Source code for bio2bel.sources.pid

# -*- coding: utf-8 -*-

"""PID Importer."""

import logging
from itertools import product
from typing import Iterable, Tuple

from pyobo import get_filtered_xrefs, get_name, get_name_id_mapping
from pyobo.ndex_utils import CX, iterate_aspect
from pyobo.sources.pid import get_obo, iter_networks
from pyobo.struct.typedef import pathway_has_part
from sqlalchemy import Column, ForeignKey, Integer, String, Table
from sqlalchemy.ext.declarative import DeclarativeMeta, declarative_base
from sqlalchemy.orm import relationship
from tqdm import tqdm

import pybel
import pybel.dsl
from pybel import BELGraph
from ..compath import CompathManager, CompathPathwayMixin, CompathProteinMixin
from ..utils import get_data_dir

logger = logging.getLogger(__name__)

MODULE_NAME = 'pid'
DIRECTORY = get_data_dir(MODULE_NAME)

URL = 'https://github.com/NCIP/pathway-interaction-database/raw/master/download/NCI-Pathway-Info.xlsx'


def _get_hgnc_id_from_name(name):
    return get_name_id_mapping('hgnc').get(name)


def _map_hgnc_to_entrez(hgnc_id):
    return get_filtered_xrefs('hgnc', 'ncbigene').get(hgnc_id)


def _get_gene_name(protein_id: str, web_fallback: bool = True):
    from protmapper.uniprot_client import get_gene_name
    return get_gene_name(protein_id, web_fallback=web_fallback)


relation_to_adder = {
    'controls-state-change-of': BELGraph.add_regulates,
}

namespace_to_dsl = {
    'cas': pybel.dsl.Abundance,
    'uniprot': pybel.dsl.Protein,
    'hprd': pybel.dsl.Protein,
    'chebi': pybel.dsl.Abundance,
    'hgnc': pybel.dsl.Protein,
}

UNMAPPED = set()

MAPPING = {
    'RAS Family': pybel.dsl.Protein('fplx', 'RAS'),
    'Cyclin D': pybel.dsl.Protein('fplx', 'Cyclin_D'),
    'Gi family': pybel.dsl.Protein('fplx', 'G_i'),
}


[docs]def iterate_graphs() -> Iterable[Tuple[str, BELGraph]]: """List network uuids.""" for network_uuid, cx in tqdm(iter_networks(), desc='networks'): yield network_uuid, get_graph_from_cx(network_uuid, cx)
[docs]def get_graph_from_cx(network_uuid: str, cx: CX) -> BELGraph: # noqa: C901 """Get a PID network from NDEx.""" metadata = {} for entry in iterate_aspect(cx, 'networkAttributes'): member_name = entry['n'] if member_name == 'name': metadata['name'] = entry['v'] elif member_name == 'version': metadata['version'] = entry['v'] elif member_name == 'description': metadata['description'] = entry['v'] graph = BELGraph(**metadata) id_to_type = {} id_to_members = {} id_to_alias = {} # TODO nodeAttributes have list of protein definitions for some things for entry in iterate_aspect(cx, 'nodeAttributes'): node_id = entry['po'] member_name = entry['n'] if member_name == 'type': id_to_type[node_id] = entry['v'] elif member_name == 'alias': id_to_alias[node_id] = entry['v'] elif member_name == 'member': id_to_members[node_id] = entry['v'] else: logger.warning(f'unhandled node attribute: {member_name}') id_to_citations = {} for entry in iterate_aspect(cx, 'edgeAttributes'): if entry['n'] == 'citation': id_to_citations[entry['po']] = [x[len('pubmed:'):] for x in entry['v']] id_to_dsl = {} for node in iterate_aspect(cx, 'nodes'): node_id = node['@id'] reference = node['r'] if reference in MAPPING: id_to_dsl[node_id] = [MAPPING[reference]] continue if node_id in id_to_members: node_type = id_to_type[node_id] members = id_to_members[node_id] if node_type != 'proteinfamily': logger.warning(f'unhandled node: {node_id} type={node_type} members={members}') _rv = [] for member in members: if not member.startswith('hgnc.symbol:'): logger.warning(f'unhandled member for node: {node_id} -> {member}') continue member_name = member[len('hgnc.symbol:'):] member_identifier = _get_hgnc_id_from_name(member_name) if member_identifier is None: logger.warning(f'unhandled member for node: {node_id} -> {member}') continue _rv.append(pybel.dsl.Protein(namespace='hgnc', identifier=member_identifier, name=member_name)) id_to_dsl[node_id] = _rv continue if ':' not in reference: logger.warning(f'no curie: {node_id} {reference}') UNMAPPED.add(reference) continue prefix, identifier = reference.split(':') if prefix == 'hprd': # nodes.write(f'unhandled hprd:{identifier}') continue elif prefix == 'cas': # nodes.write(f'unhandled cas:{identifier}') continue # not sure what to do with this elif prefix == 'CHEBI': name = get_name('chebi', identifier) id_to_dsl[node_id] = [pybel.dsl.Abundance(namespace='chebi', identifier=identifier, name=name)] elif prefix == 'uniprot': name = node['n'] hgnc_id = _get_hgnc_id_from_name(name) if hgnc_id: name = _get_gene_name(identifier) if name is None: logger.warning('could not map uniprot to name') if identifier is None: logger.warning(f'could not map HGNC symbol {name}') continue id_to_dsl[node_id] = [pybel.dsl.Protein(namespace='hgnc', identifier=identifier, name=name)] else: logger.warning(f'unexpected prefix: {prefix}') continue for edge in iterate_aspect(cx, 'edges'): source_id, target_id = edge['s'], edge['t'] if source_id not in id_to_dsl or target_id not in id_to_dsl: continue edge_type = edge['i'] edge_id = edge['@id'] sources = id_to_dsl[source_id] targets = id_to_dsl[target_id] citations = id_to_citations.get(edge_id, [('ndex', network_uuid)]) for source, target, citation in product(sources, targets, citations): if edge_type == 'in-complex-with': graph.add_binds(source, target, citation=citation, evidence=edge_id) elif edge_type == 'controls-phosphorylation-of': graph.add_regulates( source, target.with_variants(pybel.dsl.ProteinModification('Ph')), citation=citation, evidence=edge_id, ) elif edge_type in {'controls-transport-of', 'controls-transport-of-chemical'}: graph.add_regulates( source, target, citation=citation, evidence=edge_id, # object_modifier=pybel.dsl.translocation(), ) elif edge_type == 'chemical-affects': graph.add_regulates( source, target, citation=citation, evidence=edge_id, object_modifier=pybel.dsl.activity(), ) elif edge_type in {'controls-expression-of', 'controls-production-of', 'consumption-controlled-by', 'controls-state-change-of', 'catalysis-precedes'}: graph.add_regulates(source, target, citation=citation, evidence=edge_id) elif edge_type == 'used-to-produce': graph.add_node_from_data(pybel.dsl.Reaction( reactants=source, products=target, )) elif edge_type == 'reacts-with': graph.add_binds(source, target, citation=citation, evidence=edge_id) # graph.add_node_from_data(pybel.dsl.Reaction( # reactants=[source, target], # )) else: logger.warning(f'unhandled edge type: {source} {edge_type} {target}') return graph
# Manager, models PATHWAY_TABLE = f'{MODULE_NAME}_pathway' PROTEIN_TABLE = f'{MODULE_NAME}_protein' PATHWAY_PROTEIN_TABLE = f'{MODULE_NAME}_pathway_protein' Base: DeclarativeMeta = declarative_base() pathway_protein = Table( PATHWAY_PROTEIN_TABLE, Base.metadata, Column('pathway_id', Integer, ForeignKey(f'{PATHWAY_TABLE}.id'), primary_key=True), Column('protein_id', Integer, ForeignKey(f'{PROTEIN_TABLE}.id'), primary_key=True), )
[docs]class Protein(Base, CompathProteinMixin): """Protein from PID.""" __tablename__ = PROTEIN_TABLE id = Column(Integer, primary_key=True) # noqa:A003 entrez_id = Column(String(255), doc='entrez id of the protein') hgnc_id = Column(String(255), doc='HGNC id of the protein') hgnc_symbol = Column(String(255), doc='HGN symbol of the protein')
[docs] def to_pybel(self) -> pybel.dsl.Protein: """Return a protein.""" return pybel.dsl.Protein(namespace='hgnc', name=self.hgnc_symbol, identifier=self.hgnc_id)
[docs]class Pathway(Base, CompathPathwayMixin): """Pathway from PID.""" __tablename__ = PATHWAY_TABLE prefix = 'pid.pathway' id = Column(Integer, primary_key=True) # noqa:A003 identifier = Column(String(255), doc='HGNC gene family id of the protein') name = Column(String(255), doc='HGNC gene family name of the protein') proteins = relationship( Protein, secondary=pathway_protein, backref='pathways', )
[docs]class Manager(CompathManager): """Manager for PID.""" module_name = MODULE_NAME _base = Base flask_admin_models = [Pathway, Protein] namespace_model = pathway_model = Pathway edge_model = pathway_protein protein_model = Protein
[docs] def populate(self, *args, **kwargs) -> None: """Populate the PID database.""" obo = get_obo() x = { reference.identifier: Protein( entrez_id=_map_hgnc_to_entrez(reference.identifier), hgnc_id=reference.identifier, hgnc_symbol=reference.name, ) for term in obo for reference in term.get_relationships(pathway_has_part) } logger.info('extracted %d proteins from pid.pathway', len(x)) for term in obo: pathway = Pathway( identifier=term.identifier, name=term.name, proteins=[ x[reference.identifier] for reference in term.get_relationships(pathway_has_part) ], ) self.session.add(pathway) self.session.commit()
main = Manager.get_cli() # def main(): # """Get and output graphs to desktop.""" # import os # directory = os.path.join(os.path.expanduser('~'), 'Desktop', 'pid') # os.makedirs(directory, exist_ok=True) # for network_uuid, graph in iterate_graphs(): # pybel.to_nodelink_file(graph, os.path.join(directory, f'{network_uuid}.bel.nodelink.json'), indent=2) # with open(os.path.join(directory, 'UNMAPPED.txt'), 'w') as file: # for unmapped in sorted(UNMAPPED): # print(unmapped, file=file) if __name__ == '__main__': main()