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API Documentation

Access Orphanet data as pandas data frames. High level utility for convenient access to each of the supported data frames.

Source code in orphanet_parser/orphanet.py 
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class OrphanetData:
    """
    Access Orphanet data as pandas data frames. High level utility for convenient access
    to each of the supported data frames.

    """
    def __init__(self, version: Literal["2024-07", "2023-12", "2023-06", "2022-12"] = "2024-07"):
        """

        Args:
            version: Data release version.

        """
        self.version = version

        self.associated_phenotypes_parser = AssociatedPhenotypesParser(self.version)
        self.functional_consequences_parser = FunctionalConsequencesParser(self.version)
        self.gene_assocationes_parser = GeneAssociationParser(self.version)
        self.prevalence_parser = PrevalenceParser(self.version)
        self.natural_history_parser = NaturalHistoryParser(self.version)

    def associated_phenotypes(self) -> pd.DataFrame:
        """
        Get associated phenotypes data
        """
        return self.associated_phenotypes_parser.parse()

    def functional_consequences(self) -> pd.DataFrame:
        """
        Get functional consequences data
        """
        return self.functional_consequences_parser.parse()

    def gene_associations(self) -> pd.DataFrame:
        """
        Get gene association data
        """
        return self.gene_assocationes_parser.parse()

    def prevalence(self) -> pd.DataFrame:
        """
        Get prevalence data
        """
        return self.prevalence_parser.parse()

    def natural_history(self) -> pd.DataFrame:
        """
        Get natural history data
        """
        return self.natural_history_parser.parse()

__init__(version='2024-07')

Parameters:

Name Type Description Default
version Literal['2024-07', '2023-12', '2023-06', '2022-12']

Data release version.

 '2024-07'
Source code in orphanet_parser/orphanet.py 
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def __init__(self, version: Literal["2024-07", "2023-12", "2023-06", "2022-12"] = "2024-07"):
    """

    Args:
        version: Data release version.

    """
    self.version = version

    self.associated_phenotypes_parser = AssociatedPhenotypesParser(self.version)
    self.functional_consequences_parser = FunctionalConsequencesParser(self.version)
    self.gene_assocationes_parser = GeneAssociationParser(self.version)
    self.prevalence_parser = PrevalenceParser(self.version)
    self.natural_history_parser = NaturalHistoryParser(self.version)

functional_consequences()

Get functional consequences data

Source code in orphanet_parser/orphanet.py 
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def functional_consequences(self) -> pd.DataFrame:
    """
    Get functional consequences data
    """
    return self.functional_consequences_parser.parse()

gene_associations()

Get gene association data

Source code in orphanet_parser/orphanet.py 
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def gene_associations(self) -> pd.DataFrame:
    """
    Get gene association data
    """
    return self.gene_assocationes_parser.parse()

prevalence()

Get prevalence data

Source code in orphanet_parser/orphanet.py 
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def prevalence(self) -> pd.DataFrame:
    """
    Get prevalence data
    """
    return self.prevalence_parser.parse()

natural_history()

Get natural history data

Source code in orphanet_parser/orphanet.py 
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def natural_history(self) -> pd.DataFrame:
    """
    Get natural history data
    """
    return self.natural_history_parser.parse()