+ for i in range(0,len(test_txt)):
551
+ fout.write(test_txt[i]+'\n')
552
+ fout.write('\n')
553
+
554
+ return fout.getvalue()
555
+
556
+ def ml_tagging(ssplit_token,ml_model,Threshold):
557
+ # startTime=time.time()
558
+ ml_input, ml_input_txt,ml_input_index=build_ngram_testset_filted(ssplit_token)
559
+ # print('ml-ngrambuild:',time.time()-startTime)
560
+ #print('ml_input:')
561
+ #print(ml_input)
562
+ # startTime=time.time()
563
+ if len(ml_input_index)>0:
564
+ ml_pre_tsv=model_predict(ml_input,ml_model,ml_input_txt,ml_input_index,Threshold)
565
+ else:
566
+ ml_pre_tsv=output_txt(ml_input_txt)
567
+ # print('ml-modelpred:',time.time()-startTime)
568
+ return ml_pre_tsv
569
+
570
+ def ml_tagging_allngram(ssplit_token,ml_model,Threshold):
571
+ ml_input, ml_input_txt,ml_input_index=build_all_ngram_testset_filted(ssplit_token)
572
+ #print('ml_input:')
573
+ #print(ml_input)
574
+ if len(ml_input_index)>0:
575
+ ml_pre_tsv=model_predict_old(ml_input,ml_model,ml_input_txt,ml_input_index,Threshold)
576
+ else:
577
+ ml_pre_tsv=output_txt(ml_input_txt)
578
+ return ml_pre_tsv
src/nn_model.py ADDED
@@ -0,0 +1,150 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Thu Mar 26 09:04:13 2020
4
+
5
+ @author: luol2
6
+ """
7
+
8
+ import time
9
+ import sys
10
+ import numpy as np
11
+ import keras
12
+ from src.nn_represent import CNN_RepresentationLayer,BERT_RepresentationLayer
13
+ from keras.layers import *
14
+ from keras.models import Model
15
+ from keras_bert import load_trained_model_from_checkpoint
16
+
17
+
18
+
19
+
20
+ class bioTag_CNN():
21
+ def __init__(self, model_files):
22
+ self.model_type='cnn'
23
+ model_test_type='cnn'
24
+ self.fea_dict = {'word': 1,
25
+ 'char': 1,
26
+ 'lemma':0,
27
+ 'pos':0}
28
+
29
+ self.hyper = {'sen_max' :20,
30
+ 'word_max' :40,
31
+ 'charvec_size' :50,
32
+ 'pos_size' :50}
33
+
34
+ self.w2vfile=model_files['w2vfile']
35
+ self.charfile=model_files['charfile']
36
+ self.labelfile=model_files['labelfile']
37
+ self.posfile=model_files['posfile']
38
+
39
+ vocab={'char':self.charfile,'label':self.labelfile,'pos':self.posfile}
40
+ print('loading w2v model.....')
41
+ self.rep = CNN_RepresentationLayer(self.w2vfile,vocab_file=vocab, frequency=400000)
42
+
43
+ print('building model......')
44
+ all_fea = []
45
+ fea_list = []
46
+
47
+ if self.fea_dict['word'] == 1:
48
+ word_input = Input(shape=(self.hyper['sen_max'],), dtype='int32', name='word_input')
49
+ all_fea.append(word_input)
50
+ word_fea = Embedding(self.rep.vec_table.shape[0], self.rep.vec_table.shape[1], weights=[self.rep.vec_table], trainable=True,mask_zero=False, input_length=self.hyper['sen_max'], name='word_emd')(word_input)
51
+ fea_list.append(word_fea)
52
+
53
+ if self.fea_dict['char'] == 1:
54
+ char_input = Input(shape=(self.hyper['sen_max'],self.hyper['word_max']), dtype='int32', name='char_input')
55
+ all_fea.append(char_input)
56
+ char_fea = TimeDistributed(Embedding(self.rep.char_table_size, self.hyper['charvec_size'], trainable=True,mask_zero=False), name='char_emd')(char_input)
57
+ char_fea = TimeDistributed(Conv1D(self.hyper['charvec_size']*2, 3, padding='same',activation='relu'), name="char_cnn")(char_fea)
58
+ char_fea_max = TimeDistributed(GlobalMaxPooling1D(), name="char_pooling_max")(char_fea)
59
+ fea_list.append(char_fea_max)
60
+
61
+ if self.fea_dict['lemma'] == 1:
62
+ lemma_input = Input(shape=(self.hyper['sen_max'],), dtype='int32', name='lemma_input')
63
+ all_fea.append(lemma_input)
64
+ lemma_fea = Embedding(self.rep.vec_table.shape[0], self.rep.vec_table.shape[1], weights=[self.rep.vec_table], trainable=True,mask_zero=False, input_length=self.hyper['sen_max'], name='lemma_emd')(lemma_input)
65
+ fea_list.append(lemma_fea)
66
+
67
+ if self.fea_dict['pos'] == 1:
68
+ pos_input = Input(shape=(self.hyper['sen_max'],), dtype='int32', name='pos_input')
69
+ all_fea.append(pos_input)
70
+ pos_fea = Embedding(self.rep.pos_table_size, self.hyper['pos_size'], trainable=True,mask_zero=False, input_length=self.hyper['sen_max'], name='pos_emd')(pos_input)
71
+ fea_list.append(pos_fea)
72
+
73
+ if len(fea_list) == 1:
74
+ concate_vec = fea_list[0]
75
+ else:
76
+ concate_vec = Concatenate()(fea_list)
77
+
78
+ concate_vec = Dropout(0.4)(concate_vec)
79
+
80
+ # model
81
+ if model_test_type=='cnn':
82
+ cnn = Conv1D(1024, 1, padding='valid', activation='relu',name='cnn1')(concate_vec)
83
+ cnn = GlobalMaxPooling1D()(cnn)
84
+ elif model_test_type=='lstm':
85
+ bilstm = Bidirectional(LSTM(200, return_sequences=True, implementation=2, dropout=0.4, recurrent_dropout=0.4), name='bilstm1')(concate_vec)
86
+ cnn = GlobalMaxPooling1D()(bilstm)
87
+
88
+
89
+ dense = Dense(1024, activation='relu')(cnn)
90
+ dense= Dropout(0.4)(dense)
91
+ output = Dense(self.rep.label_table_size, activation='softmax')(dense)
92
+ self.model = Model(inputs=all_fea, outputs=output)
93
+ def load_model(self,model_file):
94
+ self.model.load_weights(model_file)
95
+ #self.model.summary()
96
+ print('load cnn model done!')
97
+
98
+ class bioTag_BERT():
99
+ def __init__(self, model_files):
100
+ self.model_type='bert'
101
+ self.maxlen = 64
102
+ config_path = model_files['config_path']
103
+ checkpoint_path = model_files['checkpoint_path']
104
+ vocab_path = model_files['vocab_path']
105
+ self.label_file=model_files['labelfile']
106
+
107
+ self.rep = BERT_RepresentationLayer( vocab_path, self.label_file)
108
+
109
+
110
+ bert_model = load_trained_model_from_checkpoint(config_path, checkpoint_path, training=False, trainable=True,seq_len=self.maxlen)
111
+
112
+ x1_in = Input(shape=(None,))
113
+ x2_in = Input(shape=(None,))
114
+ x = bert_model([x1_in, x2_in])
115
+ x = Lambda(lambda x: x[:, 0])(x)
116
+ outputs = Dense(self.rep.label_table_size, activation='softmax')(x)
117
+
118
+ self.model = Model(inputs=[x1_in,x2_in], outputs=outputs)
119
+
120
+ def load_model(self,model_file):
121
+ self.model.load_weights(model_file)
122
+ #self.model.summary()
123
+
124
+ class bioTag_Bioformer():
125
+ def __init__(self, model_files):
126
+ self.model_type='bioformer'
127
+ self.maxlen = 32
128
+ config_path = model_files['config_path']
129
+ checkpoint_path = model_files['checkpoint_path']
130
+ vocab_path = model_files['vocab_path']
131
+ self.label_file=model_files['labelfile']
132
+
133
+ self.rep = BERT_RepresentationLayer( vocab_path, self.label_file)
134
+
135
+
136
+ bert_model = load_trained_model_from_checkpoint(config_path, checkpoint_path, training=False, trainable=True,seq_len=self.maxlen)
137
+
138
+ x1_in = Input(shape=(None,))
139
+ x2_in = Input(shape=(None,))
140
+ x = bert_model([x1_in, x2_in])
141
+ x = Lambda(lambda x: x[:, 0])(x)
142
+ outputs = Dense(self.rep.label_table_size, activation='softmax')(x)
143
+
144
+ self.model = Model(inputs=[x1_in,x2_in], outputs=outputs)
145
+
146
+ def load_model(self,model_file):
147
+ self.model.load_weights(model_file)
148
+ #self.model.summary()
149
+ print('load bioformer model done!')
150
+
src/nn_represent.py ADDED
@@ -0,0 +1,338 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Fri Jun 12 10:02:20 2020
4
+
5
+ @author: luol2
6
+ """
7
+ import time
8
+ import os, sys
9
+ import numpy as np
10
+ from keras.preprocessing.sequence import pad_sequences
11
+ from keras_bert import Tokenizer
12
+
13
+
14
+ class CNN_RepresentationLayer(object):
15
+
16
+
17
+ def __init__(self, wordvec_file, vocab_file=[],\
18
+ vec_size=50, word_size=10000, frequency=10000):
19
+
20
+ '''
21
+ wordvec_file ： the file path of word embedding
22
+ vec_size : the dimension size of word vector
23
+ learned by word2vec tool
24
+
25
+ word_size : the size of word vocabulary
26
+
27
+ frequency : the threshold for the words left according to
28
+ their frequency appeared in the text
29
+ for example, when frequency is 10000, the most
30
+ frequent appeared 10000 words are considered
31
+
32
+ '''
33
+ #load word embedding
34
+ file = open(wordvec_file)
35
+ first_line = file.readline().strip()
36
+ file.close()
37
+ self.word_size = int(first_line.split()[0])
38
+ self.vec_size = int(first_line.split()[1])
39
+ self.frequency = frequency
40
+
41
+ if self.frequency>self.word_size:
42
+ self.vec_table = np.zeros((self.word_size + 2, self.vec_size))
43
+ else:
44
+ self.vec_table = np.zeros((self.frequency + 2, self.vec_size))
45
+ self.word_2_index = {}
46
+ self.load_wordvecs(wordvec_file)
47
+
48
+ #other fea
49
+ self.char_2_index={}
50
+ self.char_table_size=0
51
+ if 'char' in vocab_file.keys():
52
+ self.load_fea_vocab(vocab_file['char'],self.char_2_index)
53
+ self.char_table_size=len(self.char_2_index)
54
+ #print(self.char_table_size)
55
+ #print(self.char_2_index)
56
+
57
+ self.label_2_index={}
58
+ self.label_table_size=0
59
+ if 'label' in vocab_file.keys():
60
+ self.load_label_vocab(vocab_file['label'],self.label_2_index)
61
+ self.label_table_size=len(self.label_2_index)
62
+ #print(self.label_table_size)
63
+ #print(self.char_2_index)
64
+
65
+ self.pos_2_index={}
66
+ self.pos_table_size=0
67
+ if 'pos' in vocab_file.keys():
68
+ self.load_fea_vocab(vocab_file['pos'],self.pos_2_index)
69
+ self.pos_table_size=len(self.pos_2_index)
70
+ #print(self.pos_table_size)
71
+
72
+
73
+
74
+ def load_wordvecs(self, wordvec_file):
75
+
76
+ file = open(wordvec_file,'r',encoding='utf-8')
77
+ file.readline()
78
+ #print(self.word_size)
79
+ #print(self.vec_size)
80
+ row = 0
81
+ self.word_2_index['padding_0'] = row #oov-zero vector
82
+ row+=1
83
+ for line in file:
84
+ if row <= self.word_size and row <= self.frequency:
85
+ line_split = line.strip().split(' ')
86
+ self.word_2_index[line_split[0]] = row
87
+ for col in range(self.vec_size):
88
+ self.vec_table[row][col] = float(line_split[col + 1])
89
+ row += 1
90
+ else:
91
+ break
92
+
93
+ self.word_2_index['sparse_vectors'] = row #oov-zero vector
94
+ file.close()
95
+
96
+ def load_fea_vocab(self,fea_file,fea_index):
97
+ fin=open(fea_file,'r',encoding='utf-8')
98
+ i=0
99
+ fea_index['padding_0']=i
100
+ i+=1
101
+ fea_index['oov_padding']=i
102
+ i+=1
103
+ for line in fin:
104
+ fea_index[line.strip()]=i
105
+ i+=1
106
+ fin.close()
107
+
108
+ def load_label_vocab(self,fea_file,fea_index):
109
+ fin=open(fea_file,'r',encoding='utf-8')
110
+ i=0
111
+ for line in fin:
112
+ fea_index[line.strip()]=i
113
+ i+=1
114
+ fin.close()
115
+
116
+ def generate_label_list(self,labels):
117
+ label_list=[]
118
+
119
+ for label in labels:
120
+ temp_label=[0]*self.label_table_size
121
+ temp_label[self.label_2_index[label]]=1
122
+ label_list.append(temp_label)
123
+ return label_list
124
+
125
+ def represent_instances_all_feas(self, instances, labels, word_max_len=100, char_max_len=50):
126
+
127
+ x_text_list=[]
128
+ x_word_list=[]
129
+ x_char_list=[]
130
+
131
+ x_lemma_np=[]
132
+ x_pos_np=[]
133
+ y_np=[]
134
+ startTime=time.time()
135
+ for sentence in instances:
136
+ sentence_list=[]
137
+ sentence_word_list=[]
138
+ sentence_lemma_list=[]
139
+ sentence_pos_list=[]
140
+ sentence_text=[]
141
+ for j in range(0,len(sentence)):
142
+ word=sentence[j]
143
+ #char fea
144
+ char_list=[0]*char_max_len
145
+ for i in range(len(word[0])):
146
+ if i<char_max_len:
147
+ if word[0][i] in self.char_2_index.keys():
148
+ char_list[i]=self.char_2_index[word[0][i]]
149
+ else:
150
+ char_list[i]=self.char_2_index['oov_padding']
151
+ sentence_word_list.append(char_list)
152
+
153
+ #word fea
154
+ sentence_text.append(word[0].lower())
155
+ if word[0].lower() in self.word_2_index.keys():
156
+ sentence_list.append(self.word_2_index[word[0].lower()])
157
+ else:
158
+ sentence_list.append(self.word_2_index['sparse_vectors'])
159
+ """
160
+ #lemma fea
161
+ if word[1].lower() in self.word_2_index.keys():
162
+ sentence_lemma_list.append(self.word_2_index[word[1].lower()])
163
+ else:
164
+ sentence_lemma_list.append(self.word_2_index['sparse_vectors'])
165
+
166
+ #pos fea
167
+ if word[3] in self.pos_2_index.keys():
168
+ sentence_pos_list.append(self.pos_2_index[word[3]])
169
+ else:
170
+ sentence_pos_list.append(self.pos_2_index['oov_padding'])
171
+ """
172
+ x_text_list.append(sentence_text)
173
+ x_word_list.append(sentence_list)
174
+ x_char_list.append(sentence_word_list)
175
+ # x_lemma_list.append(sentence_lemma_list)
176
+ # x_pos_list.append(sentence_pos_list)
177
+
178
+
179
+ #print('\nword:',x_word_list)
180
+ #print('\nchar:',x_char_list)
181
+ #print('\nlemma:',x_lemma_list)
182
+ #print('\npos:',x_pos_list)
183
+ #y_list=self.generate_label_list(labels)
184
+ #print('\ny_list:',y_list)
185
+
186
+ x_word_np = pad_sequences(x_word_list, word_max_len, value=0, padding='post',truncating='post') # right padding
187
+ x_char_np = pad_sequences(x_char_list, word_max_len, value=0, padding='post',truncating='post')
188
+ #x_lemma_np = pad_sequences(x_lemma_list, word_max_len, value=0, padding='post',truncating='post')
189
+ #x_pos_np = pad_sequences(x_pos_list, word_max_len, value=0, padding='post',truncating='post')
190
+ #y_np = np.array(y_list)
191
+ return [x_word_np, x_char_np, x_lemma_np, x_pos_np, x_text_list], y_np
192
+
193
+ def represent_instances_all_feas_myself(self, instances, labels, word_max_len=100, char_max_len=50):
194
+
195
+ x_text_list=[]
196
+ x_word_list=[]
197
+ x_char_list=[]
198
+ x_lemma_list=[]
199
+ x_pos_list=[]
200
+
201
+ y_list=[]
202
+ startTime=time.time()
203
+ for sentence in instances:
204
+ sentence_list=[0]*word_max_len
205
+ sentence_word_list=[[0]*char_max_len for i in range(word_max_len)]
206
+ sentence_lemma_list=[0]*word_max_len
207
+ sentence_pos_list=[0]*word_max_len
208
+ sentence_text=[]
209
+ for j in range(0,len(sentence)):
210
+ word=sentence[j]
211
+
212
+ sentence_text.append(word[0].lower())
213
+
214
+ if j<word_max_len:
215
+ #char fea
216
+ for i in range(len(word[0])):
217
+ if i<char_max_len:
218
+ if word[0][i] in self.char_2_index.keys():
219
+ sentence_word_list[j][i]=self.char_2_index[word[0][i]]
220
+ else:
221
+ sentence_word_list[j][i]=self.char_2_index['oov_padding']
222
+
223
+ #word fea
224
+ if word[0].lower() in self.word_2_index.keys():
225
+ sentence_list[j]=self.word_2_index[word[0].lower()]
226
+ else:
227
+ sentence_list[j]=self.word_2_index['sparse_vectors']
228
+
229
+ #lemma fea
230
+ if word[1].lower() in self.word_2_index.keys():
231
+ sentence_lemma_list[j]=self.word_2_index[word[1].lower()]
232
+ else:
233
+ sentence_lemma_list[j]=self.word_2_index['sparse_vectors']
234
+
235
+ #pos fea
236
+ if word[3] in self.pos_2_index.keys():
237
+ sentence_pos_list[j]=self.pos_2_index[word[3]]
238
+ else:
239
+ sentence_pos_list[j]=self.pos_2_index['oov_padding']
240
+
241
+ x_text_list.append(sentence_text)
242
+ x_word_list.append(sentence_list)
243
+ x_char_list.append(sentence_word_list)
244
+ x_lemma_list.append(sentence_lemma_list)
245
+ x_pos_list.append(sentence_pos_list)
246
+
247
+ print('ml-model-represent-list:',time.time()-startTime)
248
+ startTime=time.time()
249
+ #print('\nword:',x_word_list)
250
+ #print('\nchar:',x_char_list)
251
+ #print('\nlemma:',x_lemma_list)
252
+ #print('\npos:',x_pos_list)
253
+ y_list=self.generate_label_list(labels)
254
+ #print('\ny_list:',y_list)
255
+ # x_word_np = pad_sequences2(x_word_list, word_max_len, value=0, padding='post',truncating='post') # right padding
256
+ # x_char_np = pad_sequences2(x_char_list, word_max_len, value=0, padding='post',truncating='post')
257
+ # x_lemma_np = pad_sequences2(x_lemma_list, word_max_len, value=0, padding='post',truncating='post')
258
+ # x_pos_np = pad_sequences2(x_pos_list, word_max_len, value=0, padding='post',truncating='post')
259
+
260
+ x_word_np = np.array(x_word_list) # right padding
261
+ x_char_np = pad_sequences2(x_char_list)
262
+ x_lemma_np = np.array(x_lemma_list)
263
+ x_pos_np = np.array(x_pos_list)
264
+ y_np = np.array(y_list)
265
+ print('ml-model-represent-pad:',time.time()-startTime)
266
+ return [x_word_np, x_char_np, x_lemma_np, x_pos_np, x_text_list], y_np
267
+
268
+
269
+
270
+ class BERT_RepresentationLayer(object):
271
+
272
+
273
+ def __init__(self, vocab_path, label_file):
274
+
275
+
276
+ #load vocab
277
+ self.bert_vocab_dict = {}
278
+ self.load_bert_vocab(vocab_path,self.bert_vocab_dict)
279
+ self.tokenizer = Tokenizer(self.bert_vocab_dict)
280
+
281
+ #load label
282
+ self.label_2_index={}
283
+ self.label_table_size=0
284
+ self.load_label_vocab(label_file,self.label_2_index)
285
+ self.label_table_size=len(self.label_2_index)
286
+
287
+ def load_label_vocab(self,fea_file,fea_index):
288
+ fin=open(fea_file,'r',encoding='utf-8')
289
+ i=0
290
+ for line in fin:
291
+ fea_index[line.strip()]=i
292
+ i+=1
293
+ fin.close()
294
+ def load_bert_vocab(self,vocab_file,vocab_dict):
295
+ fin=open(vocab_file,'r',encoding='utf-8')
296
+ i=0
297
+ for line in fin:
298
+ vocab_dict[line.strip()]=i
299
+ i+=1
300
+ fin.close()
301
+
302
+ def generate_label_list(self,labels):
303
+ label_list=[]
304
+
305
+ for label in labels:
306
+ temp_label=[0]*self.label_table_size
307
+ temp_label[self.label_2_index[label]]=1
308
+ label_list.append(temp_label)
309
+ return label_list
310
+
311
+ def load_data(self,instances, labels, word_max_len=100):
312
+
313
+ x_index=[]
314
+ x_seg=[]
315
+ y_np=[]
316
+
317
+ for sentence in instances:
318
+ sentence_text_list=[]
319
+ for j in range(0,len(sentence)):
320
+ sentence_text_list.append(sentence[j][0])
321
+ sentence_text=' '.join(sentence_text_list)
322
+ #print(self.tokenizer.tokenize(first=sentence_text))
323
+ x1, x2 = self.tokenizer.encode(first=sentence_text)
324
+ x_index.append(x1)
325
+ x_seg.append(x2)
326
+
327
+ # y_list=self.generate_label_list(labels)
328
+
329
+ x1_np = pad_sequences(x_index, word_max_len, value=0, padding='post',truncating='post') # right padding
330
+ x2_np = pad_sequences(x_seg, word_max_len, value=0, padding='post',truncating='post')
331
+ # y_np = np.array(y_list)
332
+
333
+ return [x1_np, x2_np], y_np
334
+
335
+ if __name__ == '__main__':
336
+ pass
337
+
338
+
src/post_processing.py ADDED
@@ -0,0 +1,58 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Thu Jun 18 20:08:30 2020
4
+
5
+ @author: luol2
6
+ """
7
+
8
+ def combine_overlap(mention_list):
9
+
10
+ entity_list=[]
11
+ if len(mention_list)>2:
12
+
13
+ first_entity=mention_list[0]
14
+ nest_list=[first_entity]
15
+ max_eid=int(first_entity[1])
16
+ for i in range(1,len(mention_list)):
17
+ segs=mention_list[i]
18
+ if int(segs[0])> max_eid:
19
+ if len(nest_list)==1:
20
+ entity_list.append(nest_list[0])
21
+ nest_list=[]
22
+ nest_list.append(segs)
23
+ if int(segs[1])>max_eid:
24
+ max_eid=int(segs[1])
25
+ else:
26
+ tem=find_max_entity(nest_list)#find max entity
27
+ entity_list.append(tem)
28
+ nest_list=[]
29
+ nest_list.append(segs)
30
+ if int(segs[1])>max_eid:
31
+ max_eid=int(segs[1])
32
+
33
+ else:
34
+ nest_list.append(segs)
35
+ if int(segs[1])>max_eid:
36
+ max_eid=int(segs[1])
37
+ if nest_list!=[]:
38
+ if len(nest_list)==1:
39
+ entity_list.append(nest_list[0])
40
+
41
+ else:
42
+ tem=find_max_entity(nest_list)#find max entity
43
+ entity_list.append(tem)
44
+ else:
45
+ entity_list=mention_list
46
+
47
+ return entity_list
48
+
49
+ def find_max_entity(nest_list):
50
+ max_len=0
51
+ max_entity=[]
52
+ for i in range(0, len(nest_list)):
53
+ length=int(nest_list[i][1])-int(nest_list[i][0])
54
+ if length>max_len:
55
+ max_len=length
56
+ max_entity=nest_list[i]
57
+
58
+ return max_entity
src/restore_index.py ADDED
@@ -0,0 +1,109 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Sun Jun 14 17:19:02 2020
4
+
5
+ @author: luol2
6
+ """
7
+
8
+ import io
9
+ import sys
10
+
11
+ def restore_index_nest_fn(ori_text,file_pre):
12
+
13
+
14
+ fin_pre=io.StringIO(file_pre)
15
+ #print(file_pre)
16
+ all_pre=fin_pre.read().strip().split('\n\n')
17
+ fin_pre.close()
18
+ #print(len(all_pre))
19
+
20
+ new_sentence=''
21
+ restore_result=[]
22
+
23
+ sentence_ori=ori_text.lower().replace('``','" ')
24
+ sentence_ori=sentence_ori.replace("''",'" ')
25
+ for pre_i in range(0,len(all_pre)):
26
+ pre_lines=all_pre[pre_i].split('\n')
27
+ #print(pre_lines)
28
+ # print(sentence_ori)
29
+ if len(pre_lines)>1:
30
+ #print(pre_lines)
31
+ sentence_pre=pre_lines[0].lower().replace('``','"')
32
+ sentence_pre=sentence_pre.replace("''",'"')
33
+ sentence_pre=sentence_pre.split()
34
+ pre_result=[]
35
+ for i in range(1,len(pre_lines)):
36
+ pre_result.append(pre_lines[i].split('\t'))
37
+
38
+ restore_sid=0
39
+ restore_eid=0
40
+ each_word_id=[]
41
+
42
+ for i in range(0,len(sentence_pre)):
43
+
44
+ temp_id=sentence_ori.find(sentence_pre[i])
45
+ if temp_id<0:
46
+ if sentence_pre[i].find('"')>=0:
47
+ temp_id = sentence_ori.find(sentence_pre[i].replace('"','" '))
48
+ else:
49
+ #print('ori:',sentence_ori)
50
+ print('resotr index error:',sentence_pre[i])
51
+ new_sentence+=sentence_ori[0:temp_id]
52
+
53
+ restore_sid=len(new_sentence)
54
+ restore_eid=len(new_sentence)+len(sentence_pre[i])
55
+ each_word_id.append([str(restore_sid),str(restore_eid)])
56
+ new_sentence+=sentence_ori[temp_id:temp_id+len(sentence_pre[i])]
57
+ sentence_ori=sentence_ori[temp_id+len(sentence_pre[i]):]
58
+ # print('each_word:',each_word_id)
59
+ for pre_ele in pre_result:
60
+ # if len(pre_ele)>4:
61
+ # temp_pre_result=[each_word_id[int(pre_ele[0])][0],each_word_id[int(pre_ele[1])][1],pre_ele[3].split('|')[0],pre_ele[4]]
62
+ # else:
63
+ # temp_pre_result=[each_word_id[int(pre_ele[0])][0],each_word_id[int(pre_ele[1])][1],pre_ele[3].split('|')[0],'1.00']
64
+ temp_pre_result=[each_word_id[int(pre_ele[0])][0],each_word_id[int(pre_ele[1])][1],pre_ele[3].split('|')[0],pre_ele[4]]
65
+ if temp_pre_result not in restore_result:
66
+ restore_result.append(temp_pre_result)
67
+ else:
68
+ sentence_pre=pre_lines[0].lower().replace('``','"')
69
+ sentence_pre=sentence_pre.replace("''",'"')
70
+ sentence_pre=sentence_pre.split()
71
+
72
+ for i in range(0,len(sentence_pre)):
73
+
74
+ temp_id=sentence_ori.find(sentence_pre[i])
75
+ if temp_id<0:
76
+ if sentence_pre[i].find('"')>=0:
77
+ temp_id = sentence_ori.find(sentence_pre[i].replace('"','" '))
78
+ else:
79
+ print('resotr index error:',sentence_pre[i])
80
+ new_sentence+=sentence_ori[0:temp_id]
81
+ new_sentence+=sentence_ori[temp_id:temp_id+len(sentence_pre[i])]
82
+ sentence_ori=sentence_ori[temp_id+len(sentence_pre[i]):]
83
+ # print('resotre:',restore_result)
84
+ return restore_result
85
+
86
+ if __name__=='__main__':
87
+ path='//panfs/pan1/bionlp/lulab/luoling/HPO_project/bioTag/data/test/gsc/result/'
88
+ fin=open(path+'GSCplus_Nest_biobert.tsv','r',encoding='utf-8')
89
+ fout=open(path+'GSCplus_Nest_restore_biobert.tsv','w',encoding='utf-8')
90
+ all_context=fin.read().strip().split('\n\n\n\n')
91
+ fin.close()
92
+ file_num=0
93
+ for doc in all_context:
94
+ file_num+=1
95
+ print('file_num:',file_num)
96
+ doc_ele=doc.split('\n\n')
97
+ first_line = doc_ele[0].split('\n')
98
+ pmid=first_line[0]
99
+ ori_text=first_line[1]
100
+ pre_result='\n\n'.join(doc_ele[1:])
101
+ # print('pmid:',pmid)
102
+ # print('ori:',ori_text)
103
+ # print('pre:',pre_result)
104
+ final_result=restore_index_nest_fn(ori_text,pre_result)
105
+ fout.write(pmid+'\n'+ori_text+'\n')
106
+ for ele in final_result:
107
+ fout.write('\t'.join(ele)+'\t'+ori_text[int(ele[0]):int(ele[1])]+'\n')
108
+ fout.write('\n')
109
+ fout.close()
src/ssplit_tokenzier.py ADDED
@@ -0,0 +1,45 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Fri Jun 12 15:26:44 2020
4
+
5
+ @author: luol2
6
+ """
7
+
8
+ import nltk
9
+ from nltk.stem import WordNetLemmatizer
10
+ from nltk.corpus import wordnet
11
+ from nltk.stem.porter import PorterStemmer
12
+ lemmatizer = WordNetLemmatizer()
13
+ stemmer = PorterStemmer()
14
+ import io
15
+
16
+ def get_wordnet_pos(treebank_tag):
17
+ if treebank_tag.startswith('J'):
18
+ return wordnet.ADJ
19
+ elif treebank_tag.startswith('V'):
20
+ return wordnet.VERB
21
+ elif treebank_tag.startswith('N'):
22
+ return wordnet.NOUN
23
+ elif treebank_tag.startswith('R') or treebank_tag=='IN':
24
+ return wordnet.ADV
25
+ else:
26
+ return wordnet.NOUN
27
+
28
+ def ssplit_token_pos_lemma(in_text):
29
+
30
+ fout=io.StringIO()
31
+
32
+ line=in_text.strip()
33
+ line=line.replace('-',' - ').replace('/',' / ')
34
+ sentences = nltk.sent_tokenize(line)
35
+ sentences = [nltk.word_tokenize(sent) for sent in sentences]
36
+ # print(sentences)
37
+ for sent in sentences:
38
+ token_pos = nltk.pos_tag(sent)
39
+ for token in token_pos:
40
+ lemma = lemmatizer.lemmatize(token[0].lower(), get_wordnet_pos(token[1]))
41
+ stem = stemmer.stem(token[0].lower())
42
+ fout.write(token[0]+'\t'+lemma+'\t'+stem+'\t'+token[1]+'\n')
43
+ fout.write('\n')
44
+
45
+ return fout.getvalue()
src/tagging_text.py ADDED
@@ -0,0 +1,102 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # -*- coding: utf-8 -*-
2
+ """
3
+ Created on Mon Aug 24 16:21:23 2020
4
+
5
+ @author: luol2
6
+ """
7
+
8
+ import argparse
9
+ from src.ssplit_tokenzier import ssplit_token_pos_lemma
10
+ from src.ml_ner import ml_tagging,ml_tagging_allngram
11
+ from src.combine_result import combine_ml_dict
12
+ from src.restore_index import restore_index_nest_fn
13
+ from src.dic_ner import dic_ont
14
+ from src.post_processing import combine_overlap
15
+ from src.abbre_resolution import postprocess_abbr
16
+ import os
17
+ import time
18
+ import json
19
+
20
+ #hybrid method
21
+ def bioTag(text,biotag_dic,ml_model,onlyLongest=False, abbrRecog=False, Threshold=0.95):
22
+
23
+ # startTime=time.time()
24
+ ssplit_token=ssplit_token_pos_lemma(text)
25
+ # print(ssplit_token)
26
+ # print('ssplit token:',time.time()-startTime)
27
+
28
+ # startTime=time.time()
29
+ dict_tsv=biotag_dic.matching(ssplit_token)
30
+ # print('dict tsv:\n',dict_tsv)
31
+ # print('dict ner:',time.time()-startTime)
32
+
33
+ # startTime=time.time()
34
+ ml_tsv=ml_tagging(ssplit_token,ml_model,Threshold)
35
+ #print('ml_tsv:\n',ml_tsv)
36
+ # print('ml ner:',time.time()-startTime)
37
+
38
+ # startTime=time.time()
39
+ combine_tsv=combine_ml_dict(dict_tsv,ml_tsv)
40
+ #combine_tsv=combine_ml_dict_fn(ml_tsv,dict_tsv)
41
+ #print('combine:\n',combine_tsv)
42
+ # print('combine:',time.time()-startTime)
43
+
44
+ # startTime=time.time()
45
+ final_result= restore_index_nest_fn(text,combine_tsv)
46
+ # print('final ner:',time.time()-startTime)
47
+ if onlyLongest==True:
48
+ final_result=combine_overlap(final_result)
49
+ if abbrRecog==True:
50
+ final_result=postprocess_abbr(final_result,text)
51
+ # print('final result:')
52
+ # print(final_result)
53
+ # print('final ner:',time.time()-startTime)
54
+
55
+ return final_result
56
+
57
+ # only machine learning-based method
58
+ def bioTag_ml(text,ml_model,onlyLongest=False,abbrRecog=False, Threshold=0.95):
59
+
60
+ # startTime=time.time()
61
+ ssplit_token=ssplit_token_pos_lemma(text)
62
+ # print(ssplit_token)
63
+ # print('ssplit token:',time.time()-startTime)
64
+
65
+ # startTime=time.time()
66
+ ml_tsv=ml_tagging_allngram(ssplit_token,ml_model,Threshold)
67
+ # print('ml_tsv:\n',ml_tsv)
68
+ # print('ml ner:',time.time()-startTime)
69
+
70
+ final_result= restore_index_nest_fn(text,ml_tsv)
71
+ # print('final ner:',time.time()-startTime)
72
+ if onlyLongest==True:
73
+ final_result=combine_overlap(final_result)
74
+
75
+ if abbrRecog==True:
76
+ final_result=postprocess_abbr(final_result,text)
77
+
78
+ return final_result
79
+
80
+ # only dict method
81
+ def bioTag_dic(text,biotag_dic,onlyLongest=False, abbrRecog=False):
82
+
83
+ # startTime=time.time()
84
+ ssplit_token=ssplit_token_pos_lemma(text)
85
+ # print(ssplit_token)
86
+ # print('ssplit token:',time.time()-startTime)
87
+
88
+ # startTime=time.time()
89
+ dict_tsv=biotag_dic.matching(ssplit_token)
90
+ # print('dict tsv:\n',dict_tsv)
91
+ # print('dict ner:',time.time()-startTime)
92
+
93
+ final_result= restore_index_nest_fn(text,dict_tsv)
94
+ # print('final ner:',time.time()-startTime)
95
+ if onlyLongest==True:
96
+ final_result=combine_overlap(final_result)
97
+
98
+ if abbrRecog==True:
99
+ final_result=postprocess_abbr(final_result,text)
100
+
101
+ return final_result
102
+