def test_vicinityResolution_5(self):
input = "In fact, apart from the very recent discovery of the occurrence of a superconducting " \
"phase at 200 K in sulfur hydride systems under ultrahigh pressures (up to 150 GPa) , " \
"the highest T c materials found up until now can be grouped into two families: the " \
"cuprates, with T c of up to 164 K [5] (in HgBa 2 Ca 2 Cu 3 O 9 at 30 GPa), and " \
"Fe-pnictides and -chalcogenides (FPC) with T c of up to 55 K [6]."
spans = [("200 K", "<tcValue>"), ("sulfur hydride", "<material>"), ("highest T c", "<tc>"),
("cuprates", "<class>"), ("T c", "<tc>"), ("up to 164 K", "<tcValue>"),
("HgBa 2 Ca 2 Cu 3 O 9", "<material>"), ("Fe-pnictides and -chalcogenides", "<class>"),
("T c", "<tc>"), ("up to 55 K", "<tcValue>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = VicinityResolutionResolver().find_relationships(doc, materials, tc_values)
assert len(relationships) == 2
assert str(relationships[0][0]) == "sulfur hydride"
assert str(relationships[0][1]) == "200 K"
assert str(relationships[1][0]) == "HgBa 2 Ca 2 Cu 3 O 9"
assert str(relationships[1][1]) == "up to 164 K"
def test_find_closer_to_pivot(self):
input = "Havinga et al systematically changed n from 3.00 to 4.00 by synthesizing LaTl 3" \
" (n=3.00, T c =1.6 K), LaPb 3 (n=3.75, T c =4.1 K), and " \
"ThPb 3 (n=4.00, T c =5.6 K) and the solid solutions " \
"La (Tl 1−x Pb x ) 3 and (La 1−x Th x )Pb 3 ."
spans = [("LaTl 3", "<material>"), ("T c", "<tc>"), ("1.6 K", "<tcValue>"),
("LaPb 3", "<material>"), ("T c", "<tc>"), ("4.1 K", "<tcValue>"),
("ThPb 3", "<material>"), ("T c", "<tc>"), ("5.6 K", "<tcValue>"),
("La (Tl 1−x Pb x ) 3", "<material>"), ("(La 1−x Th x )Pb 3", "<material>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
target = VicinityResolutionResolver()
closer_entity = target.find_closer_to_pivot(materials[0], tc_values)
assert closer_entity != None
assert closer_entity.text == "1.6 K"
closer_entity = target.find_closer_to_pivot(materials[1], tc_values)
assert closer_entity != None
assert closer_entity.text == "1.6 K"
def test_vicinityResolution_respectively_4(self):
input = "In this paper, we look at the Bi-based materials that have the chemical formula " \
"Bi 2 Sr 2 Ca n-1 Cu n O 2n+4 (BiSCCO) where n=1, 2, 3 gives the first three members of this " \
"class: Bi 2 Sr 2 CuO 6 , Bi 2 Sr 2 CaCu 2 O 8 and Bi 2 Sr 2 Ca 2 Cu 3 O 10 , with critical " \
"temperatures ( ) T c of 20 K, 85 K and 110 K respectively."
spans = [("Bi 2 Sr 2 Ca n-1 Cu n O 2n+4 (BiSCCO)", "<material>"),
("Bi 2 Sr 2 CuO 6", "<material>"), ("Bi 2 Sr 2 CaCu 2 O 8", "<material>"),
("Bi 2 Sr 2 Ca 2 Cu 3 O 10", "<material>"),
("T c", "<tc>"), ("20 K", "<tcValue>"), ("85 K", "<tcValue>"), ("110 K", "<tcValue>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = VicinityResolutionResolver().find_relationships(doc, materials, tc_values)
assert len(relationships) == 3
assert str(relationships[0][0]) == "Bi 2 Sr 2 CuO 6"
assert str(relationships[0][1]) == "20 K"
assert str(relationships[1][0]) == "Bi 2 Sr 2 CaCu 2 O 8"
assert str(relationships[1][1]) == "85 K"
assert str(relationships[2][0]) == "Bi 2 Sr 2 Ca 2 Cu 3 O 10"
assert str(relationships[2][1]) == "110 K"
def test_vicinityResolution_1(self):
input = "It is also interesting to note that a Y-based ternary germanide, namely, Y 2 PdGe 3 , " \
"crystallized in the hexagonal AlB 2 structure, was found to be a type-II superconductor " \
"with transition temperature T C =3 K."
spans = [("Y 2 PdGe 3", "<material>"), ("AlB 2", "<material>"), ("superconductor", "<tc>"),
("T C", "<tcValue>"),
("3 K", "<tcValue>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = SimpleResolutionResolver().find_relationships(materials, tc_values)
print(relationships)
def test_markCriticalTemperature_relative_critical_temperature_3(self):
input = "The material BaClE2 has Tc at 30K higher than 77K."
spans = [("BaClE2", "<material>"), ("<tc>", "<tc>"),
("30K", "<tcValue>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 0
def test_vicinityResolution_respectively_2(self):
input = "The critical temperature T C = 4.7 K discovered for La 3 Ir 2 Ge 2 in this work is by about 1.2 K " \
"higher than that found for La 3 Rh 2 Ge 2 ."
spans = [("critical temperature", "<tc>"), ("T C", "<tc>"), ("4.7 K", "<tcValue>"),
("La 3 Ir 2 Ge 2", "<material>"),
("La 3 Rh 2 Ge 2", "<material>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = VicinityResolutionResolver().find_relationships(doc, materials, tc_values)
assert len(relationships) == 1
assert str(relationships[0][0]) == "La 3 Ir 2 Ge 2"
assert str(relationships[0][1]) == "4.7 K"
def test_markCriticalTemperature_1(self):
input = "We also plot in values of U 0 obtained from flux-creep in a BaFe 2−x Ni x As 2 crystal with " \
"similar T c for H c-axis at T = 8 K and for H ab-planes at T = 13 K."
spans = [("BaFe 2−x Ni x As 2 crystal", "<material>"), ("T c", "<tc>"),
("8 K", "<tcValue>"), ("13 K", "<tcValue>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 0
def test_vicinityResolution_respectively_missingEntities_1(self):
input = "Ba 1−x K x BiO 3−δ (BKBO) and BaPb 1−x Bi x O 3−δ (BPBO) are two such compounds that show T c 's " \
"of 30 K [1] and 13 K [2], respectively, with carrier concentrations as low as 2×10 " \
"21 cm −3 ."
spans = [("BaPb 1−x Bi x O 3−δ (BPBO)", "<material>"),
("T c", "<tc>"), ("30 K", "<tcValue>"), ("13 K", "<tcValue>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = VicinityResolutionResolver().find_relationships(doc, materials, tc_values)
assert len(relationships) == 1
assert str(relationships[0][0]) == "BaPb 1−x Bi x O 3−δ (BPBO)"
assert str(relationships[0][1]) == "30 K"
def test_markCriticalTemperature_2(self):
input = "(Color online) Effect of electron irradiation on the low-temperature penetration depth ∆λ of two " \
"samples of BaFe2(As1−xPx)2: (a) Tc0 = 28 K and (b) Tc0 = 29 K."
spans = [("BaFe2(As1−xPx)2", "<material>"), ("Tc0", "<tc>"),
("28 K", "<tcValue>"), ("Tc0", "<tc>"), ("29 K", "<tcValue>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 2
def test_markCriticalTemperature_simple_3(self):
input = "We are explaining some important notions. The material BaClE2 superconducts at 30K. What about going for a beer?"
spans = [("<tc>", "<tc>"), ("BaClE2", "<material>"),
("30K", "<tcValue>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 1
assert tcValues[0].text == "30K"
def test_markCriticalTemperature_simple_2(self):
input = "The material BaClE2 superconducts at 30K."
spans = [("BaClE2", "<material>"), ("superconducts", "<tc>"),
("30K", "<tcValue>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 1
assert tcValues[0].text == "30K"
def test_vicinityResolution_3(self):
input = "Havinga et al systematically changed n from 3.00 to 4.00 by synthesizing LaTl 3" \
" (n=3.00, T c =1.6 K), LaPb 3 (n=3.75, T c =4.1 K), and " \
"ThPb 3 (n=4.00, T c =5.6 K) and the solid solutions " \
"La (Tl 1−x Pb x ) 3 and (La 1−x Th x )Pb 3 ."
spans = [("LaTl 3", "<material>"), ("T c", "<tc>"), ("1.6 K", "<tcValue>"),
("LaPb 3", "<material>"), ("T c", "<tc>"), ("4.1 K", "<tcValue>"),
("ThPb 3", "<material>"), ("T c", "<tc>"), ("5.6 K", "<tcValue>"),
("La (Tl 1−x Pb x ) 3", "<material>"), ("(La 1−x Th x )Pb 3", "<material>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = VicinityResolutionResolver().find_relationships(doc, materials, tc_values)
assert len(relationships) == 3
def test_calculate_distances_2(self):
input = "Havinga et al systematically changed n from 3.00 to 4.00 by synthesizing LaTl 3. " \
"T c = 1.6 K is then found in LaPb 3."
spans = [("LaTl 3", "<material>"), ("T c", "<tc>"), ("1.6 K", "<tcValue>"),
("LaPb 3", "<material>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
target = VicinityResolutionResolver()
distances = target.calculate_distances(materials, tc_values, doc)
assert len(distances) == 2
assert distances[materials[0]][tc_values[0]] == 27.0
assert distances[materials[1]][tc_values[0]] == 23.5
def test_markCriticalTemperature_relative_critical_temperature_2(self):
input = "The critical temperature T C = 4.7 K discovered for La 3 Ir 2 Ge 2 in this work is by about 1.2 K " \
"higher than that found for La 3 Rh 2 Ge 2 ."
spans = [("critical temperature", "<tc>"), ("T C", "<tc>"),
("4.7 K", "<tcValue>"), ("La 3 Ir 2 Ge 2", "<material>"),
("La 3 Rh 2 Ge 2", "<material>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 1
assert tcValues[0].text == "4.7 K"
def test_markCriticalTemperature_relative_critical_temperature(self):
input = "The R versus T curves (figure 2(c) for samples B1 and B2 (with 6 wt% Ag) show that the HIP process " \
"increases T c by 0.8 K and reduces the resistance in the normal state by about 10%."
spans = [
("B1", "<material>"),
("B2 (with 6 wt% Ag)", "<material>"),
("0.8 K", "<tcValue>"),
]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 0
def test_vicinityResolution_missingOneEntity_1(self):
input = "Superconductivity has been discovered in metal diborides like MgB 2 (T c =39 K ), (Mo 0.96 Zr 0.04 ) " \
"0.85 B 2 (T c =8.2 K ), NbB 2 (T c =5.2 K [3]) and various other ternary borides ."
spans = [("MgB 2", "<material>"), ("T c", "<tc>"),
("(Mo 0.96 Zr 0.04 ) 0.85 B 2", "<material>"), ("T c", "<tc>"), ("8.2 K", "<tcValue>"),
("NbB 2", "<material>"), ("T c", "<tc>"), ("5.2 K", "<tcValue>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = VicinityResolutionResolver().find_relationships(doc, materials, tc_values)
assert len(relationships) == 2
assert str(relationships[0][0]) == "(Mo 0.96 Zr 0.04 ) 0.85 B 2"
assert str(relationships[0][1]) == "8.2 K"
assert str(relationships[1][0]) == "NbB 2"
assert str(relationships[1][1]) == "5.2 K"
def test_markCriticalTemperature_3(self):
input = "It is also worth noticing that the T C of this structure is slightly lower (about 5 K lower) than " \
"the T C for the 2×7 superlattice where the two BCO/CCO interfaces are far apart (seven unit " \
"cells of CCO) and no sizeable intralayer interaction is expected.It is also worth noticing that " \
"the T C of this structure is slightly lower (about 5 K lower) than the T C for the 2×7 " \
"superlattice where the two BCO/CCO interfaces are far apart (seven unit cells of CCO) and no " \
"sizeable intralayer interaction is expected."
spans = [("BCO/CCO", "<material>"), ("CCO)", "<material>"),
("T C", "<tc>"), ("5 K", "<tcValue>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 0
def test_find_following_entity(self):
input = "Havinga et al systematically changed n from 3.00 to 4.00 by synthesizing LaTl 3" \
" (n=3.00, T c =1.6 K), LaPb 3 (n=3.75, T c =4.1 K), and " \
"ThPb 3 (n=4.00, T c =5.6 K) and the solid solutions " \
"La (Tl 1−x Pb x ) 3 and (La 1−x Th x )Pb 3 ."
spans = [("LaTl 3", "<material>"), ("T c", "<tc>"), ("1.6 K", "<tcValue>"),
("LaPb 3", "<material>"), ("T c", "<tc>"), ("4.1 K", "<tcValue>"),
("ThPb 3", "<material>"), ("T c", "<tc>"), ("5.6 K", "<tcValue>"),
("La (Tl 1−x Pb x ) 3", "<material>"), ("(La 1−x Th x )Pb 3", "<material>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
target = VicinityResolutionResolver()
following = target.find_following_entity(materials[1], tc_values)
assert following is not None
assert following.text == "4.1 K"
all_entities = list(filter(lambda w: w.ent_type_ is not "", doc))
following = target.find_following_entity(materials[2], all_entities)
assert following is not None
assert following.text == "T c"
following = target.find_following_entity(materials[4], all_entities)
assert following is None
following = target.find_following_entity(tc_values[0], tc_values, "<material>")
assert following is None
following = target.find_following_entity(tc_values[2], all_entities, "<material>")
assert following is not None
assert following.text == "La (Tl 1−x Pb x ) 3"
def test_vicinityResolution_respectively_1(self):
input = "In the best cases a transition temperature of 38 K (zero resistance point), 25 K (zero " \
"resistance point) and 38 K (midpoint) were measured for CCO/STO, CCO/BCO and LSCO/LCO, " \
"respectively."
spans = [("38 K", "<tcValue>"), ("25 K", "<tcValue>"), ("38 K", "<tcValue>"),
("CCO/STO", "<material>"), ("CCO/BCO", "<material>"), ("LSCO/LCO", "<material>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = VicinityResolutionResolver().find_relationships(doc, materials, tc_values)
assert len(relationships) == 3
assert str(relationships[0][0]) == "CCO/STO"
assert str(relationships[0][1]) == "38 K"
assert str(relationships[1][0]) == "CCO/BCO"
assert str(relationships[1][1]) == "25 K"
assert str(relationships[2][0]) == "LSCO/LCO"
assert str(relationships[2][1]) == "38 K"
def test_markCriticalTemperature_respectively_1(self):
input = "The T C values for YBCO + BSO2%, YBCO + BSO2% + YOA, and YBCO + BSO2% + YOB fi lms are 89.7 K, 86.7 K, and 89.7 K respectively"
spans = [("T C", "<tc>"), ("YBCO + BSO2%", "<material>"),
("YBCO + BSO2% + YOA", "<material>"),
("YBCO + BSO2% + YOB", "<material>"), ("89.7 K", "<tcValue>"),
("86.7 K", "<tcValue>"), ("89.7 K", "<tcValue>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 3
assert tcValues[0].text == "89.7 K"
assert tcValues[1].text == "86.7 K"
assert tcValues[2].text == "89.7 K"
def test_markCriticalTemperature_complex_case(self):
input = "Tc varies from 2.7 K in CsFe2As2 to 38 K in A1−xKxFe2As2 (A = Ba, Sr). Meanwhile, superconductivity " \
"could also be induced in the parent phase by high pressure or by replacing some of the Fe by Co. " \
"More excitingly, large single crystals could be obtained by the Sn flux method in this family to " \
"study the rather low melting temperature and the intermetallic characteristics."
spans = [("Tc", "<tc>"), ("2.7 K", "<tcValue>"),
("CsFe2As2", "<material>"), ("38 K", "<tcValue>"),
("A1−xKxFe2As2", "<material>")]
target = CriticalTemperatureClassifier()
doc = prepare_doc(input, spans)
doc2 = target.process_doc(doc)
tcValues = [
entity for entity in filter(
lambda w: w.ent_type_ in ['<tcValue>'] and w._.linkable is
True, doc2)
]
assert len(tcValues) == 1
assert tcValues[0].text == "2.7 K"
def test_calculate_distances(self):
input = "Havinga et al systematically changed n from 3.00 to 4.00 by synthesizing LaTl 3" \
" (n=3.00, T c =1.6 K), LaPb 3 (n=3.75, T c =4.1 K), and " \
"ThPb 3 with T c =5.6 K and the solid solutions " \
"La (Tl 1−x Pb x ) 3 and (La 1−x Th x )Pb 3 ."
spans = [("LaTl 3", "<material>"), ("T c", "<tc>"), ("1.6 K", "<tcValue>"),
("LaPb 3", "<material>"), ("T c", "<tc>"), ("4.1 K", "<tcValue>"),
("ThPb 3", "<material>"), ("T c", "<tc>"), ("5.6 K", "<tcValue>"),
("La (Tl 1−x Pb x ) 3", "<material>"), ("(La 1−x Th x )Pb 3", "<material>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
target = VicinityResolutionResolver()
distances = target.calculate_distances(materials, tc_values, doc)
assert len(distances) == 5
assert distances[materials[0]][tc_values[0]] == 7.5
assert distances[materials[1]][tc_values[1]] == 7.5
assert distances[materials[2]][tc_values[2]] == 18
def test_vicinityResolution_4(self):
input = "The investigated MnSi films are in a thickness regime where the magnetic transition " \
"temperature T c assumes a thickness-independent enhanced value of 43 K as compared with " \
"that of bulk MnSi, where T c ≈ 29 K. A detailed refinement of the EXAFS data reveals that " \
"the Mn positions are unchanged, whereas the Si positions vary along the out-of-plane " \
"direction, alternating in orientation from unit cell to unit cell."
spans = [("MnSi films", "<material>"), ("T c", "<tc>"), ("43 K", "<tcValue>"),
("MnSi", "<material>"), ("T c", "<tc>"), ("29 K", "<tcValue>")]
doc = prepare_doc(input, spans)
materials = [entity for entity in filter(lambda w: w.ent_type_ in ['<material>'], doc)]
tc_values = [entity for entity in filter(lambda w: w.ent_type_ in ['<tcValue>'], doc)]
relationships = VicinityResolutionResolver().find_relationships(doc, materials, tc_values)
assert len(relationships) == 2
assert str(relationships[0][0]) == "MnSi films"
assert str(relationships[0][1]) == "43 K"
assert str(relationships[1][0]) == "MnSi"
assert str(relationships[1][1]) == "29 K"
