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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 16-36 Disease denotes SARS-CoV-2 pneumonia MESH:C000657245
6 139-149 Species denotes SARS-CoV-2 Tax:2697049
7 433-443 Species denotes SARS-CoV-2 Tax:2697049
8 79-109 Disease denotes 2019-novel coronavirus disease MESH:C000657245
9 111-119 Disease denotes COVID-19 MESH:C000657245
30 461-483 Species denotes 2019-novel coronavirus Tax:2697049
31 485-495 Species denotes SARS-CoV-2 Tax:2697049
32 921-927 Species denotes people Tax:9606
33 977-982 Species denotes human Tax:9606
34 986-991 Species denotes human Tax:9606
35 1240-1250 Species denotes SARS-CoV-2 Tax:2697049
36 1386-1394 Species denotes patients Tax:9606
37 1595-1605 Species denotes SARS-CoV-2 Tax:2697049
38 518-527 Disease denotes pneumonia MESH:D011014
39 529-537 Disease denotes COVID-19 MESH:C000657245
40 837-858 Disease denotes SARS-CoV-2 infections MESH:C000657245
41 933-937 Disease denotes died MESH:D003643
42 949-957 Disease denotes COVID-19 MESH:C000657245
43 1115-1124 Disease denotes pneumonia MESH:D011014
44 1308-1313 Disease denotes Fever MESH:D005334
45 1315-1324 Disease denotes dry cough MESH:D003371
46 1330-1337 Disease denotes fatigue MESH:D005221
47 1370-1378 Disease denotes COVID-19 MESH:C000657245
48 1400-1411 Disease denotes lymphopenia MESH:D008231
49 1565-1578 Disease denotes viral disease MESH:D001102
52 3684-3690 Species denotes humans Tax:9606
53 3717-3725 Disease denotes toxicity MESH:D064420
64 1900-1904 Gene denotes Hu-1 Gene:3215
65 1882-1892 Species denotes SARS-CoV-2 Tax:2697049
66 2063-2073 Species denotes SARS-CoV-2 Tax:2697049
67 2379-2389 Species denotes SARS-CoV-2 Tax:2697049
68 2782-2792 Species denotes SARS-CoV-2 Tax:2697049
69 1851-1860 Species denotes influenza Tax:11320
70 2234-2246 Chemical denotes formaldehyde MESH:D005557
71 2252-2267 Chemical denotes β-propiolactone MESH:D011420
72 2440-2451 Disease denotes lung injury MESH:D055370
73 2013-2023 CellLine denotes MN908947.3 CVCL:U508
99 4547-4548 Gene denotes E Gene:43740570
100 4551-4559 Gene denotes membrane Gene:43740571
101 4561-4562 Gene denotes M Gene:43740571
102 4579-4580 Gene denotes N Gene:43740575
103 4587-4592 Gene denotes spike Gene:43740568
104 4594-4595 Gene denotes S Gene:43740568
105 4691-4694 Gene denotes CD4 Gene:920
106 4696-4699 Gene denotes CD8 Gene:925
107 4565-4577 Gene denotes nucleocapsid Gene:43740575
108 3895-3905 Species denotes SARS-CoV-2 Tax:2697049
109 4144-4154 Species denotes SARS-CoV-2 Tax:2697049
110 4176-4184 Species denotes SARS-CoV Tax:694009
111 4189-4244 Species denotes Middle East respiratory syndrome coronavirus (MERS-CoV) Tax:1335626
112 4488-4498 Species denotes SARS-CoV-2 Tax:2697049
113 4848-4857 Disease denotes hepatitis MESH:D056486
114 3948-3958 CellLine denotes MN908947.3 CVCL:U508
115 3960-3970 CellLine denotes MN975262.1 CVCL:U508
116 3985-3995 CellLine denotes MN997409.1 CVCL:U508
117 3997-4007 CellLine denotes MN985325.1 CVCL:U508
118 4009-4019 CellLine denotes MN988669.1 CVCL:U508
119 4021-4031 CellLine denotes MN988668.1 CVCL:U508
120 4033-4043 CellLine denotes MN994468.1 CVCL:U508
121 4045-4055 CellLine denotes MN994467.1 CVCL:U508
122 4057-4067 CellLine denotes MN988713.1 CVCL:U508
123 4073-4083 CellLine denotes MN938384.1 CVCL:U508
152 6731-6762 Gene denotes angiotensin-converting enzyme 2 Gene:59272
153 6764-6768 Gene denotes ACE2 Gene:59272
154 6052-6053 Gene denotes S Gene:43740568
155 5986-5987 Gene denotes S Gene:43740568
156 5371-5382 Species denotes coronavirus Tax:11118
157 5491-5495 Species denotes CoVs Tax:11118
158 5560-5568 Species denotes SARS-CoV Tax:694009
159 5572-5580 Species denotes MERS-CoV Tax:1335626
160 5727-5735 Species denotes SARS-CoV Tax:694009
161 5779-5782 Species denotes CoV Tax:11118
162 5905-5915 Species denotes SARS-CoV-2 Tax:2697049
163 5991-6001 Species denotes SARS-CoV-2 Tax:2697049
164 6075-6085 Species denotes SARS-CoV-2 Tax:2697049
165 6201-6211 Species denotes SARS-CoV-2 Tax:2697049
166 6261-6270 Species denotes SARS-CoVs Tax:694009
167 6570-6587 Species denotes influenza A virus Tax:11320
168 6800-6809 Species denotes 2019-nCoV Tax:2697049
169 6849-6854 Species denotes human Tax:9606
170 6855-6864 Species denotes SARS-CoVs Tax:694009
171 7337-7346 Species denotes SARS-CoVs Tax:694009
172 7396-7417 Species denotes African green monkeys Tax:9534
173 7452-7460 Species denotes SARS-CoV Tax:694009
174 7505-7513 Species denotes SARS-CoV Tax:694009
175 7543-7551 Species denotes SARS-CoV Tax:694009
176 7736-7746 Species denotes SARS-CoV-2 Tax:2697049
177 6450-6459 Species denotes influenza Tax:11320
178 5947-5956 Disease denotes infection MESH:D007239
179 7139-7154 Disease denotes viral infection MESH:D001102
184 8433-8441 Gene denotes membrane Gene:43740571
185 8090-8100 Species denotes SARS-CoV-2 Tax:2697049
186 8232-8242 Species denotes SARS-CoV-2 Tax:2697049
187 8023-8050 Disease denotes respiratory tract infection MESH:D012141
193 8760-8762 Gene denotes S1
194 8965-8968 Gene denotes GSK
195 8797-8807 Species denotes SARS-CoV-2 Tax:2697049
196 9373-9383 Species denotes SARS-CoV-2 Tax:2697049
197 8624-8632 Disease denotes COVID-19 MESH:C000657245
199 9826-9827 Gene denotes S Gene:43740568

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1458-1463 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T2 2440-2444 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T3 2472-2482 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T4 2523-2531 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T5 3579-3582 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T6 3729-3733 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T7 3906-3913 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T8 4293-4296 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T9 4310-4316 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T10 4335-4346 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T11 4519-4527 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T12 4610-4618 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T13 4703-4707 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T14 4962-4965 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T15 4970-4974 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T16 5310-5318 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T17 5394-5401 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T18 5425-5428 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 5456-5463 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 5598-5605 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T21 5646-5653 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T22 5699-5706 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T23 5707-5710 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T24 5764-5771 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T25 5894-5901 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T26 5973-5985 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T27 6064-6071 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 6169-6176 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T29 6309-6316 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T30 6402-6412 Body_part denotes Antibodies http://purl.org/sig/ont/fma/fma62871
T31 6708-6713 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T32 6789-6796 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T33 6902-6913 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T34 7228-7235 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T35 7264-7272 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T36 7441-7448 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T37 7556-7564 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T38 8023-8040 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T39 8272-8275 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T40 8302-8305 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T41 8763-8770 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T42 9403-9407 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1458-1463 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T2 2046-2051 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 2440-2444 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T4 8023-8040 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 27-36 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 518-527 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 1115-1124 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T4 1308-1313 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945
T5 1315-1324 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T6 1330-1337 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T7 1400-1411 Phenotype denotes lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T8 4848-4857 Phenotype denotes hepatitis http://purl.obolibrary.org/obo/HP_0012115
T9 8023-8050 Phenotype denotes respiratory tract infection http://purl.obolibrary.org/obo/HP_0011947

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p10944s31 2453-2463 NegReg denotes diminished
p10944s33 2472-2489 CPA denotes neutrophil influx
p10944s41 2523-2543 MPA denotes cytokine expressions
p10963s4 5464-5473 NegReg denotes abrogated
p10963s6 5478-5487 MPA denotes virulence

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 16-24 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 27-36 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T3 111-119 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 139-147 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 433-441 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 485-493 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 518-527 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T8 529-537 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 837-845 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 848-858 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T11 949-957 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 1115-1124 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T13 1240-1248 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 1400-1411 Disease denotes lymphopenia http://purl.obolibrary.org/obo/MONDO_0003783
T15 1565-1578 Disease denotes viral disease http://purl.obolibrary.org/obo/MONDO_0005108
T16 1595-1603 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 1851-1860 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T18 1882-1890 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 2063-2071 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 2379-2387 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 2445-2451 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T22 2782-2790 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 3895-3903 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 4144-4152 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 4176-4184 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 4488-4496 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 4848-4859 Disease denotes hepatitis B http://purl.obolibrary.org/obo/MONDO_0005344
T28 4848-4857 Disease denotes hepatitis http://purl.obolibrary.org/obo/MONDO_0002251
T29 5560-5568 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 5727-5735 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 5905-5913 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 5991-5999 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 6075-6083 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 6201-6209 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 6261-6265 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T36 6450-6459 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T37 6570-6579 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T38 6855-6859 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T39 7139-7154 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T40 7145-7154 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T41 7165-7169 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T42 7337-7341 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T43 7452-7460 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 7505-7513 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 7543-7551 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 7736-7744 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 8023-8050 Disease denotes respiratory tract infection http://purl.obolibrary.org/obo/MONDO_0024355
T48 8041-8050 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T49 8090-8098 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 8232-8240 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 8624-8632 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T52 8797-8805 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 9373-9381 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 150-153 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T2 183-186 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T3 203-204 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 539-542 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T5 586-589 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T6 808-809 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T7 974-982 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes by human
T8 986-991 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T9 1010-1011 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 1299-1300 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 1458-1463 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T12 1550-1551 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1654-1659 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T14 1737-1742 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T15 2116-2121 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T16 2300-2305 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T17 2440-2444 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T18 2440-2444 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T19 2612-2617 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T20 2760-2768 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T21 2950-2955 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T22 3103-3108 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T23 3684-3690 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T24 4114-4119 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T25 4297-4302 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T26 4308-4309 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 4479-4480 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T28 4499-4502 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T29 4551-4559 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T30 4691-4694 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T31 4696-4699 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T32 4701-4707 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T33 4858-4859 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T34 4937-4943 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T35 5369-5370 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 5586-5587 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 5815-5816 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 6021-6026 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T39 6122-6124 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T40 6130-6132 http://purl.obolibrary.org/obo/CLO_0001627 denotes aa
T41 6138-6140 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T42 6138-6140 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T43 6146-6148 http://purl.obolibrary.org/obo/CLO_0001627 denotes aa
T44 6166-6168 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T45 6166-6168 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T46 6212-6219 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T47 6257-6260 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T48 6306-6308 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T49 6306-6308 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T50 6376-6383 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T51 6387-6393 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T52 6580-6581 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T53 6608-6610 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T54 6681-6686 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T55 6708-6713 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T56 6786-6788 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T57 6849-6854 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T58 7019-7024 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T59 7079-7080 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 7081-7086 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T61 7102-7103 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 7298-7299 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 7410-7417 http://purl.obolibrary.org/obo/NCBITaxon_9479 denotes monkeys
T64 7470-7477 http://purl.obolibrary.org/obo/NCBITaxon_9479 denotes monkeys
T65 7656-7662 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T66 7722-7724 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T67 7815-7821 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T68 8012-8013 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 8265-8266 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T70 8332-8337 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T71 8406-8414 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T72 8433-8441 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T73 8567-8572 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T74 8660-8665 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T75 8760-8762 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T76 9006-9007 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 9151-9152 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 9367-9368 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 9403-9407 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T80 9429-9436 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 276-285 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T2 377-385 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T3 1489-1498 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T4 2234-2246 Chemical denotes formaldehyde http://purl.obolibrary.org/obo/CHEBI_16842
T5 2752-2759 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T6 2760-2768 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T7 3440-3449 Chemical denotes adjuvants http://purl.obolibrary.org/obo/CHEBI_60809
T8 3579-3582 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T9 4335-4346 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T10 4519-4527 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T11 4610-4618 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T12 4632-4640 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T13 4792-4801 Chemical denotes adjuvants http://purl.obolibrary.org/obo/CHEBI_60809
T14 4868-4875 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T15 4962-4965 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T16 5235-5243 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T17 5310-5318 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T18 5394-5401 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T19 5456-5463 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T20 5598-5605 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T21 5646-5653 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T22 5699-5706 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T23 5707-5710 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T24 5764-5771 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T25 5894-5901 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T26 5973-5985 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T27 6064-6071 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T28 6138-6140 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T29 6166-6168 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T30 6169-6176 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T31 6306-6308 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T32 6309-6316 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T33 6346-6355 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T34 6731-6742 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T35 6789-6796 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T36 6902-6913 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T37 6902-6907 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T38 6908-6913 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T39 7228-7235 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T40 7441-7448 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T41 7556-7564 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T42 7989-7998 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T43 8272-8275 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T44 8302-8305 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T45 8763-8770 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T46 8906-8915 Chemical denotes adjuvants http://purl.obolibrary.org/obo/CHEBI_60809
T47 8924-8928 Chemical denotes alum http://purl.obolibrary.org/obo/CHEBI_74768
T48 8943-8952 Chemical denotes adjuvants http://purl.obolibrary.org/obo/CHEBI_60809
T49 8982-8991 Chemical denotes adjuvants http://purl.obolibrary.org/obo/CHEBI_60809
T50 9787-9790 Chemical denotes PLA http://purl.obolibrary.org/obo/CHEBI_53407|http://purl.obolibrary.org/obo/CHEBI_60159

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2403-2415 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis
T2 3149-3165 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses
T3 3319-3343 http://purl.obolibrary.org/obo/GO_0006959 denotes humoral immune responses
T4 3512-3536 http://purl.obolibrary.org/obo/GO_0006959 denotes humoral immune responses
T5 3664-3680 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses
T6 3804-3820 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses
T7 4417-4426 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T8 5351-5365 http://purl.obolibrary.org/obo/GO_0019068 denotes viral assembly
T9 5478-5487 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T10 5478-5487 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence
T11 5670-5685 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T12 7139-7154 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection
T13 8181-8205 http://purl.obolibrary.org/obo/GO_0002385 denotes mucosal immune responses
T14 9267-9283 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-61 Sentence denotes The outbreak of SARS-CoV-2 pneumonia calls for viral vaccines
T2 63-254 Sentence denotes The outbreak of 2019-novel coronavirus disease (COVID-19) that is caused by SARS-CoV-2 has spread rapidly in China, and has developed to be a Public Health Emergency of International Concern.
T3 255-327 Sentence denotes However, no specific antiviral treatments or vaccines are available yet.
T4 328-444 Sentence denotes This work aims to share strategies and candidate antigens to develop safe and effective vaccines against SARS-CoV-2.
T5 446-633 Sentence denotes An outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes atypical pneumonia (COVID-19) has raged in China since mid-December 2019 and has spread to 26 countries (February 20, 2020).
T6 634-807 Sentence denotes The epidemic was identified by the first four cases confirmed on December 29, 2019 and was traced to the Huanan Seafood Wholesale Market, Wuhan city, Hubei Province, China1.
T7 808-948 Sentence denotes A total of 75,465 cases with SARS-CoV-2 infections have been confirmed up to date (February 20, 2020), and 2,236 people have died in China2.
T8 949-1158 Sentence denotes COVID-19 spreads rapidly by human-to-human transmission with a median incubation period of 3.0 days (range, 0 to 24.0), and the time from symptom onset to developing pneumonia is 4.0 days (range, 2.0 to 7.0)3.
T9 1159-1307 Sentence denotes Respiratory droplets and direct contact are conventional transmission routes for SARS-CoV-2, and fecal-to-oral transmission might also have a role3.
T10 1308-1380 Sentence denotes Fever, dry cough, and fatigue are common symptoms at onset of COVID-194.
T11 1381-1476 Sentence denotes Most patients have lymphopenia and bilateral ground-glass opacity changes on chest CT scans4,5.
T12 1477-1579 Sentence denotes No specific antiviral treatments or vaccines are available because it is a new emerging viral disease.
T13 1580-1642 Sentence denotes Development of SARS-CoV-2-based vaccines is urgently required.
T14 1643-1871 Sentence denotes The entire virus particle-based preparation of vaccines, including inactivated and attenuated virus vaccines is advisable, because it is based on previous studies about the prevention and control of seasonal influenza vaccines6.
T15 1872-2012 Sentence denotes The first SARS-CoV-2 (Wuhan-Hu-1) was successfully sequenced and its genomic sequence submitted to GenBank on January 5, 2020 (Accession no.
T16 2013-2026 Sentence denotes MN908947.3)7.
T17 2027-2269 Sentence denotes Subsequently large-scale culture of SARS-CoV-2 was quickly performed, and an inactivated virus vaccine could be prepared through the employment of established physical and chemical methods such as UV light, formaldehyde, and β-propiolactone8.
T18 2270-2579 Sentence denotes The development of attenuated-virus vaccines is also possible by carefully screening the serially propagated SARS-CoV-2 with reduced pathogenesis such as induced minimal lung injury, diminished limited neutrophil influx, and increased anti-inflammatory cytokine expressions compared with the wild-type virus9.
T19 2580-2683 Sentence denotes Both inactivated and attenuated virus vaccines have their own disadvantages and side effects (Table 1).
T20 2684-2814 Sentence denotes Alternatively, new vaccine designs based on the putative protective antigen/peptides derived from SARS-CoV-2 should be considered.
T21 2815-2884 Sentence denotes Table 1 Advantages and disadvantages of different vaccine strategies.
T22 2885-2937 Sentence denotes Vaccine strategy Advantages Disadvantages References
T23 2938-3091 Sentence denotes Inactivated virus vaccines Easy to prepare; safety; high-titer neutralizing antibodies Potential inappropriate for highly immunosuppressed individuals 25
T24 3092-3241 Sentence denotes Attenuated virus vaccines Rapid development; induce high immune responses Phenotypic or genotypic reversion possible; can still cause some disease 25
T25 3242-3455 Sentence denotes Subunit vaccines High safety; consistent production; can induce cellular and humoral immune responses; high-titer neutralizing antibodies High cost; lower immunogenicity; require repeated doses and adjuvants 12,14
T26 3456-3578 Sentence denotes Viral vector vaccines Safety; induces high cellular and humoral immune responses Possibly present pre-existing immunity 12
T27 3579-3728 Sentence denotes DNA vaccines Easier to design; high safety; high-titer neutralizing antibodies Lower immune responses in humans; repeated doses may cause toxicity 23
T28 3729-3870 Sentence denotes mRNA vaccines Easier to design; high degree of adaptability; induce strong immune responses Highly unstable under physiological conditions 23
T29 3871-4143 Sentence denotes Accumulated releases of SARS-CoV-2 genomes such as GenBank accession numbers MN908947.3, MN975262.1, NC_045512.2, MN997409.1, MN985325.1, MN988669.1, MN988668.1, MN994468.1, MN994467.1, MN988713.1, and MN938384.1 facilitate the development of virus-based subunit vaccines.
T30 4144-4478 Sentence denotes SARS-CoV-2, which is similar to SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), is an enveloped, single- and positive-stranded RNA virus with a genome comprising 29,891 nucleotides, which encode the 12 putative open reading frames responsible for the synthesis of viral structural and nonstructural proteins7,10.
T31 4479-4599 Sentence denotes A mature SARS-CoV-2 has four structural proteins, namely, envelope (E), membrane (M), nucleocapsid (N), and spike (S)10.
T32 4600-4721 Sentence denotes All these proteins may serve as antigens to stimulate neutralizing antibodies and increase CD4+/CD8+ T-cell responses8,9.
T33 4722-4957 Sentence denotes However, subunit vaccines require multiple booster shots and suitable adjuvants to work, and certain subunit vaccines such as hepatitis B surface antigen, PreS1, and PreS2 may fail to yield protective response when tested clinically11.
T34 4958-5076 Sentence denotes The DNA and mRNA vaccines that are easier to design and proceed into clinical trials very quickly remain experimental.
T35 5077-5174 Sentence denotes The viral vector-based vaccines could also be quickly constructed and used without an adjuvant12.
T36 5175-5297 Sentence denotes However, development of such vaccines might not start until antigens containing the neutralizing epitopes are identified8.
T37 5298-5441 Sentence denotes The E and M proteins have important functions in the viral assembly of a coronavirus, and the N protein is necessary for viral RNA synthesis13.
T38 5442-5639 Sentence denotes Deletion of E protein abrogated the virulence of CoVs, and several studies have explored the potential of recombinant SARS-CoV or MERS-CoV with a mutated E protein as live attenuated vaccines13,14.
T39 5640-5959 Sentence denotes The M protein can augment the immune response induced by N protein DNA vaccine against SARS-CoV;15 however, the conserved N protein across CoV families implies that it is not a suitable candidate for vaccine development, and the antibodies against the N protein of SARS-CoV-2 do not provide immunity to the infection16.
T40 5960-6047 Sentence denotes The critical glycoprotein S of SARS-CoV-2 is responsible for virus binding and entry16.
T41 6048-6161 Sentence denotes The S precursor protein of SARS-CoV-2 can be proteolytically cleaved into S1 (685 aa) and S2 (588 aa) subunits10.
T42 6162-6273 Sentence denotes The S2 protein is well conserved among SARS-CoV-2 viruses and shares 99% identity with that of bat SARS-CoVs10.
T43 6274-6401 Sentence denotes The vaccine design based on the S2 protein may boost the broad-spectrum antiviral effect and is worth testing in animal models.
T44 6402-6590 Sentence denotes Antibodies against the conserved stem region of influenza hemagglutinin have been found to exhibit broadly cross-reactive immunity, but are less potent in neutralizing influenza A virus17.
T45 6591-6781 Sentence denotes In contrast, the S1 subunit consists of the receptor-binding domain (RBD), which mediates virus entry into sensitive cells through the host angiotensin-converting enzyme 2 (ACE2) receptor18.
T46 6782-6865 Sentence denotes The S1 protein of 2019-nCoV shares about 70% identity with that of human SARS-CoVs.
T47 6866-7048 Sentence denotes The highest number of variations of amino acids in the RBD is located in the external subdomain, which is responsible for the direct interaction between virus and host receptor10,18.
T48 7049-7155 Sentence denotes Blocking the initial entry of a virus is proposed as a successful strategy in controlling viral infection.
T49 7156-7349 Sentence denotes Based on SARS vaccine development, most vaccine candidates target the S protein, which induces neutralizing antibody responses and stimulates a protective cellular immunity against SARS-CoVs12.
T50 7350-7524 Sentence denotes Bukreyev et al.19 showed that immunization of African green monkeys with the full-length S protein of SARS-CoV protects monkeys from subsequent homologous SARS-CoV challenge.
T51 7525-7672 Sentence denotes Administration of SARS-CoV RBD proteins can also induce highly potent neutralizing antibodies and long-term protective immunity in animal models20.
T52 7673-7874 Sentence denotes Thus, the generation of antibodies targeting the S1 subunit of SARS-CoV-2 would be an important preventive and treatment strategy that can be tested further in suitable models before clinical trials10.
T53 7875-8008 Sentence denotes Vaccine delivery modality and immunization strategy are important issues to be considered for achieving effective antiviral immunity.
T54 8009-8264 Sentence denotes As a cause of respiratory tract infection and as demonstrated by the findings of SARS-CoV-2 in stools1,21, administration of vaccines by oral or aerosol routes will induce mucosal immune responses and are possible modes of SARS-CoV-2 vaccine immunization.
T55 8265-8547 Sentence denotes A safe DNA vector for preparation of DNA vaccines22, an attenuated virus strain for design of chimeric viral vaccines23, and engineered safe bacteria for production of membrane vesicle-vaccines24 could be explored for vaccine delivery and are worth investigating in the near future.
T56 8548-8633 Sentence denotes We can assume that virus-based vaccines should prove valuable in combatting COVID-19.
T57 8634-8854 Sentence denotes In addition to the entire virus particle-associated inactivated or attenuated viral vaccines, the subunit candidates, such as S1 protein and/or the RBD element of SARS-CoV-2, are also valuable targets for vaccine design.
T58 8855-9147 Sentence denotes Combining subunit vaccines with established or new adjuvants such as alum versus modern adjuvants such as the GSK AS series of adjuvants may represent a faster and safer strategy to move through early clinical development with the caveat that the protective efficacy may not be strong enough.
T59 9148-9305 Sentence denotes As a result, immunizing the subunit vaccines with proper delivery platforms and immunization strategies to enhance the immune responses should be considered.
T60 9306-9466 Sentence denotes We expect researchers who are racing against time will bring a new SARS-CoV-2-based vaccine from gene sequence to clinical testing in approximately 16–20 weeks.
T61 9468-9603 Sentence denotes Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
T62 9605-9621 Sentence denotes Acknowledgements
T63 9622-9801 Sentence denotes This work was supported by the National Key Biosafety Technology Research and Development Program of China (2017YFC1200404-4), and the Biosafety Research Program of PLA (17SAZ08).
T64 9803-9823 Sentence denotes Author contributions
T65 9824-9896 Sentence denotes W.S. and Y.R. wrote the manuscript: Y.Y. and X.R. edited the manuscript.
T66 9898-9917 Sentence denotes Competing interests
T67 9918-9961 Sentence denotes The authors declare no competing interests.