def test_regulate_amount4_subj_act():
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='HGNC')
g = BELGraph()
g.add_increases(mek, erk, subject_modifier=activity(name='tscript'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
assert isinstance(pbp.statements[0], IncreaseAmount)
subj = pbp.statements[0].subj
assert subj.name == 'MAP2K1'
assert isinstance(subj.activity, ActivityCondition)
assert subj.activity.activity_type == 'transcription'
assert subj.activity.is_active
assert len(pbp.statements[0].evidence) == 1
g = BELGraph()
g.add_increases(mek, erk, subject_modifier=activity(name='act'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
assert isinstance(pbp.statements[0], IncreaseAmount)
subj = pbp.statements[0].subj
assert subj.name == 'MAP2K1'
assert isinstance(subj.activity, ActivityCondition)
assert subj.activity.activity_type == 'activity'
assert subj.activity.is_active
assert len(pbp.statements[0].evidence) == 1
def test_conversion():
enz = protein(name='PLCG1', namespace='HGNC')
react_1 = abundance('SCHEM', '1-Phosphatidyl-D-myo-inositol 4,5-bisphosphate')
p1 = abundance('SCHEM', 'Diacylglycerol')
p2 = abundance('SCHEM', 'Inositol 1,4,5-trisphosphate')
rxn = reaction(
reactants=react_1,
products=[p1, p2],
)
g = BELGraph()
g.add_directly_increases(enz, rxn,
subject_modifier=activity(name='activity'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
stmt = pbp.statements[0]
assert isinstance(stmt, Conversion)
assert stmt.subj.name == 'PLCG1'
assert stmt.subj.activity.activity_type == 'activity'
assert stmt.subj.activity.is_active is True
assert len(stmt.obj_from) == 1
assert isinstance(stmt.obj_from[0], Agent)
assert stmt.obj_from[0].name == '1-Phosphatidyl-D-myo-inositol ' \
'4,5-bisphosphate'
assert len(stmt.obj_to) == 2
# why do these not appear in alphabetical order?
# PyBEL sorts the nodes based on their BEL, and
# Inositol 1,4,5-trisphosphate gets quoted.
assert stmt.obj_to[0].name == 'Inositol 1,4,5-trisphosphate'
assert stmt.obj_to[1].name == 'Diacylglycerol'
assert len(stmt.evidence) == 1
def test_phosphorylation_one_site_with_evidence():
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='HGNC',
variants=[pmod('Ph', position=185, code='Thr')])
g = BELGraph()
ev_text = 'Some evidence.'
ev_pmid = '123456'
edge_hash = g.add_directly_increases(mek, erk, evidence=ev_text, citation=ev_pmid,
annotations={"TextLocation": 'Abstract'})
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
assert isinstance(pbp.statements[0], Phosphorylation)
assert pbp.statements[0].residue == 'T'
assert pbp.statements[0].position == '185'
enz = pbp.statements[0].enz
sub = pbp.statements[0].sub
assert enz.name == 'MAP2K1'
assert enz.mods == []
assert sub.name == 'MAPK1'
assert sub.mods == []
# Check evidence
assert len(pbp.statements[0].evidence) == 1
ev = pbp.statements[0].evidence[0]
assert ev.source_api == 'bel'
assert ev.source_id == edge_hash
assert ev.pmid == ev_pmid
assert ev.text == ev_text
assert ev.annotations == {'bel': 'p(HGNC:MAP2K1) directlyIncreases '
'p(HGNC:MAPK1, pmod(Ph, Thr, 185))'}
assert ev.epistemics == {'direct': True, 'section_type': 'abstract'}
def test_regulate_amount1_prot_obj():
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='HGNC')
g = BELGraph()
g.add_increases(mek, erk, evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
assert isinstance(pbp.statements[0], IncreaseAmount)
assert len(pbp.statements[0].evidence) == 1
def test_regulate_amount2_rna_obj():
# FIXME: Create a transcription-specific statement for p->rna
mek = protein(name='MAP2K1', namespace='HGNC')
erk = rna(name='MAPK1', namespace='HGNC')
g = BELGraph()
g.add_increases(mek, erk, evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
assert isinstance(pbp.statements[0], IncreaseAmount)
assert len(pbp.statements[0].evidence) == 1
def test_controlled_transloc_loc_cond():
"""Controlled translocations are currently not handled."""
subj = protein(name='MAP2K1', namespace='HGNC')
obj = protein(name='MAPK1', namespace='HGNC')
g = BELGraph()
transloc = translocation(from_loc=Entity('GOCC', 'intracellular'),
to_loc=Entity('GOCC', 'extracellular space'))
g.add_increases(subj, obj, object_modifier=transloc,
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert not pbp.statements
def test_regulate_amount3_deg():
# FIXME: Create a stability-specific statement for p->deg(p(Foo))
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='HGNC')
g = BELGraph()
g.add_increases(mek, erk, object_modifier=degradation(),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
assert isinstance(pbp.statements[0], DecreaseAmount)
assert len(pbp.statements[0].evidence) == 1
def test_activation_bioprocess():
bax = protein(name='BAX', namespace='HGNC')
apoptosis = bioprocess(name='apoptosis', namespace='GOBP')
g = BELGraph()
g.add_increases(bax, apoptosis, evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
stmt = pbp.statements[0]
assert isinstance(stmt, Activation)
assert stmt.subj.name == 'BAX'
assert stmt.obj.name == 'apoptosis'
assert stmt.obj.db_refs == {} # FIXME: Update when GO lookup is implemented
assert len(pbp.statements[0].evidence) == 1
def test_subject_transloc_loc_cond():
"""Translocations of the subject are treated as location conditions on the
subject (using the to_loc location as the condition)"""
subj = protein(name='MAP2K1', namespace='HGNC')
obj = protein(name='MAPK1', namespace='HGNC')
transloc = translocation(from_loc=Entity('GOCC', 'intracellular'),
to_loc=Entity('GOCC', 'extracellular space'))
g = BELGraph()
g.add_increases(subj, obj, subject_modifier=transloc,
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
stmt = pbp.statements[0]
assert isinstance(stmt, IncreaseAmount)
assert stmt.subj.name == 'MAP2K1'
assert stmt.subj.location == 'extracellular space'
assert stmt.obj.name == 'MAPK1'
def test_gap():
sos = protein(name='RASA1', namespace='HGNC')
kras = protein(name='KRAS', namespace='HGNC')
g = BELGraph()
g.add_directly_decreases(sos, kras,
subject_modifier=activity(name='activity'),
object_modifier=activity(name='gtp'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
stmt = pbp.statements[0]
assert isinstance(stmt, Gap)
assert stmt.gap.name == 'RASA1'
assert stmt.ras.name == 'KRAS'
assert stmt.gap.activity.activity_type == 'activity'
assert stmt.gap.activity.is_active is True
assert stmt.ras.activity is None
assert len(pbp.statements[0].evidence) == 1
def test_indirect_gef_is_activation():
sos = protein(name='SOS1', namespace='HGNC')
kras = protein(name='KRAS', namespace='HGNC')
g = BELGraph()
g.add_increases(sos, kras, subject_modifier=activity(name='activity'),
object_modifier=activity(name='gtp'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
stmt = pbp.statements[0]
assert isinstance(stmt, Activation)
assert stmt.subj.name == 'SOS1'
assert stmt.obj.name == 'KRAS'
assert stmt.subj.activity.activity_type == 'activity'
assert stmt.subj.activity.is_active is True
assert stmt.obj.activity is None
assert stmt.obj_activity == 'gtpbound'
assert len(pbp.statements[0].evidence) == 1
def test_gtpactivation():
kras = protein(name='KRAS', namespace='HGNC')
braf = protein(name='BRAF', namespace='HGNC')
g = BELGraph()
g.add_directly_increases(kras, braf,
subject_modifier=activity(name='gtp'),
object_modifier=activity(name='kin'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
stmt = pbp.statements[0]
assert isinstance(stmt, GtpActivation)
assert stmt.subj.name == 'KRAS'
assert stmt.subj.activity.activity_type == 'gtpbound'
assert stmt.subj.activity.is_active is True
assert stmt.obj.name == 'BRAF'
assert stmt.obj.activity is None
assert stmt.obj_activity == 'kinase'
assert len(stmt.evidence) == 1
def test_phosphorylation_two_sites():
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='HGNC',
variants=[pmod('Ph', position=185, code='Thr'),
pmod('Ph', position=187, code='Tyr')])
g = BELGraph()
g.add_directly_increases(mek, erk, evidence="Some evidence.",
citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 2
stmt1 = pbp.statements[0]
stmt2 = pbp.statements[1]
assert stmt1.residue == 'T'
assert stmt1.position == '185'
assert stmt2.residue == 'Y'
assert stmt2.position == '187'
assert stmt1.sub.mods == []
assert stmt2.sub.mods == []
assert len(pbp.statements[0].evidence) == 1
def test_regulate_activity():
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='HGNC')
g = BELGraph()
g.add_increases(mek, erk, subject_modifier=activity(name='kin'),
object_modifier=activity(name='kin'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
assert isinstance(pbp.statements[0], Activation)
subj = pbp.statements[0].subj
assert subj.name == 'MAP2K1'
assert isinstance(subj.activity, ActivityCondition)
assert subj.activity.activity_type == 'kinase'
assert subj.activity.is_active
obj = pbp.statements[0].obj
assert obj.name == 'MAPK1'
assert obj.activity is None
assert pbp.statements[0].obj_activity == 'kinase'
assert len(pbp.statements[0].evidence) == 1
def test_subject_transloc_active_form():
"""ActiveForms where the subject is a translocation--should draw on the
to-location of the subject."""
subj = protein(name='MAP2K1', namespace='HGNC')
obj = protein(name='MAP2K1', namespace='HGNC')
transloc = translocation(from_loc=Entity('GOCC', 'intracellular'),
to_loc=Entity('GOCC', 'extracellular space'))
g = BELGraph()
g.add_increases(subj, obj, subject_modifier=transloc,
object_modifier=activity(name='kin'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
stmt = pbp.statements[0]
assert isinstance(stmt, ActiveForm)
assert stmt.agent.name == 'MAP2K1'
assert stmt.agent.location == 'extracellular space'
assert stmt.agent.activity is None
assert stmt.activity == 'kinase'
assert stmt.is_active is True
def test_active_form():
p53_pmod = protein(name='TP53', namespace='HGNC',
variants=[pmod('Ph', position=33, code='Ser')])
p53_obj = protein(name='TP53', namespace='HGNC')
g = BELGraph()
g.add_increases(p53_pmod, p53_obj, object_modifier=activity(name='tscript'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 1
stmt = pbp.statements[0]
assert isinstance(stmt, ActiveForm)
assert stmt.activity == 'transcription'
assert stmt.is_active is True
ag = stmt.agent
assert ag.name == 'TP53'
assert len(ag.mods) == 1
mc = ag.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'S'
assert mc.position == '33'
assert len(pbp.statements[0].evidence) == 1
def test_complex_stmt_with_activation():
raf = protein(name='BRAF', namespace='HGNC')
mek = protein(name='MAP2K1', namespace='HGNC')
erk = protein(name='MAPK1', namespace='HGNC')
cplx = complex_abundance([raf, mek])
g = BELGraph()
g.add_directly_increases(cplx, erk,
object_modifier=activity(name='kin'),
evidence="Some evidence.", citation='123456')
pbp = bel.process_pybel_graph(g)
assert pbp.statements
assert len(pbp.statements) == 2
stmt1 = pbp.statements[0]
assert isinstance(stmt1, Complex)
assert len(stmt1.agent_list()) == 2
assert sorted([ag.name for ag in stmt1.agent_list()]) == ['BRAF', 'MAP2K1']
assert stmt1.evidence
stmt2 = pbp.statements[1]
assert isinstance(stmt2, Activation)
assert stmt2.subj.name == 'BRAF'
assert stmt2.subj.bound_conditions[0].agent.name == 'MAP2K1'
assert stmt2.obj.name == 'MAPK1'
assert stmt2.obj.activity is None
assert stmt2.obj_activity == 'kinase'
def test_process_pybel():
pbp = bel.process_pybel_graph(egf_graph)
assert pbp.statements
def test_process_pybel():
pbp = bel.process_pybel_graph(egf_graph)
assert pbp.statements