TRIPS (indra.trips)

TRIPS API (indra.trips.trips_api)

indra.trips.trips_api.process_text(text, save_xml_name='trips_output.xml', save_xml_pretty=True)[source]

Return a TripsProcessor by processing text.

Parameters:
  • text (str) – The text to be processed.
  • save_xml_name (Optional[str]) – The name of the file to save the returned TRIPS extraction knowledge base XML. Default: trips_output.xml
  • save_xml_pretty (Optional[bool]) – If True, the saved XML is pretty-printed. Some third-party tools require non-pretty-printed XMLs which can be obtained by setting this to False. Default: True
Returns:

tp – A TripsProcessor containing the extracted INDRA Statements in tp.statements.

Return type:

TripsProcessor

indra.trips.trips_api.process_xml(xml_string)[source]

Return a TripsProcessor by processing a TRIPS EKB XML string.

Parameters:xml_string (str) – A TRIPS extraction knowledge base (EKB) string to be processed. http://trips.ihmc.us/parser/api.html
Returns:tp – A TripsProcessor containing the extracted INDRA Statements in tp.statements.
Return type:TripsProcessor

TRIPS Processor (indra.trips.processor)

class indra.trips.processor.TripsProcessor(xml_string)[source]

The TripsProcessor extracts INDRA Statements from a TRIPS XML.

For more details on the TRIPS EKB XML format, see http://trips.ihmc.us/parser/cgi/drum

Parameters:xml_string (str) – A TRIPS extraction knowledge base (EKB) in XML format as a string.
tree

xml.etree.ElementTree.Element – An ElementTree object representation of the TRIPS EKB XML.

statements

list[indra.statements.Statement] – A list of INDRA Statements that were extracted from the EKB.

doc_id

str – The PubMed ID of the paper that the extractions are from.

sentences

dict[str: str] – The list of all sentences in the EKB with their IDs

paragraphs

dict[str: str] – The list of all paragraphs in the EKB with their IDs

par_to_sec

dict[str: str] – A map from paragraph IDs to their associated section types

extracted_events

list[xml.etree.ElementTree.Element] – A list of Event elements that have been extracted as INDRA Statements.

get_activations()[source]

Extract direct Activation INDRA Statements.

get_activations_causal()[source]

Extract causal Activation INDRA Statements.

get_activations_stimulate()[source]

Extract Activation INDRA Statements via stimulation.

get_active_forms()[source]

Extract ActiveForm INDRA Statements.

get_active_forms_state()[source]

Extract ActiveForm INDRA Statements.

get_all_events()[source]

Make a list of all events in the TRIPS EKB.

The events are stored in self.all_events.

get_complexes()[source]

Extract Complex INDRA Statements.

get_degradations()[source]

Extract Degradation INDRA Statements.

get_modifications()[source]

Extract all types of Modification INDRA Statements.

get_regulate_amounts()[source]

Extract Increase/DecreaseAmount Statements.

get_syntheses()[source]

Extract IncreaseAmount INDRA Statements.

TRIPS Client (indra.trips.trips_client)

indra.trips.trips_client.get_xml(html)[source]

Extract the EKB XML from the HTML output of the TRIPS web service.

Parameters:html (str) – The HTML output from the TRIPS web service.
Returns:
  • The extraction knowledge base (EKB) XML that contains the event and term
  • extractions.
indra.trips.trips_client.save_xml(xml_str, file_name, pretty=True)[source]

Save the TRIPS EKB XML in a file.

Parameters:
  • xml_str (str) – The TRIPS EKB XML string to be saved.
  • file_name (str) – The name of the file to save the result in.
  • pretty (Optional[bool]) – If True, the XML is pretty printed.
indra.trips.trips_client.send_query(text, query_args=None)[source]

Send a query to the TRIPS web service.

Parameters:
  • text (str) – The text to be processed.
  • query_args (Optional[dict]) – A dictionary of arguments to be passed with the query.
Returns:

html – The HTML result returned by the web service.

Return type:

str