Source code for indra.preassembler.grounding_mapper.gilda

"""This module implements a client to the Gilda grounding web service,
and contains functions to help apply it during the course of INDRA assembly."""
import logging
import requests
from urllib.parse import urljoin
from indra.preassembler.grounding_mapper.standardize \
    import standardize_agent_name
from indra.config import get_config, has_config
from indra.pipeline import register_pipeline
from .adeft import _get_text_for_grounding

logger = logging.getLogger(__name__)

grounding_service_url = get_config('GILDA_URL', failure_ok=True) \
    if has_config('GILDA_URL') else 'http://grounding.indra.bio/'


[docs]def get_grounding(txt, context=None, mode='web'): """Return the top Gilda grounding for a given text. Parameters ---------- txt : str The text to ground. context : Optional[str] Any context for the grounding. mode : Optional[str] If 'web', the web service given in the GILDA_URL config setting or environmental variable is used. Otherwise, the gilda package is attempted to be imported and used. Default: web Returns ------- dict If no grounding was found, it is an empty dict. Otherwise, it's a dict with the top grounding returned from Gilda. list The list of ScoredMatches """ grounding = {} if mode == 'web': resp = requests.post(urljoin(grounding_service_url, 'ground'), json={'text': txt, 'context': context}) results = resp.json() if results: grounding = {results[0]['term']['db']: results[0]['term']['id']} else: from gilda import ground results = ground(txt, context) if results: grounding = {results[0].term.db: results[0].term.id} results = [sm.to_json() for sm in results] return grounding, results
[docs]def get_gilda_models(mode='web'): """Return a list of strings for which Gilda has a disambiguation model. Parameters ---------- mode : Optional[str] If 'web', the web service given in the GILDA_URL config setting or environmental variable is used. Otherwise, the gilda package is attempted to be imported and used. Default: web Returns ------- list[str] A list of entity strings. """ if mode == 'web': res = requests.post(urljoin(grounding_service_url, 'models')) models = res.json() return models else: from gilda import get_models return get_models()
[docs]def ground_agent(agent, txt, context=None, mode='web'): """Set the grounding of a given agent, by re-grounding with Gilda. This function changes the agent in place without returning a value. Parameters ---------- agent : indra.statements.Agent The Agent whose db_refs shuld be changed. txt : str The text by which the Agent should be grounded. context : Optional[str] Any additional text context to help disambiguate the sense associated with txt. mode : Optional[str] If 'web', the web service given in the GILDA_URL config setting or environmental variable is used. Otherwise, the gilda package is attempted to be imported and used. Default: web """ gr, results = get_grounding(txt, context, mode) if gr: db_refs = {'TEXT': txt} db_refs.update(gr) agent.db_refs = db_refs standardize_agent_name(agent, standardize_refs=True) return results
[docs]def ground_statement(stmt, mode='web', ungrounded_only=False): """Set grounding for Agents in a given Statement using Gilda. This function modifies the original Statement/Agents in place. Parameters ---------- stmt : indra.statements.Statement A Statement to ground mode : Optional[str] If 'web', the web service given in the GILDA_URL config setting or environmental variable is used. Otherwise, the gilda package is attempted to be imported and used. Default: web ungrounded_only : Optional[str] If True, only ungrounded Agents will be grounded, and ones that are already grounded will not be modified. Default: False """ if stmt.evidence and stmt.evidence[0].text: context = stmt.evidence[0].text else: context = None for agent in stmt.agent_list(): if agent is not None and 'TEXT' in agent.db_refs: txt = agent.db_refs['TEXT'] gr = agent.get_grounding() if not ungrounded_only or gr[0] is None: ground_agent(agent, txt, context, mode=mode)
[docs]@register_pipeline def ground_statements(stmts, mode='web', sources=None, ungrounded_only=False): """Set grounding for Agents in a list of Statements using Gilda. This function modifies the original Statements/Agents in place. Parameters ---------- stmts : list[indra.statements.Statement] A list of Statements to ground mode : Optional[str] If 'web', the web service given in the GILDA_URL config setting or environmental variable is used. Otherwise, the gilda package is attempted to be imported and used. Default: web sources : Optional[list] If given, only statements from the given sources are grounded. The sources have to correspond to valid source_api entries, e.g., 'reach', 'sparser', etc. If not given, statements from all sources are grounded. ungrounded_only : Optional[str] If True, only ungrounded Agents will be grounded, and ones that are already grounded will not be modified. Default: False Returns ------- list[indra.statement.Statements] The list of Statements that were changed in place by reference. """ source_filter = set(sources) if sources else set() for stmt in stmts: if not source_filter or (stmt.evidence and stmt.evidence[0].source_api in source_filter): ground_statement(stmt, mode=mode, ungrounded_only=ungrounded_only) return stmts
[docs]def run_gilda_disambiguation(stmt, agent, idx, mode='web'): """Run Gilda disambiguation on an Agent in a given Statement. This function looks at the evidence of the given Statement and attempts to look up the full paper or the abstract for the evidence. If both of those fail, the evidence sentence itself is used for disambiguation. The disambiguation model corresponding to the Agent text is then called, and the highest scoring returned grounding is set as the Agent's new grounding. The Statement's annotations as well as the Agent are modified in place and no value is returned. Parameters ---------- stmt : indra.statements.Statement An INDRA Statement in which the Agent to be disambiguated appears. agent : indra.statements.Agent The Agent (potentially grounding mapped) which we want to disambiguate in the context of the evidence of the given Statement. idx : int The index of the new Agent's position in the Statement's agent list (needed to set annotations correctly). mode : Optional[str] If 'web', the web service given in the GILDA_URL config setting or environmental variable is used. Otherwise, the gilda package is attempted to be imported and used. Default: web Returns ------- bool True if disambiguation was successfully applied, and False otherwise. Reasons for a False response can be the lack of evidence as well as failure to obtain text for grounding disambiguation. """ success = False # If the Statement doesn't have evidence for some reason, then there is # no text to disambiguate by # NOTE: we might want to try disambiguating by other agents in the # Statement if not stmt.evidence: return False # Initialize annotations if needed so predicted # probabilities can be added to Agent annotations annots = stmt.evidence[0].annotations agent_txt = agent.db_refs['TEXT'] if 'agents' in annots: if 'gilda' not in annots['agents']: annots['agents']['gilda'] = \ [None for _ in stmt.agent_list()] else: annots['agents'] = {'gilda': [None for _ in stmt.agent_list()]} grounding_text = _get_text_for_grounding(stmt, agent_txt) if grounding_text: gilda_result = ground_agent(agent, agent_txt, grounding_text, mode) if gilda_result: logger.debug('Disambiguated %s to: %s' % (agent_txt, agent.name)) annots['agents']['gilda'][idx] = gilda_result success = True return success