Source code for indra.sources.drugbank.processor

import logging
from xml.etree import ElementTree
from indra.statements import *
from indra.databases.identifiers import ensure_chebi_prefix, \
from indra.statements.validate import assert_valid_db_refs
from indra.ontology.standardize import standardize_name_db_refs, \

logger = logging.getLogger(__name__)

drugbank_ns = {'db': ''}

[docs]class DrugbankProcessor: """Processor to extract INDRA Statements from DrugBank content. The processor assumes that an ElementTree is available which it then traverses to find drug-target information. Parameters ---------- xml_tree : xml.etree.ElementTree.ElementTree An XML ElementTree representing DrugBank XML content. Attributes ---------- statements : list of indra.statements.Statement A list of INDRA Statements that were extracted from DrugBank content. """ def __init__(self, xml_tree: ElementTree.ElementTree): self.xml_tree = xml_tree self.statements = [] def extract_statements(self): root = self.xml_tree.getroot() for drug in db_findall(root, 'db:drug'): for stmt in self._extract_statements_for_drug(drug): self.statements.append(stmt) @staticmethod def _extract_statements_for_drug(drug_element): drug = DrugbankProcessor._get_drug_agent(drug_element) for target_element in db_findall(drug_element, 'db:targets/db:target'): actions = {a.text for a in db_findall(target_element, 'db:actions/db:action')} if not actions: actions = {'N/A'} for action in actions: stmt_type = DrugbankProcessor._get_statement_type(action) if not stmt_type: continue annotations = {'drugbank_action': action} evs = DrugbankProcessor._get_evidences(target_element) for ev in evs: ev.annotations = annotations target = DrugbankProcessor._get_target_agent(target_element) yield stmt_type(drug, target, evidence=evs) @staticmethod def _get_statement_type(action): if action in neutral_actions: return None elif action in activation_actions: return Activation elif action in inhibition_actions: return Inhibition elif action in decrease_amount_actions: return DecreaseAmount elif action in increase_amount_actions: return IncreaseAmount elif action == 'N/A': return Inhibition else: return None @staticmethod def _get_target_agent(target_element): name_tag = db_find(target_element, 'db:name') name = name_tag.text db_refs = {} # Get Drugbank target ID target_id = db_find(target_element, 'db:id').text db_refs['DRUGBANKV4.TARGET'] = target_id # Extract other xrefs for xref_tag in db_findall(target_element, 'db:polypeptide/' 'db:external-identifiers/' 'db:external-identifier'): resource = db_find(xref_tag, 'db:resource').text identifier = db_find(xref_tag, 'db:identifier').text if resource == 'HUGO Gene Nomenclature Committee (HGNC)': db_refs['HGNC'] = identifier[5:] elif resource == 'UniProtKB': db_refs['UP'] = identifier return get_standard_agent(name, db_refs=db_refs) @staticmethod def _get_drug_agent(drug_element): name_tag = db_find(drug_element, 'db:name') name = name_tag.text db_refs = {} # Extract the DrugBank ID drugbank_id_tags = db_findall(drug_element, 'db:drugbank-id') # We do a sort here because sometimes there's more than one # DrugBank ID and we choose the "smaller" one here drugbank_id = sorted([di.text for di in drugbank_id_tags if di.text.startswith('DB')])[0] db_refs['DRUGBANK'] = drugbank_id # Extract CAS ID cas_tag = db_find(drug_element, 'db:cas-number') if cas_tag is not None and cas_tag.text is not None: db_refs['CAS'] = cas_tag.text # Extract other xrefs for xref_tag in db_findall(drug_element, 'db:external-identifiers/' 'db:external-identifier'): resource = db_find(xref_tag, 'db:resource').text identifier = db_find(xref_tag, 'db:identifier').text if resource == 'ChEMBL': db_refs['CHEMBL'] = ensure_chembl_prefix(identifier) elif resource == 'PubChem Compound': db_refs['PUBCHEM'] = identifier elif resource == 'ChEBI': db_refs['CHEBI'] = ensure_chebi_prefix(identifier) assert_valid_db_refs(db_refs) return get_standard_agent(name, db_refs) @staticmethod def _get_evidences(target_element): # TODO: is there a source ID we can use here? # TODO: is there context we can extract? # refs also has: textbooks, attachments pmids = db_findall(target_element, 'db:references/db:articles/db:article/db:pubmed-id') urls = db_findall(target_element, 'db:references/db:links/db:link/db:url') if pmids: evs = [Evidence(source_api='drugbank', pmid=pmid.text) for pmid in pmids] elif urls: evs = [Evidence(source_api='drugbank', text_refs={'URL': url.text}) for url in urls] else: evs = [Evidence(source_api='drugbank')] return evs
def db_find(element, path): return element.find(path, namespaces=drugbank_ns) def db_findall(element, path): return element.findall(path, namespaces=drugbank_ns) activation_actions = {'substrate', 'agonist', 'inducer', 'potentiator', 'stimulator', 'cofactor', 'activator', 'ligand', 'chaperone', 'partial agonist', 'protector', 'positive allosteric modulator', 'positive modulator'} inhibition_actions = {'antagonist', 'inhibitor', 'binder', 'antibody', 'inactivator', 'binding', 'blocker', 'negative modulator', 'inverse agonist', 'neutralizer', 'weak inhibitor', 'suppressor', 'disruptor', 'inhibitory allosteric modulator'} decrease_amount_actions = {'downregulator', 'metabolizer', 'chelator', 'degradation', 'incorporation into and destabilization'} increase_amount_actions = {'stabilization'} neutral_actions = {'modulator', 'other/unknown', 'unknown', 'other', 'regulator'}