Tabular output (
Assembles Statements into a set of tabular files for export or curation.
Currently designed for use with “raw” Statements, i.e., Statements with a single evidence entry. Exports Statements into a single tab-separated file with the following columns:
- A 1-indexed integer identifying the statement.
- The UUID of the Statement.
- Statement type, given by the name of the class in indra.statements.
- String representation of the Statement. Contains most relevant information for curation including any additional statement data beyond the Statement type and Agents.
- For Statements extracted from text, the text in the sentence corresponding to the first agent (i.e., the ‘TEXT’ entry in the db_refs dictionary). For all other Statements, the Agent name is given. Empty field if the Agent is None.
- Groundings for the first agent given as a comma-separated list of identifiers.org links. Empty if the Agent is None.
- String representation of the first agent, including additional agent context (e.g. modification, mutation, location, and bound conditions). Empty if the Agent is None.
- AG_B_TEXT, AG_B_LINKS, AG_B_STR
- As above for the second agent. Note that the Agent may be None (and these fields left empty) if the Statement consists only of a single Agent (e.g., SelfModification, ActiveForm, or Translocation statement).
- PMID of the first entry in the evidence list for the Statement.
- Evidence text for the Statement.
- Whether the Statement represents a “hypothesis”, as flagged by some reading systems and recorded in the evidence.epistemics[‘hypothesis’] field.
- Whether the Statement represents a direct physical interactions, as recorded by the evidence.epistemics[‘direct’] field.
In addition, if the add_curation_cols flag is set when calling
TsvAssembler.make_model(), the following additional (empty) columns will be added, to be filled out by curators:
- Correctness of Agent A grounding.
- Correctness of Agent A context (e.g., modification, bound, and other conditions).
- AG_B_IDS_CORRECT, AG_B_STATE_CORRECT
- As above, for Agent B.
- Whether the event is supported by the evidence text if the entities (Agents A and B) are considered as placeholders (i.e., ignoring the correctness of their grounding).
- For Modification statements, whether the amino acid residue indicated by the Statement is supported by the evidence.
- For Modification statements, whether the amino acid position indicated by the Statement is supported by the evidence.
- For Activation/Inhibition Statements, whether the activity indicated for the subject (Agent A) is supported by the evidence.
- For Activation/Inhibition Statements, whether the activity indicated for the object (Agent B) is supported by the evidence.
- Whether the Statement is correctly flagged as a hypothesis.
- Whether the Statement is correctly flagged as direct.
Parameters: stmts (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to be assembled.
A list of INDRA Statements to be assembled.
make_model(output_file, add_curation_cols=False, up_only=False)¶
Export the statements into a tab-separated text file.
- output_file (str) – Name of the output file.
- add_curation_cols (bool) – Whether to add columns to facilitate statement curation. Default is False (no additional columns).
- up_only (bool) – Whether to include identifiers.org links only for the Uniprot grounding of an agent when one is available. Because most spreadsheets allow only a single hyperlink per cell, this can makes it easier to link to Uniprot information pages for curation purposes. Default is False.