bibliome / obo-utils Goto Github PK
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License: MIT License
Python library and scripts to manipulate and convert OBO files
License: MIT License
The is_a relationships seems reversed after the umls2obo: the isa are more hasForChild.
For instance:
[Term]
id: C0556144
name: purine or derivative
synonym: "purines and derivatives" EXACT []
synonym: "purine or purine derivative (substance)" EXACT []
synonym: "purine or purine derivative" EXACT []
is_a: C0034136 ! nucleosides, purine
is_a: C0034137 ! nucleotides, purine
is_a: C0039771 ! theophyllin
is_a: C0041980 ! acid, uric
is_a: C0043314 ! xanthine
is_a: C0043315 ! xanthine or xanthine derivative
is_a: C0045643 ! 2,8-dihydroxyadenine
is_a: C0066447 ! methylxanthines
is_a: C0220903 ! purines
is_a: C0935936 ! urates
is_a: C1630404 ! purine derivative diuretic
and the correct in the UMLS should be:
[Term]
id: C1630404
name: purine derivative diuretic
synonym: "purine derivative diuretic (substance)" EXACT []
is_a: C0556144 ! purine or derivative
is_a: C0012798 ! diuretic
@rbossy je viens de constater que tes derniéres modifs concernant python3 ont causé des problémes à l'utilisation du script https://github.com/Bibliome/obo-utils/blob/master/obo2obo.py dans pipeline omnicrobe.
J'ai une ontology vide comme résultat quand j'utilise la version actuelle du code avec python2 et une erreur "AttributeError: 'dict' object has no attribute 'itervalues'" quand j'utilise python3
Le dernier commit qui fonctionne pour moi est la suivante 06ae8a1 et c'est avec Python 2.7.15
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