def test_get_agent():
# Protein/gene
test_ag = Agent('RELA',
db_refs={
'HGNC': hgnc_client.get_hgnc_id('RELA'),
'UP': 'Q04206'
})
sp_ag = SignorProcessor._get_agent(test_row.ENTITYA, test_row.TYPEA,
test_row.IDA, test_row.DATABASEA)
assert test_ag.matches(sp_ag)
# Chemical
test_ag = Agent('AZD1480', db_refs={'PUBCHEM': 'CID:16659841'})
sp_ag = SignorProcessor._get_agent('AZD1480', 'chemical', 'CID:16659841',
'PUBCHEM')
assert test_ag.matches(sp_ag)
# Signor phenotype
test_ag = Agent('Cell cycle progr.', db_refs={'SIGNOR': 'SIGNOR-PH42'})
sp_ag = SignorProcessor._get_agent('Cell cycle progr.', 'phenotype',
'SIGNOR-PH42', 'SIGNOR')
assert test_ag.matches(sp_ag)
# Ungrounded -- couldn't find a real example in the dataset
test_ag = Agent('Foobar', db_refs={})
sp_ag = SignorProcessor._get_agent('Foobar', 'pathway', None, None)
assert test_ag.matches(sp_ag)
sp_ag = SignorProcessor._get_agent('Foobar', 'antibody', None, None)
assert test_ag.matches(sp_ag)
def test_process_row_destab():
test_row_destab = SignorRow(
ENTITYA='INS',
TYPEA='protein',
IDA='P01308',
DATABASEA='UNIPROT',
ENTITYB='APOB',
TYPEB='protein',
IDB='P04114',
DATABASEB='UNIPROT',
EFFECT='down-regulates quantity by destabilization',
MECHANISM='destabilization',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='BTO:0000575',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='23721961',
DIRECT='NO',
NOTES='',
ANNOTATOR='miannu',
SENTENCE='',
SIGNOR_ID='SIGNOR-252114')
stmts, no_mech = SignorProcessor._process_row(test_row_destab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], DecreaseAmount)
def test_process_row_stab():
test_row_stab = SignorRow(ENTITYA='UCHL5',
TYPEA='protein',
IDA='Q9Y5K5',
DATABASEA='UNIPROT',
ENTITYB='TGFBR1',
TYPEB='protein',
IDB='P36897',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='stabilization',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='17052192',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-150135')
stmts, no_mech = SignorProcessor._process_row(test_row_stab)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], IncreaseAmount)
def test_process_row_binding_complex():
test_row = SignorRow(ENTITYA='ATG5',
TYPEA='protein',
IDA='Q9H1Y0',
DATABASEA='UNIPROT',
ENTITYB='ATG12/5/16L1',
TYPEB='complex',
IDB='SIGNOR-C109',
DATABASEB='SIGNOR',
EFFECT='form complex',
MECHANISM='binding',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='BTO:0000007',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='18321988',
DIRECT='YES',
NOTES='',
ANNOTATOR='lperfetto',
SENTENCE='',
SIGNOR_ID='SIGNOR-226693')
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Complex)
assert len(stmts[0].agent_list()) == 2
def test_process_row():
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], IncreaseAmount)
assert stmts[0].agent_list()[0].activity.activity_type == 'transcription'
def test_process_row_chem_inh():
test_row_chem_inh = SignorRow(ENTITYA='722544-51-6',
TYPEA='chemical',
IDA='CID:16007391',
DATABASEA='PUBCHEM',
ENTITYB='AURKB',
TYPEB='protein',
IDB='Q96GD4',
DATABASEB='UNIPROT',
EFFECT='down-regulates',
MECHANISM='chemical inhibition',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='Other',
DIRECT='YES',
NOTES='Selleck',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-190245')
stmts, no_mech = SignorProcessor._process_row(test_row_chem_inh)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Inhibition)
def test_process_row_chem_act():
test_row_chem_act = SignorRow(ENTITYA='Prostaglandin E2',
TYPEA='smallmolecule',
IDA='CID:5280360',
DATABASEA='PUBCHEM',
ENTITYB='GNG12',
TYPEB='protein',
IDB='Q9UBI6',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='chemical activation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='16293724',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-141820')
stmts, no_mech = SignorProcessor._process_row(test_row_chem_act)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 1
assert isinstance(stmts[0], Activation)
def test_process_row_phos_multi_res():
test_row = SignorRow(ENTITYA='RAF1',
TYPEA='protein',
IDA='P04049',
DATABASEA='UNIPROT',
ENTITYB='MAP2K2',
TYPEB='protein',
IDB='P36507',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='phosphorylation',
RESIDUE='Ser218;Ser222',
SEQUENCE='VSGQLIDsMANSFVG;LIDSMANsFVGTRSY',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='8157000',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-36553')
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 4
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].position == '218'
assert isinstance(stmts[2], Phosphorylation)
assert stmts[2].position == '222'
af = stmts[3]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 2
mc0 = af.agent.mods[0]
assert mc0.mod_type == 'phosphorylation'
assert mc0.residue == 'S'
assert mc0.position == '218'
mc1 = af.agent.mods[1]
assert mc1.mod_type == 'phosphorylation'
assert mc1.residue == 'S'
assert mc1.position == '222'
assert af.is_active == True
def test_process_row_complex_down():
test_row = SignorRow(ENTITYA='XIAP',
TYPEA='protein',
IDA='P98170',
DATABASEA='UNIPROT',
ENTITYB='CASP3',
TYPEB='protein',
IDB='P42574',
DATABASEB='UNIPROT',
EFFECT='down-regulates activity',
MECHANISM='binding',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='10548111',
DIRECT='YES',
NOTES='',
ANNOTATOR='amattioni',
SENTENCE='',
SIGNOR_ID='SIGNOR-71954')
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert not af.is_active
def test_process_row_complex_up():
test_row = SignorRow(ENTITYA='NONO',
TYPEA='protein',
IDA='Q15233',
DATABASEA='UNIPROT',
ENTITYB='TOP1',
TYPEB='protein',
IDB='P11387',
DATABASEB='UNIPROT',
EFFECT='up-regulates',
MECHANISM='binding',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='BTO:0000017',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='9756848',
DIRECT='YES',
NOTES='',
ANNOTATOR='miannu',
SENTENCE='',
SIGNOR_ID='SIGNOR-60557')
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Complex)
cplx_agent_a = stmts[1].agent_list()[0]
cplx_agent_b = stmts[1].agent_list()[1]
af = stmts[2]
assert isinstance(af, ActiveForm)
# Won't fully match because of bound condition, so we check name
assert af.agent.name == cplx_agent_b.name
assert len(af.agent.bound_conditions) == 1
bc = af.agent.bound_conditions[0]
assert bc.agent.matches(cplx_agent_a)
assert bc.is_bound
assert af.activity == 'activity'
assert af.is_active
def test_process_row_phos_nores_down():
test_row = SignorRow(ENTITYA='CSNK1D',
TYPEA='protein',
IDA='P48730',
DATABASEA='UNIPROT',
ENTITYB='LEF1',
TYPEB='protein',
IDB='Q9UJU2',
DATABASEB='UNIPROT',
EFFECT='down-regulates',
MECHANISM='phosphorylation',
RESIDUE='',
SEQUENCE='',
TAX_ID='9606',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='15747065',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-134494')
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == False
def test_process_row_phos_nores_up():
test_row = SignorRow(ENTITYA='STK11',
TYPEA='protein',
IDA='Q15831',
DATABASEA='UNIPROT',
ENTITYB='AMPK',
TYPEB='complex',
IDB='SIGNOR-C15',
DATABASEB='SIGNOR',
EFFECT='up-regulates activity',
MECHANISM='phosphorylation',
RESIDUE='',
SEQUENCE='',
TAX_ID='-1',
CELL_DATA='',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='14976552',
DIRECT='YES',
NOTES='',
ANNOTATOR='lperfetto',
SENTENCE='',
SIGNOR_ID='SIGNOR-242602')
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].residue is None
assert stmts[1].position is None
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue is None
assert mc.position is None
assert af.is_active == True
def test_process_row_phos_down():
test_row = SignorRow(ENTITYA='PRKCD',
TYPEA='protein',
IDA='Q05655',
DATABASEA='UNIPROT',
ENTITYB='PTPN22',
TYPEB='protein',
IDB='Q9Y2R2',
DATABASEB='UNIPROT',
EFFECT='down-regulates',
MECHANISM='phosphorylation',
RESIDUE='Ser35',
SEQUENCE='FLKLKRQsTKYKADK',
TAX_ID='9606',
CELL_DATA='BTO:0000782',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='18056643',
DIRECT='YES',
NOTES='',
ANNOTATOR='llicata',
SENTENCE='',
SIGNOR_ID='SIGNOR-159591')
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Inhibition)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].residue == 'S'
assert stmts[1].position == '35'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'S'
assert mc.position == '35'
assert af.is_active == False
def test_process_row_phos_up():
test_row = SignorRow(ENTITYA='CHEK2',
TYPEA='protein',
IDA='O96017',
DATABASEA='UNIPROT',
ENTITYB='CHEK2',
TYPEB='protein',
IDB='O96017',
DATABASEB='UNIPROT',
EFFECT='up-regulates activity',
MECHANISM='phosphorylation',
RESIDUE='Thr387',
SEQUENCE='LMRTLCGtPTYLAPE',
TAX_ID='9606',
CELL_DATA='BTO:0000007',
TISSUE_DATA='',
MODULATOR_COMPLEX='',
TARGET_COMPLEX='',
MODIFICATIONA='',
MODASEQ='',
MODIFICATIONB='',
MODBSEQ='',
PMID='11901158',
DIRECT='YES',
NOTES='',
ANNOTATOR='gcesareni',
SENTENCE='',
SIGNOR_ID='SIGNOR-116131')
stmts, no_mech = SignorProcessor._process_row(test_row)
assert not no_mech
assert isinstance(stmts, list)
assert len(stmts) == 3
assert isinstance(stmts[0], Activation)
assert isinstance(stmts[1], Phosphorylation)
assert stmts[1].residue == 'T'
assert stmts[1].position == '387'
af = stmts[2]
assert isinstance(af, ActiveForm)
assert len(af.agent.mods) == 1
mc = af.agent.mods[0]
assert mc.mod_type == 'phosphorylation'
assert mc.residue == 'T'
assert mc.position == '387'
assert af.is_active == True
def test_get_evidence():
ev = SignorProcessor._get_evidence(test_row)
assert isinstance(ev, Evidence)
assert ev.pmid == '19530226'
assert ev.annotations == {
'SEQUENCE': None,
'TAX_ID': '10090',
'CELL_DATA': 'BTO:0002895',
'TISSUE_DATA': None,
'MODULATOR_COMPLEX': None,
'TARGET_COMPLEX': None,
'MODIFICATIONA': None,
'MODASEQ': None,
'MODIFICATIONB': None,
'MODBSEQ': None,
'NOTES': None,
'ANNOTATOR': 'gcesareni',
}
assert ev.epistemics['direct']
assert ev.source_api == 'signor'
assert ev.source_id == 'SIGNOR-241929'
assert ev.text == "Together, these results indicate that the Met gene " \
"is a direct target of NFkappaB and that Met " \
"participates in NFkappaB-mediated cell survival."
def test_get_agent_keyerror():
sp_ag = SignorProcessor._get_agent('foo', 'bar', None, None)
def test_parse_csv():
sp = SignorProcessor()
assert isinstance(sp._data, list)
assert isinstance(sp._data[0], SignorRow)
assert isinstance(sp.statements, list)
assert isinstance(sp.statements[0], Statement)