Tabular output (
- class indra.assemblers.tsv.assembler.TsvAssembler(statements=None)¶
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.
stmts (Optional[list[indra.statements.Statement]]) – 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.