Source code for indra.sources.ubibrowser.processor

from indra.statements import *
from indra.ontology.standardize import get_standard_agent

[docs]class UbiBrowserProcessor: """Processor for UbiBrowser data.""" def __init__(self, e3_df, dub_df): self.e3_df = e3_df self.dub_df = dub_df self.statements = [] def extract_statements(self): for df, stmt_type in [(self.e3_df, Ubiquitination), (self.dub_df, Deubiquitination)]: for _, row in df.iterrows(): stmt = self._process_row(row, stmt_type) if stmt: self.statements.append(stmt) @staticmethod def _process_row(row, stmt_type): # Note that even in the DUB table the subject of the statement # is called "E3" # There are some examples where a complex is implied (e.g., BMI1-RNF2), # for simplicity we just ignore these if '-' in row['E3AC']: return None subj_agent = get_standard_agent(row['E3GENE'], {'UP': row['E3AC']}) obj_agent = get_standard_agent(row['SUBGENE'], {'UP': row['SUBAC']}) if row['SOURCE'] == 'MEDLINE' and row['SOURCEID'] != 'UNIPROT': # Note: we sometimes get int here pmid = str(row['SOURCEID']) text = row['SENTENCE'] else: pmid = None text = None ev = Evidence(source_api='ubibrowser', pmid=pmid, text=text) stmt = stmt_type(subj_agent, obj_agent, evidence=[ev]) return stmt