grape.ensmallen.datasets.pheknowlatorkg
This sub-module offers methods to automatically retrieve the graphs from PheKnowLatorKG repository.
View Source
"""This sub-module offers methods to automatically retrieve the graphs from PheKnowLatorKG repository.""" from .pheknowlator import PheKnowLator __all__ = [ "PheKnowLator", ]
#  
def
PheKnowLator(
directed: bool = False,
preprocess: bool = True,
load_nodes: bool = True,
verbose: int = 2,
cache: bool = True,
cache_path: str = 'graphs/pheknowlatorkg',
version: str = 'v3.0.0-2021-10-02.subclass-relationsOnly-owlnets-purified',
**additional_graph_kwargs: Dict
) -> grape.ensmallen.ensmallen.Graph:
View Source
def PheKnowLator( directed: bool = False, preprocess: bool = True, load_nodes: bool = True, verbose: int = 2, cache: bool = True, cache_path: str = "graphs/pheknowlatorkg", version: str = "v3.0.0-2021-10-02.subclass-relationsOnly-owlnets-purified", **additional_graph_kwargs: Dict ) -> Graph: """Return new instance of the PheKnowLator graph. The graph is automatically retrieved from the PheKnowLatorKG 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 = "v3.0.0-2021-10-02.subclass-relationsOnly-owlnets-purified" The version of the graph to retrieve. The available versions are: - v2.0.0-2020-5-10.instance-inverseRelations-owl - v2.0.0-2020-5-10.instance-inverseRelations-owlnets - v2.0.0-2020-5-10.instance-relationsOnly-owl - v2.0.0-2020-5-10.instance-relationsOnly-owlnets - v2.0.0-2020-5-10.subclass-inverseRelations-owl - v2.0.0-2020-5-10.subclass-inverseRelations-owlnets - v2.0.0-2020-5-10.subclass-relationsOnly-owl - v2.0.0-2020-5-10.subclass-relationsOnly-owlnets - v2.0.0-2021-1-25.instance-inverseRelations-owl - v2.0.0-2021-1-25.instance-inverseRelations-owlnets - v2.0.0-2021-1-25.instance-inverseRelations-owlnets-purified - v2.0.0-2021-1-25.instance-relationsOnly-owl - v2.0.0-2021-1-25.instance-relationsOnly-owlnets - v2.0.0-2021-1-25.instance-relationsOnly-owlnets-purified - v2.0.0-2021-1-25.subclass-inverseRelations-owl - v2.0.0-2021-1-25.subclass-inverseRelations-owlnets - v2.0.0-2021-1-25.subclass-inverseRelations-owlnets-purified - v2.0.0-2021-1-25.subclass-relationsOnly-owl - v2.0.0-2021-1-25.subclass-relationsOnly-owlnets - v2.0.0-2021-1-25.subclass-relationsOnly-owlnets-purified - v2.0.0-2021-2-11.instance-inverseRelations-owl - v2.0.0-2021-2-11.instance-inverseRelations-owlnets - v2.0.0-2021-2-11.instance-inverseRelations-owlnets-purified - v2.0.0-2021-2-11.instance-relationsOnly-owl - v2.0.0-2021-2-11.instance-relationsOnly-owlnets - v2.0.0-2021-2-11.instance-relationsOnly-owlnets-purified - v2.0.0-2021-2-11.subclass-inverseRelations-owl - v2.0.0-2021-2-11.subclass-inverseRelations-owlnets - v2.0.0-2021-2-11.subclass-inverseRelations-owlnets-purified - v2.0.0-2021-2-11.subclass-relationsOnly-owl - v2.0.0-2021-2-11.subclass-relationsOnly-owlnets - v2.0.0-2021-2-11.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-5-01.instance-inverseRelations-owl - v2.1.0-2021-5-01.instance-inverseRelations-owlnets - v2.1.0-2021-5-01.instance-inverseRelations-owlnets-purified - v2.1.0-2021-5-01.instance-relationsOnly-owl - v2.1.0-2021-5-01.instance-relationsOnly-owlnets - v2.1.0-2021-5-01.instance-relationsOnly-owlnets-purified - v2.1.0-2021-5-01.subclass-inverseRelations-owl - v2.1.0-2021-5-01.subclass-inverseRelations-owlnets - v2.1.0-2021-5-01.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-5-01.subclass-relationsOnly-owl - v2.1.0-2021-5-01.subclass-relationsOnly-owlnets - v2.1.0-2021-5-01.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-6-01.instance-inverseRelations-owl - v2.1.0-2021-6-01.instance-inverseRelations-owlnets - v2.1.0-2021-6-01.instance-inverseRelations-owlnets-purified - v2.1.0-2021-6-01.instance-relationsOnly-owl - v2.1.0-2021-6-01.instance-relationsOnly-owlnets - v2.1.0-2021-6-01.instance-relationsOnly-owlnets-purified - v2.1.0-2021-6-01.subclass-inverseRelations-owl - v2.1.0-2021-6-01.subclass-inverseRelations-owlnets - v2.1.0-2021-6-01.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-6-01.subclass-relationsOnly-owl - v2.1.0-2021-6-01.subclass-relationsOnly-owlnets - v2.1.0-2021-6-01.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-7-06.instance-inverseRelations-owl - v2.1.0-2021-7-06.instance-inverseRelations-owlnets - v2.1.0-2021-7-06.instance-inverseRelations-owlnets-purified - v2.1.0-2021-7-06.instance-relationsOnly-owl - v2.1.0-2021-7-06.instance-relationsOnly-owlnets - v2.1.0-2021-7-06.instance-relationsOnly-owlnets-purified - v2.1.0-2021-7-06.subclass-inverseRelations-owl - v2.1.0-2021-7-06.subclass-inverseRelations-owlnets - v2.1.0-2021-7-06.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-7-06.subclass-relationsOnly-owl - v2.1.0-2021-7-06.subclass-relationsOnly-owlnets - v2.1.0-2021-7-06.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-8-01.instance-inverseRelations-owl - v2.1.0-2021-8-01.instance-inverseRelations-owlnets - v2.1.0-2021-8-01.instance-inverseRelations-owlnets-purified - v2.1.0-2021-8-01.instance-relationsOnly-owl - v2.1.0-2021-8-01.instance-relationsOnly-owlnets - v2.1.0-2021-8-01.instance-relationsOnly-owlnets-purified - v2.1.0-2021-8-01.subclass-inverseRelations-owl - v2.1.0-2021-8-01.subclass-inverseRelations-owlnets - v2.1.0-2021-8-01.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-8-01.subclass-relationsOnly-owl - v2.1.0-2021-8-01.subclass-relationsOnly-owlnets - v2.1.0-2021-8-01.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-9-01.instance-inverseRelations-owl - v2.1.0-2021-9-01.instance-inverseRelations-owlnets - v2.1.0-2021-9-01.instance-inverseRelations-owlnets-purified - v2.1.0-2021-9-01.instance-relationsOnly-owl - v2.1.0-2021-9-01.instance-relationsOnly-owlnets - v2.1.0-2021-9-01.instance-relationsOnly-owlnets-purified - v2.1.0-2021-9-01.subclass-inverseRelations-owl - v2.1.0-2021-9-01.subclass-inverseRelations-owlnets - v2.1.0-2021-9-01.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-9-01.subclass-relationsOnly-owl - v2.1.0-2021-9-01.subclass-relationsOnly-owlnets - v2.1.0-2021-9-01.subclass-relationsOnly-owlnets-purified - v3.0.0-2021-10-02.instance-inverseRelations-owl - v3.0.0-2021-10-02.instance-inverseRelations-owlnets - v3.0.0-2021-10-02.instance-inverseRelations-owlnets-purified - v3.0.0-2021-10-02.instance-relationsOnly-owl - v3.0.0-2021-10-02.instance-relationsOnly-owlnets - v3.0.0-2021-10-02.instance-relationsOnly-owlnets-purified - v3.0.0-2021-10-02.subclass-inverseRelations-owl - v3.0.0-2021-10-02.subclass-inverseRelations-owlnets - v3.0.0-2021-10-02.subclass-inverseRelations-owlnets-purified - v3.0.0-2021-10-02.subclass-relationsOnly-owl - v3.0.0-2021-10-02.subclass-relationsOnly-owlnets - v3.0.0-2021-10-02.subclass-relationsOnly-owlnets-purified additional_graph_kwargs: Dict Additional graph kwargs. Returns ----------------------- Instace of PheKnowLator graph. References --------------------- Please cite the following if you use the data: ```bib @article{callahan2020framework, title={A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs}, author={Callahan, Tiffany J and Tripodi, Ignacio J and Hunter, Lawrence E and Baumgartner, William A}, journal={bioRxiv}, year={2020}, publisher={Cold Spring Harbor Laboratory} } ``` """ return AutomaticallyRetrievedGraph( graph_name="PheKnowLator", repository="pheknowlatorkg", 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 PheKnowLator graph.
The graph is automatically retrieved from the PheKnowLatorKG 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 = "v3.0.0-2021-10-02.subclass-relationsOnly-owlnets-purified"):
The version of the graph to retrieve.
The available versions are: - v2.0.0-2020-5-10.instance-inverseRelations-owl - v2.0.0-2020-5-10.instance-inverseRelations-owlnets - v2.0.0-2020-5-10.instance-relationsOnly-owl - v2.0.0-2020-5-10.instance-relationsOnly-owlnets - v2.0.0-2020-5-10.subclass-inverseRelations-owl - v2.0.0-2020-5-10.subclass-inverseRelations-owlnets - v2.0.0-2020-5-10.subclass-relationsOnly-owl - v2.0.0-2020-5-10.subclass-relationsOnly-owlnets - v2.0.0-2021-1-25.instance-inverseRelations-owl - v2.0.0-2021-1-25.instance-inverseRelations-owlnets - v2.0.0-2021-1-25.instance-inverseRelations-owlnets-purified - v2.0.0-2021-1-25.instance-relationsOnly-owl - v2.0.0-2021-1-25.instance-relationsOnly-owlnets - v2.0.0-2021-1-25.instance-relationsOnly-owlnets-purified - v2.0.0-2021-1-25.subclass-inverseRelations-owl - v2.0.0-2021-1-25.subclass-inverseRelations-owlnets - v2.0.0-2021-1-25.subclass-inverseRelations-owlnets-purified - v2.0.0-2021-1-25.subclass-relationsOnly-owl - v2.0.0-2021-1-25.subclass-relationsOnly-owlnets - v2.0.0-2021-1-25.subclass-relationsOnly-owlnets-purified - v2.0.0-2021-2-11.instance-inverseRelations-owl - v2.0.0-2021-2-11.instance-inverseRelations-owlnets - v2.0.0-2021-2-11.instance-inverseRelations-owlnets-purified - v2.0.0-2021-2-11.instance-relationsOnly-owl - v2.0.0-2021-2-11.instance-relationsOnly-owlnets - v2.0.0-2021-2-11.instance-relationsOnly-owlnets-purified - v2.0.0-2021-2-11.subclass-inverseRelations-owl - v2.0.0-2021-2-11.subclass-inverseRelations-owlnets - v2.0.0-2021-2-11.subclass-inverseRelations-owlnets-purified - v2.0.0-2021-2-11.subclass-relationsOnly-owl - v2.0.0-2021-2-11.subclass-relationsOnly-owlnets - v2.0.0-2021-2-11.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-5-01.instance-inverseRelations-owl - v2.1.0-2021-5-01.instance-inverseRelations-owlnets - v2.1.0-2021-5-01.instance-inverseRelations-owlnets-purified - v2.1.0-2021-5-01.instance-relationsOnly-owl - v2.1.0-2021-5-01.instance-relationsOnly-owlnets - v2.1.0-2021-5-01.instance-relationsOnly-owlnets-purified - v2.1.0-2021-5-01.subclass-inverseRelations-owl - v2.1.0-2021-5-01.subclass-inverseRelations-owlnets - v2.1.0-2021-5-01.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-5-01.subclass-relationsOnly-owl - v2.1.0-2021-5-01.subclass-relationsOnly-owlnets - v2.1.0-2021-5-01.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-6-01.instance-inverseRelations-owl - v2.1.0-2021-6-01.instance-inverseRelations-owlnets - v2.1.0-2021-6-01.instance-inverseRelations-owlnets-purified - v2.1.0-2021-6-01.instance-relationsOnly-owl - v2.1.0-2021-6-01.instance-relationsOnly-owlnets - v2.1.0-2021-6-01.instance-relationsOnly-owlnets-purified - v2.1.0-2021-6-01.subclass-inverseRelations-owl - v2.1.0-2021-6-01.subclass-inverseRelations-owlnets - v2.1.0-2021-6-01.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-6-01.subclass-relationsOnly-owl - v2.1.0-2021-6-01.subclass-relationsOnly-owlnets - v2.1.0-2021-6-01.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-7-06.instance-inverseRelations-owl - v2.1.0-2021-7-06.instance-inverseRelations-owlnets - v2.1.0-2021-7-06.instance-inverseRelations-owlnets-purified - v2.1.0-2021-7-06.instance-relationsOnly-owl - v2.1.0-2021-7-06.instance-relationsOnly-owlnets - v2.1.0-2021-7-06.instance-relationsOnly-owlnets-purified - v2.1.0-2021-7-06.subclass-inverseRelations-owl - v2.1.0-2021-7-06.subclass-inverseRelations-owlnets - v2.1.0-2021-7-06.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-7-06.subclass-relationsOnly-owl - v2.1.0-2021-7-06.subclass-relationsOnly-owlnets - v2.1.0-2021-7-06.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-8-01.instance-inverseRelations-owl - v2.1.0-2021-8-01.instance-inverseRelations-owlnets - v2.1.0-2021-8-01.instance-inverseRelations-owlnets-purified - v2.1.0-2021-8-01.instance-relationsOnly-owl - v2.1.0-2021-8-01.instance-relationsOnly-owlnets - v2.1.0-2021-8-01.instance-relationsOnly-owlnets-purified - v2.1.0-2021-8-01.subclass-inverseRelations-owl - v2.1.0-2021-8-01.subclass-inverseRelations-owlnets - v2.1.0-2021-8-01.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-8-01.subclass-relationsOnly-owl - v2.1.0-2021-8-01.subclass-relationsOnly-owlnets - v2.1.0-2021-8-01.subclass-relationsOnly-owlnets-purified - v2.1.0-2021-9-01.instance-inverseRelations-owl - v2.1.0-2021-9-01.instance-inverseRelations-owlnets - v2.1.0-2021-9-01.instance-inverseRelations-owlnets-purified - v2.1.0-2021-9-01.instance-relationsOnly-owl - v2.1.0-2021-9-01.instance-relationsOnly-owlnets - v2.1.0-2021-9-01.instance-relationsOnly-owlnets-purified - v2.1.0-2021-9-01.subclass-inverseRelations-owl - v2.1.0-2021-9-01.subclass-inverseRelations-owlnets - v2.1.0-2021-9-01.subclass-inverseRelations-owlnets-purified - v2.1.0-2021-9-01.subclass-relationsOnly-owl - v2.1.0-2021-9-01.subclass-relationsOnly-owlnets - v2.1.0-2021-9-01.subclass-relationsOnly-owlnets-purified - v3.0.0-2021-10-02.instance-inverseRelations-owl - v3.0.0-2021-10-02.instance-inverseRelations-owlnets - v3.0.0-2021-10-02.instance-inverseRelations-owlnets-purified - v3.0.0-2021-10-02.instance-relationsOnly-owl - v3.0.0-2021-10-02.instance-relationsOnly-owlnets - v3.0.0-2021-10-02.instance-relationsOnly-owlnets-purified - v3.0.0-2021-10-02.subclass-inverseRelations-owl - v3.0.0-2021-10-02.subclass-inverseRelations-owlnets - v3.0.0-2021-10-02.subclass-inverseRelations-owlnets-purified - v3.0.0-2021-10-02.subclass-relationsOnly-owl - v3.0.0-2021-10-02.subclass-relationsOnly-owlnets - v3.0.0-2021-10-02.subclass-relationsOnly-owlnets-purified - additional_graph_kwargs (Dict): Additional graph kwargs.
Returns
- Instace of PheKnowLator graph.: References
Please cite the following if you use the data:
@article{callahan2020framework,
title={A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs},
author={Callahan, Tiffany J and Tripodi, Ignacio J and Hunter, Lawrence E and Baumgartner, William A},
journal={bioRxiv},
year={2020},
publisher={Cold Spring Harbor Laboratory}
}