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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 57-64 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T2 331-338 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 465-472 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T4 580-587 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T5 699-706 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T6 724-731 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T7 935-942 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T8 1067-1074 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T9 1179-1186 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T10 1261-1268 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T11 1348-1355 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T12 1414-1421 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T13 1454-1459 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 36-44 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 103-111 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T3 166-174 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 318-326 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 848-856 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 1470-1478 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 127-136 http://purl.obolibrary.org/obo/BFO_0000030 denotes OBJECTIVE
T2 185-188 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T3 257-260 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T4 660-662 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T5 992-993 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 1114-1116 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T7 1454-1459 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T8 1511-1512 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T9 1067-1074 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T1 57-64 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T2 331-338 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T3 465-472 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T4 580-587 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T5 660-662 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T6 699-706 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T7 724-731 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T8 935-942 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T10 1114-1116 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T11 1179-1186 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T12 1261-1268 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T13 1348-1355 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T14 1414-1421 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
6 27-32 Gene denotes Furin Gene:5045
7 36-46 Species denotes SARS-CoV-2 Tax:2697049
8 47-52 Gene denotes spike Gene:43740568
9 54-55 Gene denotes S Gene:43740568
10 65-70 Mutation denotes D614G p.D614G
11 103-113 Species denotes SARS-CoV-2 Tax:2697049
39 142-164 Disease denotes coronavirus disease-19 MESH:C000657245
40 166-174 Disease denotes COVID-19 MESH:C000657245
41 219-224 Disease denotes death MESH:D003643
42 299-305 Mutation denotes D614 G p.D614G
43 318-328 Species denotes SARS-CoV-2 Tax:2697049
44 329-338 Gene denotes S-protein Gene:43740568
45 399-405 Mutation denotes D614 G p.D614G
46 463-472 Gene denotes S-protein Gene:43740568
47 548-553 Gene denotes furin Gene:5045
48 578-587 Gene denotes S-protein Gene:43740568
49 697-706 Gene denotes S-protein Gene:43740568
50 722-731 Gene denotes S-protein Gene:43740568
51 732-737 Gene denotes furin Gene:5045
52 814-820 Mutation denotes D614 G p.D614G
53 848-858 Species denotes SARS-CoV-2 Tax:2697049
54 933-942 Gene denotes S-protein Gene:43740568
55 1041-1046 Gene denotes furin Gene:5045
56 1065-1074 Gene denotes S-protein Gene:43740568
57 1168-1173 Gene denotes furin Gene:5045
58 1177-1186 Gene denotes S-protein Gene:43740568
59 1259-1268 Gene denotes S-protein Gene:43740568
60 1288-1294 Mutation denotes D614 G p.D614G
61 1346-1355 Gene denotes S-protein Gene:43740568
62 1380-1385 Gene denotes furin Gene:5045
63 1412-1421 Gene denotes S-protein Gene:43740568
64 1470-1480 Species denotes SARS-CoV-2 Tax:2697049
65 1481-1487 Mutation denotes D614 G p.D614G

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-126 Sentence denotes Higher binding affinity of Furin to SARS-CoV-2 spike (S) protein D614G could be associated with higher SARS-CoV-2 infectivity.
T2 127-137 Sentence denotes OBJECTIVE:
T3 138-252 Sentence denotes The coronavirus disease-19 (COVID-19) pandemic has caused an exponential rise in death rates and hospitalizations.
T4 253-375 Sentence denotes The aim of this study was to characterize the D614 G mutation of SARS-CoV-2 S-protein, which may affect viral infectivity.
T5 376-384 Sentence denotes METHODS:
T6 385-510 Sentence denotes The effect of D614 G mutation on the structure and thermodynamic stability of S-protein was analyzed using DynaMut and SCooP.
T7 511-640 Sentence denotes HDOCK and PRODIGY were used to model furin protease binding to the S-protein RARR cleavage site and calculate binding affinities.
T8 641-800 Sentence denotes Molecular dynamic (MD) simulations were used to predict S-protein apo structure, S-protein-furin complex structure, and the free binding energy of the complex.
T9 801-809 Sentence denotes RESULTS:
T10 810-966 Sentence denotes The D614 G mutation in the G clade of SARS-CoV-2 strains introduced structural mobility and decreased thermal stability of S-protein (ΔΔG: -0.086 kcal/mol).
T11 967-1084 Sentence denotes The mutation resulted in a stronger binding affinity (Kd = 1.6 × 10-8) to furin which may enhance S-protein cleavage.
T12 1085-1270 Sentence denotes Results were corroborated by MD simulations demonstrating higher binding energy of furin to S-protein D614 mutant (-61.9 kcal/mol compared with -56.78 kcal/mol for wild-type S-protein).
T13 1271-1283 Sentence denotes CONCLUSIONS:
T14 1284-1460 Sentence denotes The D614 G mutation in the G clade induced the flexibility of S-protein, resulting in increased furin binding which may enhance S-protein cleave and infiltration of host cells.
T15 1461-1534 Sentence denotes As such, SARS-CoV-2 D614 G mutation may result in a more virulent strain.

LitCovid_AGAC_only

Id Subject Object Predicate Lexical cue
p237582s9 299-303 Var denotes D614
p237582s10 303-304 Var denotes  
p237582s24 346-352 Reg denotes may af
p237587s1 814-818 Var denotes D614
p237587s2 818-819 Var denotes  
p237587s15 859-869 PosReg denotes strains in
p237587s16 867-877 MPA denotes introduced
p237587s17 878-886 MPA denotes structur
p237587s19 898-907 NegReg denotes and decre
p237587s20 902-946 MPA denotes decreased thermal stability of S-protein (ΔΔ
p237589s1 971-979 Var denotes mutation
p237589s2 980-991 Reg denotes resulted in
p237589s5 994-1002 PosReg denotes stronger
p237589s6 1003-1019 MPA denotes binding affinity
p237592s7 1143-1149 PosReg denotes higher
p237592s8 1150-1157 MPA denotes binding
p237594s1 1288-1292 Var denotes D614
p237594s2 1292-1293 Var denotes  
p237594s8 1313-1320 PosReg denotes clade i
p237594s10 1327-1338 MPA denotes the flexibi
p237594s12 1343-1354 Protein denotes of S-protei
p237594s18 1367-1376 PosReg denotes in increa
p237594s19 1370-1375 Protein denotes incre
p237594s20 1380-1387 MPA denotes furin b
p237594s23 1400-1407 PosReg denotes may enh
p237594s24 1404-1405 Protein denotes e
p237594s25 1412-1420 Protein denotes S-protei
p237594s27 1414-1420 CPA denotes protei
p237594s30 1433-1454 CPA denotes infiltration of host