VirHostNet (indra.sources.virhostnet
)¶
This module implements an API for VirHostNet 2.0 (http://virhostnet.prabi.fr/).
VirHostNet API (indra.sources.virhostnet.api
)¶
- 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
- 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
- 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
VirHostNet Processor (indra.sources.virhostnet.processor
)¶
- 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
- indra.sources.virhostnet.processor.get_agent_from_grounding(grounding, up_web_fallback=False)[source]¶
Return an INDRA Agent based on a grounding annotation.
- indra.sources.virhostnet.processor.parse_psi_mi(psi_mi_str)[source]¶
Parse a PSI-MI annotation into an ID and name pair.
- indra.sources.virhostnet.processor.parse_source_ids(source_id_str)[source]¶
Parse VirHostNet source id annotations into a dict.