Source code for indra.sources.ndex_cx.processor

from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str

import logging
from indra.databases import uniprot_client, hgnc_client
from indra.statements import *


logger = logging.getLogger(__name__)


_stmt_map = {
    'phosphorylates': Phosphorylation,
    'controls-phosphorylation-of': Phosphorylation,
    'in-complex-with': Complex,
    'NEGATIVE_INFLUENCE': Inhibition,
    'POSITIVE_INFLUENCE': Activation,
    'binds': Complex,
}


def _get_dict_from_list(dict_key, list_of_dicts):
    """Retrieve a specific dict from a list of dicts.

    Parameters
    ----------
    dict_key : str
        The (single) key of the dict to be retrieved from the list.
    list_of_dicts : list
        The list of dicts to search for the specific dict.

    Returns
    -------
    dict value
        The value associated with the dict_key (e.g., a list of nodes or
        edges).
    """
    the_dict = [cur_dict for cur_dict in list_of_dicts
                if cur_dict.get(dict_key)]
    if not the_dict:
        raise ValueError('Could not find a dict with key %s' % dict_key)
    return the_dict[0][dict_key]


[docs]class NdexCxProcessor(object): """The NdexCxProcessor extracts INDRA Statements from Cytoscape CX JSON. Parameters ---------- cx : list of dicts JSON content containing the Cytoscape network in CX format. summary : Optional[dict] The network summary object which can be obtained via get_network_summary through the web service. THis contains metadata such as the owner and the creation time of the network. Attributes ---------- statements : list A list of extracted INDRA Statements. Not all edges in the network may be converted into Statements. """ def __init__(self, cx, summary=None, require_grounding=True): self.cx = cx self.statements = [] self.require_grounding = require_grounding # Initialize the dict mapping node IDs to gene names self._node_names = {} self._node_agents = {} self._network_info = {} self._edge_attributes = {} summary = summary if summary else {} self._initialize_node_attributes() self._initialize_node_agents() self._initialize_network_info(summary) self._initialize_edge_attributes() def _initialize_node_agents(self): """Initialize internal dicts containing node information.""" nodes = _get_dict_from_list('nodes', self.cx) invalid_genes = [] for node in nodes: id = node['@id'] cx_db_refs = self.get_aliases(node) node_name = node['n'] up_id = cx_db_refs.get('UP') if up_id: db_refs = {'UP': up_id, 'TEXT': node_name} hgnc_id = uniprot_client.get_hgnc_id(up_id) if hgnc_id: db_refs['HGNC'] = hgnc_id gene_name = hgnc_client.get_hgnc_name(hgnc_id) else: gene_name = uniprot_client.get_gene_name(up_id) agent = Agent(gene_name, db_refs=db_refs) self._node_names[id] = gene_name self._node_agents[id] = agent continue else: self._node_names[id] = node_name hgnc_id = hgnc_client.get_hgnc_id(node_name) db_refs = {'TEXT': node_name} if not hgnc_id: if not self.require_grounding: self._node_agents[id] = \ Agent(node_name, db_refs=db_refs) invalid_genes.append(node_name) else: db_refs.update({'HGNC': hgnc_id}) up_id = hgnc_client.get_uniprot_id(hgnc_id) # It's possible that a valid HGNC ID will not have a # Uniprot ID, as in the case of HOTAIR (HOX transcript # antisense RNA, HGNC:33510) if up_id: db_refs.update({'UP': up_id}) self._node_agents[id] = Agent(node_name, db_refs=db_refs) if invalid_genes: verb = 'Skipped' if self.require_grounding else 'Included' logger.info('%s invalid gene symbols: %s' % (verb, ', '.join(invalid_genes))) def _initialize_network_info(self, summary): self._network_info['externalId'] = summary.get('externalId') self._network_info['owner'] = summary.get('owner') def _initialize_edge_attributes(self): edge_attr = _get_dict_from_list('edgeAttributes', self.cx) for ea in edge_attr: edge_id = ea.get('po') ea_type = ea.get('n') ea_value = ea.get('v') ea_info = self._edge_attributes.get(edge_id) # If we don't have any info about this edge, initialize an empty # dict if ea_info is None: ea_info = {'pmids': []} self._edge_attributes[edge_id] = ea_info # Collect PMIDs from the various edge types if ea_type == 'ndex:citation' or ea_type == 'citation_ids': pmids = [] assert isinstance(ea_value, list) # ndex:citations are in the form 'pmid:xxxxx' for cit in ea_value: if cit.upper().startswith('PMID:'): pmid = cit[5:] if pmid: # Check for empty PMID strings! pmids.append(pmid) else: logger.info("Unexpected PMID format: %s" % cit) ea_info['pmids'] += pmids def _initialize_node_attributes(self): self._node_attributes = _get_dict_from_list('nodeAttributes', self.cx)
[docs] def get_agents(self): """Get list of grounded nodes in the network as Agents. Returns ------- list of Agents Only nodes containing sufficient information to be grounded will be contained in this list. """ return [ag for ag in self._node_agents.values()]
[docs] def get_node_names(self): """Get list of all nodes in the network by name.""" return [name for name in self._node_names.values()]
[docs] def get_pmids(self): """Get list of all PMIDs associated with edges in the network.""" pmids = [] for ea in self._edge_attributes.values(): edge_pmids = ea.get('pmids') if edge_pmids: pmids += edge_pmids return list(set(pmids))
[docs] def get_statements(self): """Convert network edges into Statements. Returns ------- list of Statements Converted INDRA Statements. """ edges = _get_dict_from_list('edges', self.cx) for edge in edges: edge_type = edge.get('i') if not edge_type: continue stmt_type = _stmt_map.get(edge_type) if stmt_type: id = edge['@id'] source_agent = self._node_agents.get(edge['s']) target_agent = self._node_agents.get(edge['t']) if not source_agent or not target_agent: logger.info("Skipping edge %s->%s: %s" % (self._node_names[edge['s']], self._node_names[edge['t']], edge)) continue ev = self._create_evidence(id) if stmt_type == Complex: stmt = stmt_type([source_agent, target_agent], evidence=ev) else: stmt = stmt_type(source_agent, target_agent, evidence=ev) self.statements.append(stmt) return self.statements
def _create_evidence(self, edge_id): """Create Evidence object for a specific edge/Statement in the network. Parameters ---------- edge_id : int ID of the edge in the underlying NDEx network. """ pmids = None edge_attr = self._edge_attributes.get(edge_id) if edge_attr: pmids = edge_attr.get('pmids') if not pmids: return [Evidence(source_api='ndex', source_id=self._network_info['externalId'], annotations={'edge_id': edge_id})] else: evidence = [] for pmid in pmids: evidence.append( Evidence(source_api='ndex', source_id=self._network_info['externalId'], pmid=pmid, annotations={'edge_id': edge_id})) return evidence def get_aliases(self, node): cx_db_refs = {} node_id = node['@id'] alias_attrs = [attr for attr in self._node_attributes if attr.get('po') == node_id and attr.get('n') == 'alias'] if not alias_attrs: return {} if len(alias_attrs) > 1: logger.warning('More than one alias attribute for node %d' % node_id) aliases = alias_attrs[0].get('v') for alias in aliases: if ':' not in alias: continue db_name, db_id = alias.split(':') db_name_mapped = cx_indra_db_map.get(db_name) if not db_name_mapped: logger.warning('DB name %s is not mapped to INDRA.' % db_name) continue cx_db_refs[db_name_mapped] = db_id return cx_db_refs
cx_indra_db_map = { 'UniProt': 'UP', 'uniprot knowledgebase': 'UP' }