grape.ensmallen.datasets.monarchinitiative
This sub-module offers methods to automatically retrieve the graphs from MonarchInitiative repository.
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"""This sub-module offers methods to automatically retrieve the graphs from MonarchInitiative repository.""" from .monarch import Monarch __all__ = [ "Monarch", ]
#  
def
Monarch(
directed: bool = False,
preprocess: bool = True,
load_nodes: bool = True,
verbose: int = 2,
cache: bool = True,
cache_path: str = 'graphs/monarchinitiative',
version: str = '202103',
**additional_graph_kwargs: Dict
) -> grape.ensmallen.ensmallen.Graph:
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def Monarch( directed: bool = False, preprocess: bool = True, load_nodes: bool = True, verbose: int = 2, cache: bool = True, cache_path: str = "graphs/monarchinitiative", version: str = "202103", **additional_graph_kwargs: Dict ) -> Graph: """Return new instance of the Monarch graph. The graph is automatically retrieved from the MonarchInitiative repository. Parameters ------------------- directed: bool = False Wether to load the graph as directed or undirected. By default false. preprocess: bool = True Whether to preprocess the graph to be loaded in optimal time and memory. load_nodes: bool = True, Whether to load the nodes vocabulary or treat the nodes simply as a numeric range. verbose: int = 2, Wether to show loading bars during the retrieval and building of the graph. cache: bool = True Whether to use cache, i.e. download files only once and preprocess them only once. cache_path: str = "graphs" Where to store the downloaded graphs. version: str = "202103" The version of the graph to retrieve. The available versions are: - 202012 - 202103 additional_graph_kwargs: Dict Additional graph kwargs. Returns ----------------------- Instace of Monarch graph. References --------------------- Please cite the following if you use the data: ```bib @article{mungall2017monarch, title={The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species}, author={Mungall, Christopher J and McMurry, Julie A and K{\"o}hler, Sebastian and Balhoff, James P and Borromeo, Charles and Brush, Matthew and Carbon, Seth and Conlin, Tom and Dunn, Nathan and Engelstad, Mark and others}, journal={Nucleic acids research}, volume={45}, number={D1}, pages={D712--D722}, year={2017}, publisher={Oxford University Press} } ``` """ return AutomaticallyRetrievedGraph( graph_name="Monarch", repository="monarchinitiative", version=version, directed=directed, preprocess=preprocess, load_nodes=load_nodes, verbose=verbose, cache=cache, cache_path=cache_path, additional_graph_kwargs=additional_graph_kwargs )()
Return new instance of the Monarch graph.
The graph is automatically retrieved from the MonarchInitiative repository.
Parameters
- directed (bool = False): Wether to load the graph as directed or undirected. By default false.
- preprocess (bool = True): Whether to preprocess the graph to be loaded in optimal time and memory.
- load_nodes (bool = True,): Whether to load the nodes vocabulary or treat the nodes simply as a numeric range.
- verbose (int = 2,): Wether to show loading bars during the retrieval and building of the graph.
- cache (bool = True): Whether to use cache, i.e. download files only once and preprocess them only once.
- cache_path (str = "graphs"): Where to store the downloaded graphs.
- version (str = "202103"):
The version of the graph to retrieve.
The available versions are: - 202012 - 202103 - additional_graph_kwargs (Dict): Additional graph kwargs.
Returns
- Instace of Monarch graph.: References
Please cite the following if you use the data:
@article{mungall2017monarch,
title={The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species},
author={Mungall, Christopher J and McMurry, Julie A and K{"o}hler, Sebastian and Balhoff, James P and Borromeo, Charles and Brush, Matthew and Carbon, Seth and Conlin, Tom and Dunn, Nathan and Engelstad, Mark and others},
journal={Nucleic acids research},
volume={45},
number={D1},
pages={D712--D722},
year={2017},
publisher={Oxford University Press}
}