VirHostNet (indra.sources.virhostnet)¶
This module implements an API for VirHostNet 2.0 (http://virhostnet.prabi.fr/).
VirHostNet API (indra.sources.virhostnet.api)¶
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indra.sources.virhostnet.api.process_from_web(query=None, up_web_fallback=False)[source]¶ Process host-virus interactions from the VirHostNet website.
Parameters: query (Optional[str]) – A query that constrains the results to a given subset of the VirHostNet database. Example: “taxid:2697049” to search for interactions for SARS-CoV-2. If not provided, By default, the “*” query is used which returns the full database. Returns: A VirhostnetProcessor object which contains a list of extracted INDRA Statements in its statements attribute. Return type: VirhostnetProcessor
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indra.sources.virhostnet.api.process_tsv(fname, up_web_fallback=False)[source]¶ Process a TSV data file obtained from VirHostNet.
Parameters: fname (str) – The path to the VirHostNet tabular data file (in the same format as the web service). Returns: A VirhostnetProcessor object which contains a list of extracted INDRA Statements in its statements attribute. Return type: VirhostnetProcessor
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indra.sources.virhostnet.api.process_df(df, up_web_fallback=False)[source]¶ Process a VirHostNet pandas DataFrame.
Parameters: df (pandas.DataFrame) – A DataFrame representing VirHostNet interactions (in the same format as the web service). Returns: A VirhostnetProcessor object which contains a list of extracted INDRA Statements in its statements attribute. Return type: VirhostnetProcessor
VirHostNet Processor (indra.sources.virhostnet.processor)¶
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class
indra.sources.virhostnet.processor.VirhostnetProcessor(df, up_web_fallback=False)[source]¶ A processor that takes a pandas DataFrame and extracts INDRA Statements.
Parameters: df (pandas.DataFrame) – A pandas DataFrame representing VirHostNet interactions. -
df¶ A pandas DataFrame representing VirHostNet interactions.
Type: pandas.DataFrame
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statements¶ A list of INDRA Statements extracted from the DataFrame.
Type: list[indra.statements.Statement]
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indra.sources.virhostnet.processor.get_agent_from_grounding(grounding, up_web_fallback=False)[source]¶ Return an INDRA Agent based on a grounding annotation.
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indra.sources.virhostnet.processor.parse_psi_mi(psi_mi_str)[source]¶ Parse a PSI-MI annotation into an ID and name pair.
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indra.sources.virhostnet.processor.parse_source_ids(source_id_str)[source]¶ Parse VirHostNet source id annotations into a dict.