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Add pathway entity #43

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Zethson opened this issue Mar 17, 2023 · 0 comments
Open
2 of 6 tasks

Add pathway entity #43

Zethson opened this issue Mar 17, 2023 · 0 comments
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@Zethson
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Zethson commented Mar 17, 2023

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/cached_property.py", line 36, in __get__
    value = obj.__dict__[self.func.__name__] = self.func(obj)
  File "/home/zeth/PycharmProjects/bionty/bionty/_entity.py", line 121, in df
    df = self._ontology_to_df(self.ontology)
  File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/cached_property.py", line 36, in __get__
    value = obj.__dict__[self.func.__name__] = self.func(obj)
  File "/home/zeth/PycharmProjects/bionty/bionty/_entity.py", line 102, in ontology
    return Ontology(handle=localpath, **kwargs)
  File "/home/zeth/PycharmProjects/bionty/bionty/_ontology.py", line 32, in __init__
    super().__init__(
  File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/ontology.py", line 283, in __init__
    cls(self).parse_from(_handle)  # type: ignore
  File "/home/zeth/miniconda3/envs/bionty/lib/python3.10/site-packages/pronto/parsers/obo.py", line 45, in parse_from
    raise SyntaxError(s.args[0], location) from None
  File "/home/zeth/PycharmProjects/bionty/bionty/_dynamic/human_pw_7.74_Pathway___download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb", line 98
    def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of the primary or standard 20 amino acids found in proteins. Amino acids are described as non-essential or essential depending on whether humans can or can not synthesize them, respectively. Chemically, they are classified based on the polarity of their side chain or R group, as non-polar and hydrophobic and hydrophilic and charged or polar uncharged. Amino acid metabolic pathways are also listed with their KEGG entries." [GO:0006520, http://www.genome.jp/kegg/ "KEGG", MCW library:Handbooks of Biochemistry]
@Zethson Zethson self-assigned this Mar 17, 2023
@Zethson Zethson transferred this issue from laminlabs/bionty-base Aug 7, 2024
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