def test_render_stmt_graph():
braf = Agent('BRAF', db_refs={'HGNC': '1097'})
mek1 = Agent('MAP2K1', db_refs={'HGNC': '6840'})
mek = Agent('MEK', db_refs={'FPLX':'MEK'})
# Statements
p0 = Phosphorylation(braf, mek)
p1 = Phosphorylation(braf, mek1)
p2 = Phosphorylation(braf, mek1, position='218')
p3 = Phosphorylation(braf, mek1, position='222')
p4 = Phosphorylation(braf, mek1, 'serine')
p5 = Phosphorylation(braf, mek1, 'serine', '218')
p6 = Phosphorylation(braf, mek1, 'serine', '222')
stmts = [p0, p1, p2, p3, p4, p5, p6]
pa = Preassembler(hierarchies, stmts=stmts)
pa.combine_related()
graph = render_stmt_graph(pa.related_stmts, reduce=False)
# One node for each statement
assert len(graph.nodes()) == 7
# Edges:
# p0 supports p1-p6 = 6 edges
# p1 supports p2-p6 = 5 edges
# p2 supports p5 = 1 edge
# p3 supports p6 = 1 edge
# p4 supports p5-p6 = 2 edges
# (p5 and p6 support none--they are top-level)
# 6 + 5 + 1 + 1 + 2 = 15 edges
assert len(graph.edges()) == 15
def test_flatten_evidence_hierarchy():
braf = Agent('BRAF')
mek = Agent('MAP2K1')
st1 = Phosphorylation(braf, mek, evidence=[Evidence(text='foo')])
st2 = Phosphorylation(braf, mek, 'S', '218',
evidence=[Evidence(text='bar')])
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa.combine_related()
assert len(pa.related_stmts) == 1
flattened = flatten_evidence(pa.related_stmts)
assert len(flattened) == 1
top_stmt = flattened[0]
assert len(top_stmt.evidence) == 2
assert 'bar' in [e.text for e in top_stmt.evidence]
assert 'foo' in [e.text for e in top_stmt.evidence]
assert len(top_stmt.supported_by) == 1
supporting_stmt = top_stmt.supported_by[0]
assert len(supporting_stmt.evidence) == 1
assert supporting_stmt.evidence[0].text == 'foo'
supporting_stmt.evidence[0].text = 'changed_foo'
assert supporting_stmt.evidence[0].text == 'changed_foo'
assert 'changed_foo' not in [e.text for e in top_stmt.evidence]
assert 'foo' in [e.text for e in top_stmt.evidence]
assert {ev.annotations.get('support_type') for ev in top_stmt.evidence} \
== {'direct', 'supported_by'}
def test_render_stmt_graph():
braf = Agent('BRAF', db_refs={'HGNC': '1097'})
mek1 = Agent('MAP2K1', db_refs={'HGNC': '6840'})
mek = Agent('MEK', db_refs={'FPLX': 'MEK'})
# Statements
p0 = Phosphorylation(braf, mek)
p1 = Phosphorylation(braf, mek1)
p2 = Phosphorylation(braf, mek1, position='218')
p3 = Phosphorylation(braf, mek1, position='222')
p4 = Phosphorylation(braf, mek1, 'serine')
p5 = Phosphorylation(braf, mek1, 'serine', '218')
p6 = Phosphorylation(braf, mek1, 'serine', '222')
stmts = [p0, p1, p2, p3, p4, p5, p6]
pa = Preassembler(bio_ontology, stmts=stmts)
pa.combine_related()
graph = render_stmt_graph(pa.related_stmts, reduce=False)
# One node for each statement
assert len(graph.nodes()) == 7
# Edges:
# p0 supports p1-p6 = 6 edges
# p1 supports p2-p6 = 5 edges
# p2 supports p5 = 1 edge
# p3 supports p6 = 1 edge
# p4 supports p5-p6 = 2 edges
# (p5 and p6 support none--they are top-level)
# 6 + 5 + 1 + 1 + 2 = 15 edges
assert len(graph.edges()) == 15
def test_translocation():
st1 = Translocation(Agent('AKT'), None, None)
st2 = Translocation(Agent('AKT'), None, 'plasma membrane')
st3 = Translocation(Agent('AKT'), None, 'nucleus')
pa = Preassembler(hierarchies, stmts=[st1, st2, st3])
pa.combine_related()
assert len(pa.related_stmts) == 2
def test_pathsfromto():
bp = biopax.process_pc_pathsfromto(['MAP2K1'], ['MAPK1'])
bp.get_phosphorylation()
assert_pmids(bp.statements)
pre = Preassembler(hierarchies, bp.statements)
pre.combine_related()
assert unicode_strs(pre.unique_stmts)
def test_pathsfromto():
bp = biopax.process_pc_pathsfromto(['MAP2K1'], ['MAPK1'])
bp.get_phosphorylation()
assert_pmids(bp.statements)
pre = Preassembler(hierarchies, bp.statements)
pre.combine_related()
assert unicode_strs(pre.unique_stmts)
def test_modification_refinement_residue_noenz():
erbb3 = Agent('Erbb3')
st1 = Phosphorylation(None, erbb3)
st2 = Phosphorylation(None, erbb3, 'Y')
pa = Preassembler(bio_ontology, stmts=[st1, st2])
pa.combine_related()
assert len(pa.related_stmts) == 1
def test_flatten_evidence_hierarchy():
braf = Agent('BRAF')
mek = Agent('MAP2K1')
st1 = Phosphorylation(braf, mek, evidence=[Evidence(text='foo')])
st2 = Phosphorylation(braf,
mek,
'S',
'218',
evidence=[Evidence(text='bar')])
pa = Preassembler(bio_ontology, stmts=[st1, st2])
pa.combine_related()
assert len(pa.related_stmts) == 1
flattened = flatten_evidence(pa.related_stmts)
assert len(flattened) == 1
top_stmt = flattened[0]
assert len(top_stmt.evidence) == 2
assert 'bar' in [e.text for e in top_stmt.evidence]
assert 'foo' in [e.text for e in top_stmt.evidence]
assert len(top_stmt.supported_by) == 1
supporting_stmt = top_stmt.supported_by[0]
assert len(supporting_stmt.evidence) == 1
assert supporting_stmt.evidence[0].text == 'foo'
supporting_stmt.evidence[0].text = 'changed_foo'
assert supporting_stmt.evidence[0].text == 'changed_foo'
assert 'changed_foo' not in [e.text for e in top_stmt.evidence]
assert 'foo' in [e.text for e in top_stmt.evidence]
assert {ev.annotations.get('support_type') for ev in top_stmt.evidence} \
== {'direct', 'supported_by'}
def test_modification_refinement_residue_noenz():
erbb3 = Agent('Erbb3')
st1 = Phosphorylation(None, erbb3)
st2 = Phosphorylation(None, erbb3, 'Y')
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa.combine_related()
assert len(pa.related_stmts) == 1
def test_translocation():
st1 = Translocation(Agent('AKT'), None, None)
st2 = Translocation(Agent('AKT'), None, 'plasma membrane')
st3 = Translocation(Agent('AKT'), None, 'nucleus')
pa = Preassembler(bio_ontology, stmts=[st1, st2, st3])
pa.combine_related()
assert len(pa.related_stmts) == 2, pa.related_stmts
def test_complex_refinement_order():
st1 = Complex([Agent('MED23'), Agent('ELK1')])
st2 = Complex([Agent('ELK1', mods=[ModCondition('phosphorylation')]),
Agent('MED23')])
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa.combine_duplicates()
pa.combine_related()
assert len(pa.related_stmts) == 1
def test_complex_agent_refinement():
ras = Agent('RAS')
raf1 = Agent('RAF', mods=[ModCondition('ubiquitination', None, None, True)])
raf2 = Agent('RAF', mods=[ModCondition('ubiquitination', None, None, False)])
st1 = Complex([ras, raf1])
st2 = Complex([ras, raf2])
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa.combine_related()
assert len(pa.unique_stmts) == 2
assert len(pa.related_stmts) == 2
def test_homodimer_refinement():
egfr = Agent('EGFR')
erbb = Agent('ERBB2')
st1 = Complex([erbb, erbb])
st2 = Complex([erbb, egfr])
pa = Preassembler(bio_ontology, stmts=[st1, st2])
pa.combine_duplicates()
assert len(pa.unique_stmts) == 2
pa.combine_related()
assert len(pa.related_stmts) == 2
def test_complex_refinement():
ras = Agent('RAS')
raf = Agent('RAF')
mek = Agent('MEK')
st1 = Complex([ras, raf])
st2 = Complex([mek, ras, raf])
pa = Preassembler(bio_ontology, stmts=[st1, st2])
pa.combine_related()
assert len(pa.unique_stmts) == 2
assert len(pa.related_stmts) == 2
def test_complex_refinement_order():
st1 = Complex([Agent('MED23'), Agent('ELK1')])
st2 = Complex([
Agent('ELK1', mods=[ModCondition('phosphorylation')]),
Agent('MED23')
])
pa = Preassembler(bio_ontology, stmts=[st1, st2])
pa.combine_duplicates()
pa.combine_related()
assert len(pa.related_stmts) == 1
def test_homodimer_refinement():
egfr = Agent('EGFR')
erbb = Agent('ERBB2')
st1 = Complex([erbb, erbb])
st2 = Complex([erbb, egfr])
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa.combine_duplicates()
assert len(pa.unique_stmts) == 2
pa.combine_related()
assert len(pa.related_stmts) == 2
def test_complex_refinement():
ras = Agent('RAS')
raf = Agent('RAF')
mek = Agent('MEK')
st1 = Complex([ras, raf])
st2 = Complex([mek, ras, raf])
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa.combine_related()
assert len(pa.unique_stmts) == 2
assert len(pa.related_stmts) == 2
def test_flatten_stmts():
st1 = Phosphorylation(Agent('MAP3K5'), Agent('RAF1'), 'S', '338')
st2 = Phosphorylation(None, Agent('RAF1'), 'S', '338')
st3 = Phosphorylation(None, Agent('RAF1'))
st4 = Phosphorylation(Agent('PAK1'), Agent('RAF1'), 'S', '338')
st5 = Phosphorylation(None, Agent('RAF1'), evidence=Evidence(text='foo'))
pa = Preassembler(hierarchies, stmts=[st1, st2, st3, st4, st5])
pa.combine_duplicates()
pa.combine_related()
assert len(pa.related_stmts) == 2
assert len(flatten_stmts(pa.unique_stmts)) == 4
assert len(flatten_stmts(pa.related_stmts)) == 4
def test_complex_agent_refinement():
ras = Agent('RAS')
raf1 = Agent('RAF',
mods=[ModCondition('ubiquitination', None, None, True)])
raf2 = Agent('RAF',
mods=[ModCondition('ubiquitination', None, None, False)])
st1 = Complex([ras, raf1])
st2 = Complex([ras, raf2])
pa = Preassembler(bio_ontology, stmts=[st1, st2])
pa.combine_related()
assert len(pa.unique_stmts) == 2
assert len(pa.related_stmts) == 2
def test_flatten_stmts():
st1 = Phosphorylation(Agent('MAP3K5'), Agent('RAF1'), 'S', '338')
st2 = Phosphorylation(None, Agent('RAF1'), 'S', '338')
st3 = Phosphorylation(None, Agent('RAF1'))
st4 = Phosphorylation(Agent('PAK1'), Agent('RAF1'), 'S', '338')
st5 = Phosphorylation(None, Agent('RAF1'), evidence=Evidence(text='foo'))
pa = Preassembler(bio_ontology, stmts=[st1, st2, st3, st4, st5])
pa.combine_duplicates()
pa.combine_related()
assert len(pa.related_stmts) == 2
assert len(flatten_stmts(pa.unique_stmts)) == 4
assert len(flatten_stmts(pa.related_stmts)) == 4
def test_activation_refinement():
subj = Agent('alcohol', db_refs={'CHEBI': 'CHEBI:16236',
'HMDB': 'HMDB00108',
'PUBCHEM': '702',
'TEXT': 'alcohol'})
obj = Agent('endotoxin', db_refs={'TEXT': 'endotoxin'})
st1 = Inhibition(subj, obj)
st2 = Activation(subj, obj)
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa.combine_duplicates()
assert len(pa.unique_stmts) == 2
pa.combine_related()
assert len(pa.related_stmts) == 2
def test_activation_refinement():
subj = Agent('alcohol',
db_refs={
'CHEBI': 'CHEBI:16236',
'HMDB': 'HMDB00108',
'PUBCHEM': '702',
'TEXT': 'alcohol'
})
obj = Agent('endotoxin', db_refs={'TEXT': 'endotoxin'})
st1 = Inhibition(subj, obj)
st2 = Activation(subj, obj)
pa = Preassembler(bio_ontology, stmts=[st1, st2])
pa.combine_duplicates()
assert len(pa.unique_stmts) == 2
pa.combine_related()
assert len(pa.related_stmts) == 2
def test_association_refinement():
health = 'UN/entities/human/health'
food = 'UN/entities/human/food'
food_security = 'UN/entities/human/food/food_security'
eh = Event(Concept('health', db_refs={'UN': [(health, 1.0)]}))
ef = Event(Concept('food', db_refs={'UN': [(food, 1.0)]}))
efs = Event(Concept('food security', db_refs={'UN': [(food_security, 1.0)]}))
st1 = Association([eh, ef], evidence=[Evidence(source_api='eidos1')])
st2 = Association([ef, eh], evidence=[Evidence(source_api='eidos2')])
st3 = Association([eh, efs], evidence=[Evidence(source_api='eidos3')])
st4 = Association([ef, efs], evidence=[Evidence(source_api='eidos4')])
eidos_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/eidos/eidos_ontology.rdf')
hm = HierarchyManager(eidos_ont, True, True)
hierarchies = {'entity': hm}
pa = Preassembler(hierarchies, [st1, st2, st3, st4])
unique_stmts = pa.combine_duplicates() # debugging
assert len(unique_stmts) == 3
rel_stmts = pa.combine_related()
assert len(rel_stmts) == 2
eh_efs_stmt = [st for st in rel_stmts if (st.members[0].concept.name in
{'health', 'food security'} and st.members[1].concept.name
in {'health', 'food security'})][0]
assert len(eh_efs_stmt.supported_by) == 1
assert (eh_efs_stmt.supported_by[0].members[0].concept.name
in {'food', 'health'})
assert (eh_efs_stmt.supported_by[0].members[1].concept.name
in {'food', 'health'})
def test_modification_refinement_noenz2():
"""A more specific modification statement should be supported by a more
generic modification statement.
Similar to test_modification_refinement_noenz for statements where one
argument is associated with a component in the hierarchy (SIRT1 in this
case) but the other is not (BECN1).
"""
sirt1 = Agent('SIRT1',
db_refs={
'HGNC': '14929',
'UP': 'Q96EB6',
'TEXT': 'SIRT1'
})
becn1 = Agent('BECN1',
db_refs={
'HGNC': '1034',
'UP': 'Q14457',
'TEXT': 'Beclin 1'
})
st1 = Deacetylation(sirt1, becn1)
st2 = Deacetylation(None, becn1)
pa = Preassembler(bio_ontology, stmts=[st1, st2])
stmts = pa.combine_related()
# The top-level list should contain only one statement, the more specific
# modification, supported by the less-specific modification.
assert (len(stmts) == 1)
assert (stmts[0].equals(st1))
assert (len(stmts[0].supported_by) == 1)
assert (stmts[0].supported_by[0].equals(st2))
assert (stmts[0].supported_by[0].supports[0].equals(st1))
def test_association_refinement():
health = 'UN/entities/human/health'
food = 'UN/entities/human/food'
food_security = 'UN/entities/human/food/food_security'
eh = Event(Concept('health', db_refs={'UN': [(health, 1.0)]}))
ef = Event(Concept('food', db_refs={'UN': [(food, 1.0)]}))
efs = Event(
Concept('food security', db_refs={'UN': [(food_security, 1.0)]}))
st1 = Association([eh, ef], evidence=[Evidence(source_api='eidos1')])
st2 = Association([ef, eh], evidence=[Evidence(source_api='eidos2')])
st3 = Association([eh, efs], evidence=[Evidence(source_api='eidos3')])
st4 = Association([ef, efs], evidence=[Evidence(source_api='eidos4')])
eidos_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/eidos/eidos_ontology.rdf')
hm = HierarchyManager(eidos_ont, True, True)
hierarchies = {'entity': hm}
pa = Preassembler(hierarchies, [st1, st2, st3, st4])
unique_stmts = pa.combine_duplicates() # debugging
assert len(unique_stmts) == 3
rel_stmts = pa.combine_related()
assert len(rel_stmts) == 2
eh_efs_stmt = [
st for st in rel_stmts
if (st.members[0].concept.name in {'health', 'food security'}
and st.members[1].concept.name in {'health', 'food security'})
][0]
assert len(eh_efs_stmt.supported_by) == 1
assert (eh_efs_stmt.supported_by[0].members[0].concept.name
in {'food', 'health'})
assert (eh_efs_stmt.supported_by[0].members[1].concept.name
in {'food', 'health'})
def test_association_refinement():
unrelated = 'wm/concept/causal_factor/wild_food_sources'
parent = 'wm/concept/causal_factor/health_and_life'
child = 'wm/concept/causal_factor/health_and_life/' \
'living_condition/food_safety'
parent_event = Event(Concept('parent', db_refs={'WM': [(parent, 1.0)]}))
unrelated_event = \
Event(Concept('unrelated', db_refs={'WM': [(unrelated, 1.0)]}))
child_event = Event(Concept('child', db_refs={'WM': [(child, 1.0)]}))
st1 = Association([parent_event, unrelated_event],
evidence=[Evidence(source_api='eidos1')])
st2 = Association([unrelated_event, parent_event],
evidence=[Evidence(source_api='eidos2')])
st3 = Association([parent_event, child_event],
evidence=[Evidence(source_api='eidos3')])
st4 = Association([unrelated_event, child_event],
evidence=[Evidence(source_api='eidos4')])
pa = Preassembler(world_ontology, [st1, st2, st3, st4])
unique_stmts = pa.combine_duplicates()
assert len(unique_stmts) == 3
top_level_stmts = pa.combine_related()
assert len(top_level_stmts) == 2, top_level_stmts
names = {
tuple(sorted(e.concept.name for e in stmt.members)): stmt
for stmt in top_level_stmts
}
stmt = names[('child', 'unrelated')]
assert len(stmt.supported_by) == 1
assert {e.concept.name for e in stmt.supported_by[0].members} == \
{'parent', 'unrelated'}
def test_return_toplevel():
src = Agent('SRC', db_refs={'HGNC': '11283'})
nras = Agent('NRAS', db_refs={'HGNC': '7989'})
st1 = Phosphorylation(src, nras, 'tyrosine', '32')
st2 = Phosphorylation(src, nras)
pa = Preassembler(bio_ontology, stmts=[st1, st2])
stmts = pa.combine_related(return_toplevel=True)
assert len(stmts) == 1
assert len(stmts[0].supported_by) == 1
assert len(stmts[0].supported_by[0].supports) == 1
stmts = pa.combine_related(return_toplevel=False)
assert len(stmts) == 2
ix = 1 if stmts[0].residue else 0
assert len(stmts[1 - ix].supported_by) == 1
assert len(stmts[1 - ix].supported_by[0].supports) == 1
assert len(stmts[ix].supports) == 1
assert len(stmts[ix].supports[0].supported_by) == 1
def test_return_toplevel():
src = Agent('SRC', db_refs = {'HGNC': '11283'})
nras = Agent('NRAS', db_refs = {'HGNC': '7989'})
st1 = Phosphorylation(src, nras, 'tyrosine', '32')
st2 = Phosphorylation(src, nras)
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related(return_toplevel=True)
assert len(stmts) == 1
assert len(stmts[0].supported_by) == 1
assert len(stmts[0].supported_by[0].supports) == 1
stmts = pa.combine_related(return_toplevel=False)
assert len(stmts) == 2
ix = 1 if stmts[0].residue else 0
assert len(stmts[1-ix].supported_by) == 1
assert len(stmts[1-ix].supported_by[0].supports) == 1
assert len(stmts[ix].supports) == 1
assert len(stmts[ix].supports[0].supported_by) == 1
def assemble_model(requester_name):
global stmts
# Performing grounding mapping on the statements
gmapper = gm.GroundingMapper(gm.default_grounding_map)
stmts = gmapper.map_agents(stmts)
pa = Preassembler(hierarchies, stmts)
pa.combine_related()
stmts = pa.related_stmts
ml = MechLinker(stmts)
linked_stmts = ml.link_statements()
if linked_stmts:
for linked_stmt in linked_stmts:
if linked_stmt.inferred_stmt:
question = mechlinker_queries.print_linked_stmt(linked_stmt)
say(question)
stmts.append(linked_stmt.inferred_stmt)
say("%s: Done, updating layout." % requester_name)
update_layout()
def test_flatten_evidence_multilevel():
braf = Agent('BRAF')
mek = Agent('MAP2K1')
st1 = Phosphorylation(braf, mek, evidence=[Evidence(text='foo')])
st2 = Phosphorylation(braf, mek, 'S',
evidence=[Evidence(text='bar')])
st3 = Phosphorylation(braf, mek, 'S', '218',
evidence=[Evidence(text='baz')])
pa = Preassembler(hierarchies, stmts=[st1, st2, st3])
pa.combine_related()
assert len(pa.related_stmts) == 1
flattened = flatten_evidence(pa.related_stmts)
assert len(flattened) == 1
top_stmt = flattened[0]
assert len(top_stmt.evidence) == 3, len(top_stmt.evidence)
anns = [ev.annotations['support_type'] for ev in top_stmt.evidence]
assert anns.count('direct') == 1
assert anns.count('supported_by') == 2
def test_flatten_evidence_multilevel():
braf = Agent('BRAF')
mek = Agent('MAP2K1')
st1 = Phosphorylation(braf, mek, evidence=[Evidence(text='foo')])
st2 = Phosphorylation(braf, mek, 'S', evidence=[Evidence(text='bar')])
st3 = Phosphorylation(braf,
mek,
'S',
'218',
evidence=[Evidence(text='baz')])
pa = Preassembler(bio_ontology, stmts=[st1, st2, st3])
pa.combine_related()
assert len(pa.related_stmts) == 1
flattened = flatten_evidence(pa.related_stmts)
assert len(flattened) == 1
top_stmt = flattened[0]
assert len(top_stmt.evidence) == 3, len(top_stmt.evidence)
anns = [ev.annotations['support_type'] for ev in top_stmt.evidence]
assert anns.count('direct') == 1
assert anns.count('supported_by') == 2
def test_conversion_refinement():
ras = Agent('RAS', db_refs={'FPLX': 'RAS'})
hras = Agent('HRAS', db_refs={'HGNC': '5173'})
gtp = Agent('GTP')
gdp = Agent('GDP')
st1 = Conversion(ras, gtp, gdp)
st2 = Conversion(hras, gtp, gdp)
st3 = Conversion(hras, [gtp, gdp], gdp)
st4 = Conversion(hras, [gdp, gtp], gdp)
pa = Preassembler(bio_ontology, stmts=[st1, st2, st3, st4])
toplevel_stmts = pa.combine_related()
assert len(toplevel_stmts) == 2
def test_conversion_refinement():
ras = Agent('RAS', db_refs={'FPLX': 'RAS'})
hras = Agent('HRAS', db_refs={'HGNC': '5173'})
gtp = Agent('GTP')
gdp = Agent('GDP')
st1 = Conversion(ras, gtp, gdp)
st2 = Conversion(hras, gtp, gdp)
st3 = Conversion(hras, [gtp, gdp], gdp)
st4 = Conversion(hras, [gdp, gtp], gdp)
pa = Preassembler(hierarchies, stmts=[st1, st2, st3, st4])
toplevel_stmts = pa.combine_related()
assert len(toplevel_stmts) == 2
def test_preassemble_related_complex():
ras = Agent('RAS', db_refs={'FPLX': 'RAS'})
kras = Agent('KRAS', db_refs={'HGNC': '6407'})
hras = Agent('HRAS', db_refs={'HGNC': '5173'})
st1 = Complex([kras, hras])
st2 = Complex([kras, ras])
st3 = Complex([hras, kras])
st4 = Complex([ras, kras])
pa = Preassembler(hierarchies, [st1, st2, st3, st4])
uniq = pa.combine_duplicates()
assert len(uniq) == 2
top = pa.combine_related()
assert len(top) == 1
def test_preassemble_related_complex():
ras = Agent('RAS', db_refs={'FPLX': 'RAS'})
kras = Agent('KRAS', db_refs={'HGNC': '6407'})
hras = Agent('HRAS', db_refs={'HGNC': '5173'})
st1 = Complex([kras, hras])
st2 = Complex([kras, ras])
st3 = Complex([hras, kras])
st4 = Complex([ras, kras])
pa = Preassembler(bio_ontology, [st1, st2, st3, st4])
uniq = pa.combine_duplicates()
assert len(uniq) == 2
top = pa.combine_related()
assert len(top) == 1
def test_flatten_evidence_hierarchy():
braf = Agent('BRAF')
mek = Agent('MAP2K1')
st1 = Phosphorylation(braf, mek, evidence=[Evidence(text='foo')])
st2 = Phosphorylation(braf,
mek,
'S',
'218',
evidence=[Evidence(text='bar')])
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa.combine_related()
assert len(pa.related_stmts) == 1
flattened = flatten_evidence(pa.related_stmts)
assert len(flattened) == 1
top_stmt = flattened[0]
assert len(top_stmt.evidence) == 2
assert 'bar' in [e.text for e in top_stmt.evidence]
assert 'foo' in [e.text for e in top_stmt.evidence]
assert len(top_stmt.supported_by) == 1
supporting_stmt = top_stmt.supported_by[0]
assert len(supporting_stmt.evidence) == 1
assert supporting_stmt.evidence[0].text == 'foo'
def test_modification_norefinement_subsfamily():
"""A more specific modification statement should be supported by a more
generic modification statement."""
src = Agent('SRC', db_refs={'HGNC': '11283'})
nras = Agent('NRAS', db_refs={'HGNC': '7989'})
ras = Agent('RAS', db_refs={'FPLX': 'RAS'})
st1 = Phosphorylation(src, nras)
st2 = Phosphorylation(src, ras, 'Y', '32', evidence=[Evidence(text='foo')])
pa = Preassembler(bio_ontology, stmts=[st1, st2])
stmts = pa.combine_related()
# Modification is less specific, enzyme more specific in st1, therefore
# these statements shouldn't be combined.
assert len(stmts) == 2
assert len(stmts[0].evidence) == 1, stmts
def test_superfamily_refinement_isa_or_partof():
src = Agent('SRC', db_refs={'HGNC': '11283'})
prkag1 = Agent('PRKAG1', db_refs={'HGNC': '9385'})
ampk = Agent('AMPK', db_refs={'FPLX': 'AMPK'})
st1 = Phosphorylation(src, ampk, 'tyrosine', '32')
st2 = Phosphorylation(src, prkag1, 'tyrosine', '32')
pa = Preassembler(bio_ontology, stmts=[st1, st2])
stmts = pa.combine_related()
# The top-level list should contain only one statement, the gene-level
# one, supported by the family one.
assert len(stmts) == 1
assert stmts[0].equals(st2)
assert len(stmts[0].supported_by) == 1
assert stmts[0].supported_by[0].equals(st1)
def extract_phos():
with open(stmts_fname, 'rb') as fh:
model = pickle.load(fh)
stmts = []
for pmid, pmid_stmts in model.items():
for stmt in pmid_stmts:
if isinstance(stmt, Phosphorylation):
stmts.append(stmt)
logger.info('%d phosphorylations in RAS Machine' % len(stmts))
stmts = [s for s in stmts if s.enz is not None]
logger.info('%d phosphorylations with enzyme in RAS Machine' % len(stmts))
stmts_grounded = filter_grounded(stmts)
logger.info('%d grounded phosphorylations in RAS Machine' %
len(stmts_grounded))
stmts_enzkinase = filter_enzkinase(stmts_grounded)
logger.info('%d phosphorylations with kinase enzyme in RAS Machine' %
len(stmts_enzkinase))
sm = SiteMapper(default_site_map)
stmts_valid, _ = sm.map_sites(stmts_enzkinase)
logger.info('%d valid-sequence phosphorylations in RAS Machine' %
len(stmts_valid))
pa = Preassembler(hierarchies, stmts_valid)
stmts_unique = pa.combine_duplicates()
logger.info('%d unique phosphorylations in RAS Machine' %
len(stmts_unique))
stmts_unique = pa.combine_related()
logger.info('%d top-level phosphorylations in RAS Machine' %
len(stmts_unique))
with open('mapped_unique_phos.pkl', 'wb') as fh:
pickle.dump(stmts_unique, fh, protocol=2)
# Filter RAS Machine statements for direct and not hypothesis
stmts = filter_direct(stmts_unique)
logger.info('%d direct phosphorylations in RAS Machine' % len(stmts))
stmts = filter_non_hypothesis(stmts)
logger.info('%d non-hypothesis phosphorylations in RAS Machine' %
len(stmts))
with open('filtered_phos.pkl', 'wb') as fh:
pickle.dump(stmts, fh, protocol=2)
return stmts
def test_superfamily_refinement_isa_or_partof():
src = Agent('SRC', db_refs = {'HGNC': '11283'})
prkag1 = Agent('PRKAG1', db_refs = {'HGNC': '9385'})
ampk = Agent('AMPK', db_refs = {'FPLX': 'AMPK'})
st1 = Phosphorylation(src, ampk, 'tyrosine', '32')
st2 = Phosphorylation(src, prkag1, 'tyrosine', '32')
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# The top-level list should contain only one statement, the gene-level
# one, supported by the family one.
assert len(stmts) == 1
assert stmts[0].equals(st2)
assert len(stmts[0].supported_by) == 1
assert stmts[0].supported_by[0].equals(st1)
def test_modification_norefinement_enzfamily():
"""A more specific modification statement should be supported by a more
generic modification statement."""
mek = Agent('MEK')
raf = Agent('RAF')
braf = Agent('BRAF')
st1 = Phosphorylation(raf, mek, 'Y', '32', evidence=[Evidence(text='foo')])
st2 = Phosphorylation(braf, mek)
pa = Preassembler(bio_ontology, stmts=[st1, st2])
stmts = pa.combine_related()
# Modification is less specific, enzyme more specific in st1, therefore
# these statements shouldn't be combined.
assert len(stmts) == 2
assert len(stmts[1].evidence) == 1
def test_modification_norefinement_noenz():
"""A more specific modification statement should be supported by a more
generic modification statement."""
src = Agent('SRC', db_refs = {'HGNC': '11283'})
nras = Agent('NRAS', db_refs = {'HGNC': '7989'})
st1 = Phosphorylation(src, nras)
st2 = Phosphorylation(None, nras, 'Y', '32',
evidence=[Evidence(text='foo')])
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# Modification is less specific, enzyme more specific in st1, therefore
# these statements shouldn't be combined.
assert len(stmts) == 2
assert len(stmts[1].evidence)==1
def test_modification_refinement():
"""A more specific modification statement should be supported by a more
generic modification statement."""
src = Agent('SRC', db_refs={'HGNC': '11283'})
nras = Agent('NRAS', db_refs={'HGNC': '7989'})
st1 = Phosphorylation(src, nras, 'tyrosine', '32')
st2 = Phosphorylation(src, nras)
pa = Preassembler(bio_ontology, stmts=[st1, st2])
stmts = pa.combine_related()
# The top-level list should contain only one statement, the more specific
# modification, supported by the less-specific modification.
assert len(stmts) == 1
assert stmts[0].equals(st1)
assert len(stmts[0].supported_by) == 1
assert stmts[0].supported_by[0].equals(st2)
def test_modification_norefinement_enzfamily():
"""A more specific modification statement should be supported by a more
generic modification statement."""
mek = Agent('MEK')
raf = Agent('RAF')
braf = Agent('BRAF')
st1 = Phosphorylation(raf, mek, 'Y', '32',
evidence=[Evidence(text='foo')])
st2 = Phosphorylation(braf, mek)
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# Modification is less specific, enzyme more specific in st1, therefore
# these statements shouldn't be combined.
assert len(stmts) == 2
assert len(stmts[1].evidence)==1
def test_bound_condition_norefinement():
"""A statement with more specific bound context should be supported by a
less specific statement."""
src = Agent('SRC', db_refs = {'HGNC': '11283'})
gtp = Agent('GTP', db_refs = {'CHEBI': '15996'})
nras = Agent('NRAS', db_refs = {'HGNC': '7989'})
nrasgtp = Agent('NRAS', db_refs = {'HGNC': '7989'},
bound_conditions=[BoundCondition(gtp, True)])
st1 = Phosphorylation(src, nras, 'tyrosine', '32')
st2 = Phosphorylation(src, nrasgtp)
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# The bound condition is more specific in st2 but the modification is less
# specific. Therefore these statements should not be combined.
assert len(stmts) == 2
def test_modification_refinement():
"""A more specific modification statement should be supported by a more
generic modification statement."""
src = Agent('SRC', db_refs = {'HGNC': '11283'})
nras = Agent('NRAS', db_refs = {'HGNC': '7989'})
st1 = Phosphorylation(src, nras, 'tyrosine', '32')
st2 = Phosphorylation(src, nras)
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# The top-level list should contain only one statement, the more specific
# modification, supported by the less-specific modification.
assert len(stmts) == 1
assert stmts[0].equals(st1)
assert len(stmts[0].supported_by) == 1
assert stmts[0].supported_by[0].equals(st2)
def test_superfamily_refinement():
"""A gene-level statement should be supported by a family-level
statement."""
src = Agent('SRC', db_refs={'HGNC': '11283'})
ras = Agent('RAS', db_refs={'FPLX': 'RAS'})
nras = Agent('NRAS', db_refs={'HGNC': '7989'})
st1 = Phosphorylation(src, ras, 'tyrosine', '32')
st2 = Phosphorylation(src, nras, 'tyrosine', '32')
pa = Preassembler(bio_ontology, stmts=[st1, st2])
stmts = pa.combine_related()
# The top-level list should contain only one statement, the gene-level
# one, supported by the family one.
assert len(stmts) == 1
assert (stmts[0].equals(st2))
assert (len(stmts[0].supported_by) == 1)
assert (stmts[0].supported_by[0].equals(st1))
def test_superfamily_refinement():
"""A gene-level statement should be supported by a family-level
statement."""
src = Agent('SRC', db_refs = {'HGNC': '11283'})
ras = Agent('RAS', db_refs = {'FPLX': 'RAS'})
nras = Agent('NRAS', db_refs = {'HGNC': '7989'})
st1 = Phosphorylation(src, ras, 'tyrosine', '32')
st2 = Phosphorylation(src, nras, 'tyrosine', '32')
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# The top-level list should contain only one statement, the gene-level
# one, supported by the family one.
assert len(stmts) == 1
assert (stmts[0].equals(st2))
assert (len(stmts[0].supported_by) == 1)
assert (stmts[0].supported_by[0].equals(st1))
def test_bound_condition_norefinement():
"""A statement with more specific bound context should be supported by a
less specific statement."""
src = Agent('SRC', db_refs={'HGNC': '11283'})
gtp = Agent('GTP', db_refs={'CHEBI': '15996'})
nras = Agent('NRAS', db_refs={'HGNC': '7989'})
nrasgtp = Agent('NRAS',
db_refs={'HGNC': '7989'},
bound_conditions=[BoundCondition(gtp, True)])
st1 = Phosphorylation(src, nras, 'tyrosine', '32')
st2 = Phosphorylation(src, nrasgtp)
pa = Preassembler(bio_ontology, stmts=[st1, st2])
stmts = pa.combine_related()
# The bound condition is more specific in st2 but the modification is less
# specific. Therefore these statements should not be combined.
assert len(stmts) == 2
def test_modification_norefinement_noenz():
"""A more specific modification statement should be supported by a more
generic modification statement."""
src = Agent('SRC', db_refs={'HGNC': '11283'})
nras = Agent('NRAS', db_refs={'HGNC': '7989'})
st1 = Phosphorylation(src, nras)
st2 = Phosphorylation(None,
nras,
'Y',
'32',
evidence=[Evidence(text='foo')])
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# Modification is less specific, enzyme more specific in st1, therefore
# these statements shouldn't be combined.
assert (len(stmts) == 2)
assert (len(stmts[1].evidence) == 1)
def run_preassembly(statements, hierarchies):
print('%d total statements' % len(statements))
# Filter to grounded only
statements = ac.filter_grounded_only(statements, score_threshold=0.4)
# Make a Preassembler with the Eidos and TRIPS ontology
pa = Preassembler(hierarchies, statements)
# Make a BeliefEngine and run combine duplicates
be = BeliefEngine()
unique_stmts = pa.combine_duplicates()
print('%d unique statements' % len(unique_stmts))
be.set_prior_probs(unique_stmts)
# Run combine related
related_stmts = pa.combine_related(return_toplevel=False)
be.set_hierarchy_probs(related_stmts)
# Filter to top-level Statements
top_stmts = ac.filter_top_level(related_stmts)
print('%d top-level statements' % len(top_stmts))
return top_stmts
def test_bound_condition_refinement():
"""A statement with more specific bound context should be supported by a
less specific statement."""
src = Agent('SRC', db_refs = {'HGNC': '11283'})
gtp = Agent('GTP', db_refs = {'CHEBI': '15996'})
nras = Agent('NRAS', db_refs = {'HGNC': '7989'})
nrasgtp = Agent('NRAS', db_refs = {'HGNC': '7989'},
bound_conditions=[BoundCondition(gtp, True)])
st1 = Phosphorylation(src, nras, 'tyrosine', '32')
st2 = Phosphorylation(src, nrasgtp, 'tyrosine', '32')
# The top-level list should contain only one statement, the more specific
# modification, supported by the less-specific modification.
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
assert len(stmts) == 1
assert stmts[0].equals(st2)
assert len(stmts[0].supported_by) == 1
assert stmts[0].supported_by[0].equals(st1)
def test_flatten_evidence_hierarchy_supports():
braf = Agent('BRAF')
mek = Agent('MAP2K1')
st1 = Phosphorylation(braf, mek, evidence=[Evidence(text='foo')])
st2 = Phosphorylation(braf, mek, 'S', '218',
evidence=[Evidence(text='bar')])
pa = Preassembler(hierarchies, stmts=[st1, st2])
pa_stmts = pa.combine_related(return_toplevel=False)
assert len(pa_stmts) == 2
flattened = flatten_evidence(pa_stmts, collect_from='supports')
assert len(flattened) == 2
top_stmt = flattened[1]
assert len(top_stmt.evidence) == 1
assert 'bar' in [e.text for e in top_stmt.evidence]
assert len(top_stmt.supported_by) == 1
supporting_stmt = top_stmt.supported_by[0]
assert len(supporting_stmt.evidence) == 2
assert set([e.text for e in supporting_stmt.evidence]) == {'foo', 'bar'}
def run_preassembly(statements, hierarchies):
print('%d total statements' % len(statements))
# Filter to grounded only
statements = map_onto(statements)
ac.dump_statements(statements, 'pi_mtg_demo_unfiltered.pkl')
statements = ac.filter_grounded_only(statements, score_threshold=0.7)
#statements = ac.filter_by_db_refs(statements, 'UN',
# ['conflict', 'food_security', 'precipitation'], policy='one',
# match_suffix=True)
statements = ac.filter_by_db_refs(
statements,
'UN', [
'conflict', 'food_security', 'flooding', 'food_production',
'human_migration', 'drought', 'food_availability', 'market',
'food_insecurity'
],
policy='all',
match_suffix=True)
assume_polarity(statements)
statements = filter_has_polarity(statements)
# Make a Preassembler with the Eidos and TRIPS ontology
pa = Preassembler(hierarchies, statements)
# Make a BeliefEngine and run combine duplicates
be = BeliefEngine()
unique_stmts = pa.combine_duplicates()
print('%d unique statements' % len(unique_stmts))
be.set_prior_probs(unique_stmts)
# Run combine related
related_stmts = pa.combine_related(return_toplevel=False)
be.set_hierarchy_probs(related_stmts)
#related_stmts = ac.filter_belief(related_stmts, 0.8)
# Filter to top-level Statements
top_stmts = ac.filter_top_level(related_stmts)
pa.stmts = top_stmts
print('%d top-level statements' % len(top_stmts))
conflicts = pa.find_contradicts()
top_stmts = remove_contradicts(top_stmts, conflicts)
ac.dump_statements(top_stmts, 'pi_mtg_demo.pkl')
return top_stmts
def extract_phos():
with open(stmts_fname, 'rb') as fh:
model = pickle.load(fh)
stmts = []
for pmid, pmid_stmts in model.items():
for stmt in pmid_stmts:
if isinstance(stmt, Phosphorylation):
stmts.append(stmt)
logger.info('%d phosphorylations in RAS Machine' % len(stmts))
stmts = [s for s in stmts if s.enz is not None]
logger.info('%d phosphorylations with enzyme in RAS Machine' % len(stmts))
stmts_grounded = filter_grounded(stmts)
logger.info('%d grounded phosphorylations in RAS Machine' % len(stmts_grounded))
stmts_enzkinase = filter_enzkinase(stmts_grounded)
logger.info('%d phosphorylations with kinase enzyme in RAS Machine' % len(stmts_enzkinase))
sm = SiteMapper(default_site_map)
stmts_valid, _ = sm.map_sites(stmts_enzkinase)
logger.info('%d valid-sequence phosphorylations in RAS Machine' % len(stmts_valid))
pa = Preassembler(hierarchies, stmts_valid)
stmts_unique = pa.combine_duplicates()
logger.info('%d unique phosphorylations in RAS Machine' % len(stmts_unique))
stmts_unique = pa.combine_related()
logger.info('%d top-level phosphorylations in RAS Machine' % len(stmts_unique))
with open('mapped_unique_phos.pkl', 'wb') as fh:
pickle.dump(stmts_unique, fh, protocol=2)
# Filter RAS Machine statements for direct and not hypothesis
stmts = filter_direct(stmts_unique)
logger.info('%d direct phosphorylations in RAS Machine' % len(stmts))
stmts = filter_non_hypothesis(stmts)
logger.info('%d non-hypothesis phosphorylations in RAS Machine' % len(stmts))
with open('filtered_phos.pkl', 'wb') as fh:
pickle.dump(stmts, fh, protocol=2)
return stmts
def test_multiprocessing():
braf = Agent('BRAF', db_refs={'HGNC': '1097'})
mek1 = Agent('MAP2K1', db_refs={'HGNC': '6840'})
mek = Agent('MEK', db_refs={'FPLX':'MEK'})
# Statements
p0 = Phosphorylation(braf, mek)
p1 = Phosphorylation(braf, mek1)
p2 = Phosphorylation(braf, mek1, position='218')
p3 = Phosphorylation(braf, mek1, position='222')
p4 = Phosphorylation(braf, mek1, 'serine')
p5 = Phosphorylation(braf, mek1, 'serine', '218')
p6 = Phosphorylation(braf, mek1, 'serine', '222')
p7 = Dephosphorylation(braf, mek1)
stmts = [p0, p1, p2, p3, p4, p5, p6, p7]
pa = Preassembler(hierarchies, stmts=stmts)
# Size cutoff set to a low number so that one group will run remotely
# and one locally
toplevel = pa.combine_related(return_toplevel=True, poolsize=1,
size_cutoff=2)
assert len(toplevel) == 3, 'Got %d toplevel statements.' % len(toplevel)
def test_influence_refinement():
tran = 'UN/entities/human/infrastructure/transportation'
truck = 'UN/entities/human/infrastructure/transportation/' + \
'transportation_methods'
agr = 'UN/entities/human/livelihood'
ctran = Event(Concept('transportation', db_refs={'UN': [(tran, 1.0)]}))
ctruck = Event(Concept('trucking', db_refs={'UN': [(truck, 1.0)]}))
cagr = Event(Concept('agriculture', db_refs={'UN': [(agr, 1.0)]}))
stmt1 = Influence(ctran, cagr, evidence=[Evidence(source_api='eidos1')])
stmt2 = Influence(ctruck, cagr, evidence=[Evidence(source_api='eidos2')])
stmt3 = Influence(cagr, ctran, evidence=[Evidence(source_api='eidos3')])
eidos_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/eidos/eidos_ontology.rdf')
hm = HierarchyManager(eidos_ont, True, True)
hierarchies = {'entity': hm}
pa = Preassembler(hierarchies, [stmt1, stmt2, stmt3])
rel_stmts = pa.combine_related()
assert len(rel_stmts) == 2
truck_stmt = [st for st in rel_stmts if st.subj.concept.name ==
'trucking'][0]
assert len(truck_stmt.supported_by) == 1
assert truck_stmt.supported_by[0].subj.concept.name == 'transportation'
def test_modification_refinement_noenz2():
"""A more specific modification statement should be supported by a more
generic modification statement.
Similar to test_modification_refinement_noenz for statements where one
argument is associated with a component in the hierarchy (SIRT1 in this
case) but the other is not (BECN1).
"""
sirt1 = Agent('SIRT1', db_refs={'HGNC':'14929', 'UP':'Q96EB6',
'TEXT':'SIRT1'})
becn1 = Agent('BECN1', db_refs={'HGNC': '1034', 'UP': 'Q14457',
'TEXT': 'Beclin 1'})
st1 = Deacetylation(sirt1, becn1)
st2 = Deacetylation(None, becn1)
pa = Preassembler(hierarchies, stmts=[st1, st2])
stmts = pa.combine_related()
# The top-level list should contain only one statement, the more specific
# modification, supported by the less-specific modification.
assert (len(stmts) == 1)
assert (stmts[0].equals(st1))
assert (len(stmts[0].supported_by) == 1)
assert (stmts[0].supported_by[0].equals(st2))
assert (stmts[0].supported_by[0].supports[0].equals(st1))
def run_assembly(stmts, folder, pmcid, background_assertions=None):
'''Run assembly on a list of statements, for a given PMCID.'''
# Folder for index card output (scored submission)
indexcard_prefix = folder + '/index_cards/' + pmcid
# Folder for other outputs (for analysis, debugging)
otherout_prefix = folder + '/other_outputs/' + pmcid
# Do grounding mapping here
# Load the TRIPS-specific grounding map and add to the default
# (REACH-oriented) grounding map:
trips_gm = load_grounding_map('trips_grounding_map.csv')
default_grounding_map.update(trips_gm)
gm = GroundingMapper(default_grounding_map)
mapped_agent_stmts = gm.map_agents(stmts)
renamed_agent_stmts = gm.rename_agents(mapped_agent_stmts)
# Filter for grounding
grounded_stmts = []
for st in renamed_agent_stmts:
if all([is_protein_or_chemical(a) for a in st.agent_list()]):
grounded_stmts.append(st)
# Instantiate the Preassembler
pa = Preassembler(hierarchies)
pa.add_statements(grounded_stmts)
print('== %s ====================' % pmcid)
print('%d statements collected in total.' % len(pa.stmts))
# Combine duplicates
unique_stmts = pa.combine_duplicates()
print('%d statements after combining duplicates.' % len(unique_stmts))
# Run BeliefEngine on unique statements
epe = BeliefEngine()
epe.set_prior_probs(pa.unique_stmts)
# Build statement hierarchy
related_stmts = pa.combine_related()
# Run BeliefEngine on hierarchy
epe.set_hierarchy_probs(related_stmts)
print('%d statements after combining related.' % len(related_stmts))
# Instantiate the mechanism linker
# Link statements
linked_stmts = MechLinker.infer_active_forms(related_stmts)
linked_stmts += MechLinker.infer_modifications(related_stmts)
linked_stmts += MechLinker.infer_activations(related_stmts)
# Run BeliefEngine on linked statements
epe.set_linked_probs(linked_stmts)
# Print linked statements for debugging purposes
print('Linked\n=====')
for ls in linked_stmts:
print(ls.inferred_stmt.belief, ls.inferred_stmt)
print('=============')
# Combine all statements including linked ones
all_statements = related_stmts + [ls.inferred_stmt for ls in linked_stmts]
# Instantiate a new preassembler
pa = Preassembler(hierarchies, all_statements)
# Build hierarchy again
pa.combine_duplicates()
# Choose the top-level statements
related_stmts = pa.combine_related()
# Remove top-level statements that came only from the prior
if background_assertions is not None:
nonbg_stmts = [stmt for stmt in related_stmts
if stmt not in background_assertions]
else:
nonbg_stmts = related_stmts
# Dump top-level statements in a pickle
with open(otherout_prefix + '.pkl', 'wb') as fh:
pickle.dump(nonbg_stmts, fh)
# Flatten evidence for statements
flattened_evidence_stmts = flatten_evidence(nonbg_stmts)
# Start a card counter
card_counter = 1
# We don't limit the number of cards reported in this round
card_lim = float('inf')
top_stmts = []
###############################################
# The belief cutoff for statements
belief_cutoff = 0.3
###############################################
# Sort by amount of evidence
for st in sorted(flattened_evidence_stmts,
key=lambda x: x.belief, reverse=True):
if st.belief >= belief_cutoff:
print(st.belief, st)
if st.belief < belief_cutoff:
print('SKIP', st.belief, st)
# If it's background knowledge, we skip the statement
if is_background_knowledge(st):
print('This statement is background knowledge - skipping.')
continue
# Assemble IndexCards
ia = IndexCardAssembler([st], pmc_override=pmcid)
ia.make_model()
# If the index card was actually made
# (not all statements can be assembled into index cards to
# this is often not the case)
if ia.cards:
# Save the index card json
ia.save_model(indexcard_prefix + '-%d.json' % card_counter)
card_counter += 1
top_stmts.append(st)
if card_counter > card_lim:
break
# Print the English-assembled model for debugging purposes
ea = EnglishAssembler(top_stmts)
print('=======================')
print(ea.make_model().encode('utf-8'))
print('=======================')
# Print the statement graph
graph = render_stmt_graph(nonbg_stmts)
graph.draw(otherout_prefix + '_graph.pdf', prog='dot')
# Print statement diagnostics
print_stmts(pa.stmts, otherout_prefix + '_statements.tsv')
print_stmts(related_stmts, otherout_prefix + '_related_statements.tsv')
def run_preassembly(self, stmts, print_summary=True):
"""Run complete preassembly procedure on the given statements.
Results are returned as a dict and stored in the attribute
:py:attr:`results`. They are also saved in the pickle file
`<basename>_results.pkl`.
Parameters
----------
stmts : list of :py:class:`indra.statements.Statement`
Statements to preassemble.
print_summary : bool
If True (default), prints a summary of the preassembly process to
the console.
Returns
-------
dict
A dict containing the following entries:
- `raw`: the starting set of statements before preassembly.
- `duplicates1`: statements after initial de-duplication.
- `valid`: statements found to have valid modification sites.
- `mapped`: mapped statements (list of
:py:class:`indra.preassembler.sitemapper.MappedStatement`).
- `mapped_stmts`: combined list of valid statements and statements
after mapping.
- `duplicates2`: statements resulting from de-duplication of the
statements in `mapped_stmts`.
- `related2`: top-level statements after combining the statements
in `duplicates2`.
"""
# First round of preassembly: remove duplicates before sitemapping
pa1 = Preassembler(hierarchies, stmts)
logger.info("Combining duplicates")
pa1.combine_duplicates()
# Map sites
logger.info("Mapping sites")
(valid, mapped) = sm.map_sites(pa1.unique_stmts)
# Combine valid and successfully mapped statements into single list
correctly_mapped_stmts = []
for ms in mapped:
if all([True if mm[1] is not None else False
for mm in ms.mapped_mods]):
correctly_mapped_stmts.append(ms.mapped_stmt)
mapped_stmts = valid + correctly_mapped_stmts
# Second round of preassembly: de-duplicate and combine related
pa2 = Preassembler(hierarchies, mapped_stmts)
logger.info("Combining duplicates again")
pa2.combine_duplicates()
pa2.combine_related()
# Fill out the results dict
self.results = {}
self.results['raw'] = stmts
self.results['duplicates1'] = pa1.unique_stmts
self.results['valid'] = valid
self.results['mapped'] = mapped
self.results['mapped_stmts'] = mapped_stmts
self.results['duplicates2'] = pa2.unique_stmts
self.results['related2'] = pa2.related_stmts
# Print summary
if print_summary:
logger.info("\nStarting number of statements: %d" % len(stmts))
logger.info("After duplicate removal: %d" % len(pa1.unique_stmts))
logger.info("Unique statements with valid sites: %d" % len(valid))
logger.info("Unique statements with invalid sites: %d" %
len(mapped))
logger.info("After post-mapping duplicate removal: %d" %
len(pa2.unique_stmts))
logger.info("After combining related statements: %d" %
len(pa2.related_stmts))
# Save the results if we're caching
if self.basename is not None:
results_filename = '%s_results.pkl' % self.basename
with open(results_filename, 'wb') as f:
pickle.dump(self.results, f, protocol=2)
return self.results