diff --git a/bioagents/mra/mra.py b/bioagents/mra/mra.py
index d7c88bad..741b2da1 100644
--- a/bioagents/mra/mra.py
+++ b/bioagents/mra/mra.py
@@ -20,6 +20,7 @@
from pysb.tools import render_reactions
from pysb.export import export
from indra.util.kappa_util import im_json_to_graph, cm_json_to_graph
+from indra.assemblers.english_assembler import EnglishAssembler
logger = logging.getLogger('MRA')
@@ -64,7 +65,8 @@ def build_model_from_ekb(self, model_ekb):
res['ambiguities'] = ambiguities
model_exec = self.assemble_pysb(stmts)
res['model_exec'] = model_exec
- res['diagrams'] = make_diagrams(model_exec, model_id)
+ res['diagrams'] = make_diagrams(model_exec, model_id,
+ self.models[model_id])
return res
def build_model_from_json(self, model_json):
@@ -77,7 +79,8 @@ def build_model_from_json(self, model_json):
return res
model_exec = self.assemble_pysb(stmts)
res['model_exec'] = model_exec
- res['diagrams'] = make_diagrams(model_exec, model_id)
+ res['diagrams'] = make_diagrams(model_exec, model_id,
+ self.models[model_id])
return res
def expand_model_from_ekb(self, model_ekb, model_id):
@@ -99,7 +102,8 @@ def expand_model_from_ekb(self, model_ekb, model_id):
res['model_new'] = new_stmts
model_exec = self.assemble_pysb(model_stmts)
res['model_exec'] = model_exec
- res['diagrams'] = make_diagrams(model_exec, new_model_id)
+ res['diagrams'] = make_diagrams(model_exec, new_model_id,
+ self.models[model_id])
return res
def expand_model_from_json(self, model_json, model_id):
@@ -116,7 +120,8 @@ def expand_model_from_json(self, model_json, model_id):
res['model_new'] = new_stmts
model_exec = self.assemble_pysb(model_stmts)
res['model_exec'] = model_exec
- res['diagrams'] = make_diagrams(model_exec, new_model_id)
+ res['diagrams'] = make_diagrams(model_exec, new_model_id,
+ self.models[model_id])
return res
def has_mechanism(self, mech_ekb, model_id):
@@ -159,7 +164,8 @@ def remove_mechanism(self, mech_ekb, model_id):
res['model_exec'] = model_exec
if removed_stmts:
res['removed'] = removed_stmts
- res['diagrams'] = make_diagrams(model_exec, model_id)
+ res['diagrams'] = make_diagrams(model_exec, model_id,
+ self.models[model_id])
self.new_model(new_stmts)
return res
@@ -181,7 +187,8 @@ def model_undo(self):
if not stmts:
return res
res['ambiguities'] = []
- res['diagrams'] = make_diagrams(model_exec, new_model_id)
+ res['diagrams'] = make_diagrams(model_exec, new_model_id,
+ self.models[new_model_id])
return res
def get_upstream(self, target, model_id):
@@ -249,11 +256,11 @@ def get_ambiguities(tp):
return all_ambiguities
-def make_diagrams(pysb_model, model_id):
+def make_diagrams(pysb_model, model_id, indra_model):
sbgn = make_sbgn(pysb_model, model_id)
rxn = draw_reaction_network(pysb_model, model_id)
cm = draw_contact_map(pysb_model, model_id)
- im = draw_influence_map(pysb_model, model_id)
+ im = draw_influence_map(pysb_model, model_id, indra_model)
diagrams = {'reactionnetwork': rxn, 'contactmap': cm,
'influencemap': im, 'sbgn': sbgn}
return diagrams
@@ -272,10 +279,12 @@ def make_sbgn(pysb_model, model_id):
return sbgn_str
-def draw_influence_map(pysb_model, model_id):
+def draw_influence_map(pysb_model, model_id, indra_model):
"""Generate a Kappa influence map, draw it and save it as a PNG."""
try:
im = make_influence_map(pysb_model)
+ im = make_influence_map_labels_natural_language(im, pysb_model,
+ indra_model)
fname = 'model%d_im' % model_id
abs_path = os.path.abspath(os.getcwd())
full_path = os.path.join(abs_path, fname + '.png')
@@ -304,6 +313,64 @@ def make_influence_map(pysb_model):
return im
+def get_statement_by_uuid(statements, uuid):
+ """Returns the first statement in statements with the given uuid, or None
+ if no such statements are in the provided list."""
+ for statement in statements:
+ if statement.uuid == uuid:
+ return statement
+ return None
+
+
+def dict_value_appears_multiple_times(d, value):
+ """Returns True iff the given value is mapped to multiple times in this
+ dictionary."""
+ count = 0
+ for k, v in d.items():
+ if v == value:
+ count += 1
+ return count > 1
+
+def make_influence_map_labels_natural_language(im, pysb_model, indra_model):
+ """Replaces the labels of the influence map with natural language labels.
+ """
+ # Get the name of all the rules in the pysb model
+ rule_names = [rule.name for rule in pysb_model.rules]
+
+ relabel_map_english = {}
+ relabel_map_english_and_rule = {}
+ for annotation in pysb_model.annotations:
+ if annotation.subject in rule_names:
+ name = annotation.subject
+ if annotation.predicate == 'from_indra_statement':
+ # We found the INDRA statement uuid corresponding to a rule
+ statement_uuid = annotation.object
+ s = get_statement_by_uuid(indra_model, statement_uuid)
+
+ # Convert the statement into English
+ assembler = EnglishAssembler([s])
+
+ english_text = assembler.make_model()
+ english_and_rule = english_text + ' (' + name + ')'
+
+ relabel_map_english[name] = english_text
+ relabel_map_english_and_rule[name] = english_and_rule
+
+ # Use only the English text if that is unambiguous, otherwise include
+ # the rule name too
+ relabel_map = {}
+ for before in relabel_map_english:
+ english_text = relabel_map_english[before]
+ if dict_value_appears_multiple_times(relabel_map_english,
+ english_text):
+ relabel_map[before] = relabel_map_english_and_rule[before]
+ else:
+ relabel_map[before] = english_text
+
+ im = networkx.relabel_nodes(im, relabel_map)
+ return im
+
+
def draw_contact_map(pysb_model, model_id):
try:
cm = make_contact_map(pysb_model)
diff --git a/bioagents/tests/ekb_cache.json b/bioagents/tests/ekb_cache.json
index fa775166..a5bf592c 100644
--- a/bioagents/tests/ekb_cache.json
+++ b/bioagents/tests/ekb_cache.json
@@ -23,6 +23,7 @@
"KRAS": "KRAS\nKRASONT::GENE-PROTEINKRASONT::GENEONT::GENEONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINKRAS",
"KRAS activates BRAF": "KRAS activates BRAF\nKRAS activates BRAFONT::ACTIVATEONT::TRUEONT::ACTIVATEKRAS activates BRAFONT::GENE-PROTEINKRASONT::GENE-PROTEINBRAFKRAS activates BRAFONT::GENE-PROTEINKRASONT::GENEONT::GENEONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINKRASONT::GENE-PROTEINBRAFONT::GENEONT::GENEONT::PROTEINBRAF",
"KRAS activates BRAF.": "KRAS activates BRAF.\nKRAS activates BRAF.ONT::ACTIVATEONT::TRUEONT::ACTIVATEKRAS activates BRAFONT::GENE-PROTEINKRASONT::GENE-PROTEINBRAFKRAS activates BRAFONT::GENE-PROTEINKRASONT::GENEONT::GENEONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINKRASONT::GENE-PROTEINBRAFONT::GENEONT::GENEONT::PROTEINBRAF",
+ "KRAS activates BRAF. Active BRAF binds MEK.": "KRAS activates BRAF. Active BRAF binds MEK.KRAS activates BRAF.Active BRAF binds MEK.ONT::ACTIVATEONT::TRUEONT::ACTIVATEKRAS activates BRAFONT::GENE-PROTEINKRASONT::GENE-PROTEINBRAFKRAS activates BRAFONT::GENE-PROTEINKRASONT::GENEONT::GENEONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINKRASONT::GENE-PROTEINBRAFONT::GENEONT::GENEONT::PROTEINBRAFONT::BINDONT::TRUEONT::BINDActive BRAF binds MEKONT::GENE-PROTEINActive BRAFONT::PROTEIN-FAMILYMEKActive BRAF binds MEKONT::GENE-PROTEINBRAFTRUEONT::GENEONT::GENEONT::PROTEINActive BRAFONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEK",
"KRAS bound to GTP phosphorylates BRAF on T373.": "KRAS bound to GTP phosphorylates BRAF on T373.\nKRAS bound to GTP phosphorylates BRAF on T373.ONT::PHOSPHORYLATIONONT::TRUEONT::PHOSPHORYLATIONKRAS bound to GTP phosphorylates BRAF on T373ONT::GENE-PROTEINKRAS bound to GTPONT::GENE-PROTEINBRAFONT::MOLECULAR-SITET373ONT::POST-TRANSLATIONAL-MODIFICATIONKRAS bound to GTP phosphorylates BRAF on T373ONT::GENE-PROTEINKRASONT::GENEONT::GENEONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINONT::PROTEINKRAS bound to GTPONT::GENE-PROTEINBRAFONT::GENEONT::GENEONT::PROTEINBRAFONT::BINDONT::TRUEONT::BINDKRAS bound to GTPONT::GENE-PROTEINKRAS bound to GTPONT::CHEMICALto GTPKRAS bound to GTPONT::CHEMICALGTPONT::CHEMICALONT::MOLECULEONT::CHEMICALONT::MOLECULEto GTPONT::MOLECULAR-SITET-373ThreonineT373T373",
"MAP2K1": "MAP2K1\nMAP2K1ONT::GENE-PROTEINMAP-2-K-1ONT::GENEONT::GENEONT::PROTEINMAP2K1",
"MAP2K1 binds MAPK1": "MAP2K1 binds MAPK1\nMAP2K1 binds MAPK1ONT::BINDONT::TRUEONT::BINDMAP2K1 binds MAPK1ONT::GENE-PROTEINMAP2K1ONT::GENE-PROTEINMAPK1MAP2K1 binds MAPK1ONT::GENE-PROTEINMAP-2-K-1ONT::GENEONT::GENEONT::PROTEINMAP2K1ONT::GENE-PROTEINMAPK-1ONT::GENEONT::GENEONT::PROTEINMAPK1",
@@ -33,6 +34,7 @@
"MAPK1-bound MAP2K1": "MAPK1-bound MAP2K1\nMAPK1-bound MAP2K1ONT::GENE-PROTEINMAP-2-K-1ONT::GENEONT::GENEONT::PROTEINMAPK1-bound MAP2K1ONT::BINDONT::TRUEONT::BINDMAPK1-bound MAP2K1ONT::GENE-PROTEINMAPK1-boundONT::GENE-PROTEINMAPK1-bound MAP2K1MAPK1-bound MAP2K1ONT::GENE-PROTEINMAPK-1ONT::GENEONT::GENEONT::PROTEINMAPK1-bound",
"MEK": "MEK\nMEKONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEK",
"MEK binds ERK": "MEK binds ERK\nMEK binds ERKONT::BINDONT::TRUEONT::BINDMEK binds ERKONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINERKMEK binds ERKONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINERKONT::PROTEIN-FAMILYONT::PROTEINONT::PROTEINONT::GENEONT::GENEONT::GENEONT::GENEONT::GENEERK",
+ "MEK binds MAPK1. MEK binds MAPK3.": "MEK binds MAPK1. MEK binds MAPK3.MEK binds MAPK1.MEK binds MAPK3.ONT::BINDONT::TRUEONT::BINDMEK binds MAPK1ONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINMAPK1MEK binds MAPK1ONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINMAPK-1ONT::GENEONT::GENEONT::PROTEINMAPK1ONT::BINDONT::TRUEONT::BINDMEK binds MAPK3ONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINMAPK3MEK binds MAPK3ONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINMAPK-3ONT::GENEONT::GENEONT::PROTEINMAPK3",
"MEK bound to ERK": "MEK bound to ERK\nMEK bound to ERKONT::BINDONT::TRUEONT::BINDMEK bound to ERKONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINto ERKMEK bound to ERKONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINERKONT::PROTEIN-FAMILYONT::PROTEINONT::PROTEINONT::GENEONT::GENEONT::GENEONT::GENEONT::GENEto ERK",
"MEK not bound to Selumetinib phosphorylates ERK. DUSP dephosphorylates ERK. Selumetinib binds MEK.": "MEK not bound to Selumetinib phosphorylates ERK. DUSP dephosphorylates ERK. Selumetinib binds MEK.\nMEK not bound to Selumetinib phosphorylates ERK.DUSP dephosphorylates ERK.Selumetinib binds MEK.ONT::PHOSPHORYLATIONONT::TRUEONT::PHOSPHORYLATIONMEK not bound to Selumetinib phosphorylates ERKONT::PROTEIN-FAMILYMEK not bound to SelumetinibONT::GENE-PROTEINERKONT::POST-TRANSLATIONAL-MODIFICATIONMEK not bound to Selumetinib phosphorylates ERKONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEK not bound to SelumetinibONT::GENE-PROTEINERKONT::PROTEIN-FAMILYONT::PROTEINONT::PROTEINONT::GENEONT::GENEONT::GENEONT::GENEONT::GENEERKONT::BIND+ONT::FALSEONT::BINDMEK not bound to SelumetinibONT::PROTEIN-FAMILYMEK not bound to SelumetinibONT::PHARMACOLOGIC-SUBSTANCEto SelumetinibMEK not bound to SelumetinibONT::PHARMACOLOGIC-SUBSTANCESELUMETINIBONT::PHARMACOLOGIC-SUBSTANCEONT::PHARMACOLOGIC-SUBSTANCEONT::PHARMACOLOGIC-SUBSTANCEto SelumetinibONT::PHOSPHORYLATIONONT::TRUEONT::MANNER-UNDODE-ONT::PHOSPHORYLATIONDUSP dephosphorylates ERKONT::GENE-PROTEINDUSPONT::GENE-PROTEINERKDUSP dephosphorylates ERKONT::GENE-PROTEINDUSPONT::PROTEIN-FAMILYONT::GENEDUSPONT::GENE-PROTEINERKONT::PROTEIN-FAMILYONT::PROTEINONT::PROTEINONT::GENEONT::GENEONT::GENEONT::GENEONT::GENEERKONT::BINDONT::TRUEONT::BINDSelumetinib binds MEKONT::PHARMACOLOGIC-SUBSTANCESelumetinibONT::PROTEIN-FAMILYMEKSelumetinib binds MEKONT::PHARMACOLOGIC-SUBSTANCESELUMETINIBONT::PHARMACOLOGIC-SUBSTANCEONT::CHEMICALONT::MOLECULESelumetinibONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEK",
"MEK phosphorylates ERK": "MEK phosphorylates ERK\nMEK phosphorylates ERKONT::PHOSPHORYLATIONONT::TRUEONT::PHOSPHORYLATIONMEK phosphorylates ERKONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINERKONT::POST-TRANSLATIONAL-MODIFICATIONMEK phosphorylates ERKONT::PROTEIN-FAMILYMEKONT::PROTEIN-FAMILYONT::PROTEIN-FAMILYMEKONT::GENE-PROTEINERKONT::PROTEIN-FAMILYONT::PROTEINONT::PROTEINONT::GENEONT::GENEONT::GENEONT::GENEONT::GENEERK",