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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 21-29 Disease denotes COVID-19 MESH:C000657245
9 95-142 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
10 144-154 Species denotes SARS-CoV-2 Tax:2697049
11 245-255 Species denotes SARS-CoV-2 Tax:2697049
12 213-221 Disease denotes COVID-19 MESH:C000657245
13 230-239 Disease denotes Infection MESH:D007239
14 577-594 Disease denotes pulmonary disease MESH:D008171
15 652-660 Disease denotes COVID-19 MESH:C000657245
25 1009-1016 Species denotes patient Tax:9606
26 1173-1186 Chemical denotes emtricitabine MESH:D000068679
27 1191-1212 Chemical denotes tenofovir alafenamide MESH:C442442
28 1316-1345 Chemical denotes tenofovir disoproxil fumarate MESH:D000068698
29 1350-1363 Chemical denotes emtricitabine MESH:D000068679
30 1423-1434 Chemical denotes oseltamivir MESH:D053139
31 829-834 Disease denotes fever MESH:D005334
32 836-841 Disease denotes cough MESH:D003371
33 847-855 Disease denotes dyspnoea MESH:D004417
35 3360-3398 Disease denotes new right upper lobe nodular opacities MESH:D003318
50 2370-2372 Gene denotes μL Gene:4591
51 2907-2909 Gene denotes μL Gene:4591
52 1660-1667 Species denotes patient Tax:9606
53 2316-2323 Species denotes patient Tax:9606
54 2533-2540 Species denotes patient Tax:9606
55 2775-2785 Species denotes SARS-CoV-2 Tax:2697049
56 2855-2865 Species denotes SARS-CoV-2 Tax:2697049
57 1994-2000 Chemical denotes Oxygen MESH:D010100
58 2157-2167 Chemical denotes vancomycin MESH:D014640
59 2195-2206 Chemical denotes ceftriaxone MESH:D002443
60 2954-2966 Chemical denotes azithromycin MESH:D017963
61 1687-1692 Disease denotes fever MESH:D005334
62 1710-1719 Disease denotes dry cough MESH:D003371
63 1725-1744 Disease denotes shortness of breath MESH:D004417
86 3952-3959 Species denotes patient Tax:9606
87 4124-4131 Species denotes patient Tax:9606
88 4700-4710 Species denotes SARS-CoV-2 Tax:2697049
89 4044-4056 Chemical denotes azithromycin MESH:D017963
90 4182-4194 Chemical denotes azithromycin MESH:D017963
91 4238-4249 Chemical denotes clindamycin MESH:D002981
92 4790-4796 Chemical denotes oxygen MESH:D010100
93 4874-4884 Chemical denotes prednisone MESH:D011241
94 5224-5237 Chemical denotes galactomannan MESH:C012990
95 3999-4004 Disease denotes cough MESH:D003371
96 4009-4017 Disease denotes dyspnoea MESH:D004417
97 4080-4085 Disease denotes fever MESH:D005334
98 4160-4168 Disease denotes coughing MESH:D003371
99 4629-4638 Disease denotes pneumonia MESH:D011014
100 4741-4746 Disease denotes cough MESH:D003371
101 4769-4774 Disease denotes fever MESH:D005334
102 4979-4988 Disease denotes pneumonia MESH:D011014
103 5104-5129 Disease denotes invasive fungal infection MESH:D000072742
104 5192-5200 Disease denotes COVID-19 MESH:C000657245
105 5406-5414 Disease denotes COVID-19 MESH:C000657245
106 5481-5489 Disease denotes COVID-19 MESH:C000657245
107 5514-5531 Disease denotes pulmonary disease MESH:D008171
112 6234-6244 Species denotes SARS-CoV-2 Tax:2697049
113 6184-6197 Chemical denotes galactomannan MESH:C012990
114 5645-5653 Disease denotes COVID-19 MESH:C000657245
115 5713-5725 Disease denotes inflammation MESH:D007249
119 7701-7713 Chemical denotes haematoxylin MESH:D006416
120 7714-7719 Chemical denotes eosin MESH:D004801
121 7546-7568 Disease denotes pneumocyte hyperplasia MESH:D006965
138 7020-7030 Species denotes SARS-CoV-2 Tax:2697049
139 7173-7180 Species denotes patient Tax:9606
140 7280-7287 Species denotes patient Tax:9606
141 6734-6752 Chemical denotes methenamine silver MESH:D008709
142 6968-6986 Chemical denotes methenamine silver MESH:D008709
143 7079-7092 Chemical denotes galactomannan MESH:C012990
144 7136-7146 Chemical denotes prednisone MESH:D011241
145 7205-7223 Chemical denotes hydroxychloroquine MESH:D006886
146 6418-6430 Disease denotes inflammation MESH:D007249
147 6450-6461 Disease denotes hyperplasia MESH:D006965
148 6550-6567 Disease denotes acute lung injury MESH:D055371
149 6630-6640 Disease denotes granulomas MESH:D006099
150 6645-6655 Disease denotes malignancy MESH:D009369
151 7306-7311 Disease denotes cough MESH:D003371
152 7316-7324 Disease denotes myalgias MESH:D063806
153 7356-7361 Disease denotes fever MESH:D005334
163 7918-7925 Species denotes patient Tax:9606
164 8126-8136 Species denotes SARS-CoV-2 Tax:2697049
165 8459-8467 Species denotes patients Tax:9606
166 8607-8614 Species denotes patient Tax:9606
167 8822-8834 Chemical denotes azithromycin MESH:D017963
168 8045-8053 Disease denotes COVID-19 MESH:C000657245
169 8376-8404 Disease denotes multifocal pulmonary disease MESH:D008171
170 8473-8481 Disease denotes COVID-19 MESH:C000657245
171 8700-8709 Disease denotes infection MESH:D007239
183 8839-8849 Species denotes SARS-CoV-2 Tax:2697049
184 9591-9598 Species denotes patient Tax:9606
185 9714-9721 Species denotes patient Tax:9606
186 9849-9859 Species denotes SARS-CoV-2 Tax:2697049
187 9379-9390 Disease denotes lung injury MESH:D055370
188 9460-9468 Disease denotes COVID-19 MESH:C000657245
189 9502-9513 Disease denotes lung injury MESH:D055370
190 9525-9540 Disease denotes alveolar damage MESH:D055370
191 9604-9612 Disease denotes COVID-19 MESH:C000657245
192 9749-9760 Disease denotes lung injury MESH:D055370
193 9897-9905 Disease denotes COVID-19 MESH:C000657245
200 10223-10233 Species denotes SARS-CoV-2 Tax:2697049
201 9972-9981 Disease denotes infection MESH:D007239
202 10010-10016 Disease denotes sepsis MESH:D018805
203 10132-10140 Disease denotes COVID-19 MESH:C000657245
204 10202-10211 Disease denotes infection MESH:D007239
205 10448-10465 Disease denotes acute lung injury MESH:D055371
211 10608-10617 Disease denotes pneumonia MESH:D011014
212 10767-10776 Disease denotes infection MESH:D007239
213 10825-10831 Disease denotes sepsis MESH:D018805
214 10907-10918 Disease denotes lung injury MESH:D055370
215 11005-11014 Disease denotes pneumonia MESH:D011014
223 11468-11476 Species denotes patients Tax:9606
224 11808-11816 Species denotes patients Tax:9606
225 12017-12024 Species denotes patient Tax:9606
226 11055-11063 Disease denotes COVID-19 MESH:C000657245
227 11298-11306 Disease denotes COVID-19 MESH:C000657245
228 11504-11512 Disease denotes COVID-19 MESH:C000657245
229 11763-11771 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 370-393 Body_part denotes lower respiratory tract http://purl.org/sig/ont/fma/fma45662
T2 1217-1220 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T3 1642-1646 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T4 1895-1900 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T5 1924-1929 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T6 2293-2301 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542
T7 2326-2342 Body_part denotes white blood cell http://purl.org/sig/ont/fma/fma62852
T8 2338-2342 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T9 2360-2365 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T10 2411-2421 Body_part denotes lymphocyte http://purl.org/sig/ont/fma/fma62863
T11 2445-2450 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T12 2510-2514 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T13 2915-2918 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T14 3060-3068 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542
T15 3101-3106 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T16 3119-3124 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T17 3159-3164 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T18 3208-3212 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T19 3239-3244 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T20 3261-3277 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T21 3336-3341 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T22 3364-3380 Body_part denotes right upper lobe http://purl.org/sig/ont/fma/fma7333
T23 3452-3468 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T24 3504-3520 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T25 3596-3611 Body_part denotes left lower lobe http://purl.org/sig/ont/fma/fma7371
T26 3670-3686 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T27 3745-3749 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T28 3827-3832 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T29 3864-3880 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T30 3915-3920 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T31 4331-4336 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T32 4375-4391 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T33 4507-4522 Body_part denotes left lower lobe http://purl.org/sig/ont/fma/fma7371
T34 4564-4580 Body_part denotes right upper lobe http://purl.org/sig/ont/fma/fma7333
T35 5218-5223 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T36 5754-5770 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T37 5930-5934 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T38 5967-5983 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T39 6382-6390 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T40 6391-6397 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T41 6432-6449 Body_part denotes type 2 pneumocyte http://purl.org/sig/ont/fma/fma62501
T42 6493-6501 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T43 6513-6525 Body_part denotes fibroblastic http://purl.org/sig/ont/fma/fma63877
T44 6526-6532 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T45 6556-6560 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T46 6623-6628 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T47 6844-6855 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T48 6862-6873 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T49 6875-6886 Body_part denotes histiocytes http://purl.org/sig/ont/fma/fma83585
T50 6903-6915 Body_part denotes fibroblastic http://purl.org/sig/ont/fma/fma63877
T51 6931-6942 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T52 7073-7078 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T53 7401-7406 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T54 7546-7556 Body_part denotes pneumocyte http://purl.org/sig/ont/fma/fma62499
T55 7605-7617 Body_part denotes fibroblastic http://purl.org/sig/ont/fma/fma63877
T56 7618-7624 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T57 7630-7638 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T58 7683-7687 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T59 7794-7806 Body_part denotes fibroblastic http://purl.org/sig/ont/fma/fma63877
T60 7821-7832 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T61 8236-8244 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T62 8423-8431 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T63 8858-8862 Body_part denotes sole http://purl.org/sig/ont/fma/fma25000
T64 9222-9226 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T65 9274-9290 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T66 9330-9335 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T67 9379-9383 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T68 9502-9506 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T69 9525-9533 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T70 9655-9667 Body_part denotes plasma cells http://purl.org/sig/ont/fma/fma70574
T71 9655-9661 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T72 9662-9667 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T73 9749-9753 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T74 9776-9780 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T75 10358-10366 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542
T76 10373-10378 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T77 10454-10458 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T78 10907-10911 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T79 11123-11131 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T80 12097-12105 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542
T81 12258-12266 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 370-393 Body_part denotes lower respiratory tract http://purl.obolibrary.org/obo/UBERON_0001558
T2 376-393 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T3 1895-1900 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T4 1924-1929 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T5 2332-2337 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T6 2445-2450 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T7 2510-2514 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T8 3101-3106 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T9 3119-3124 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T10 3159-3164 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T11 3208-3212 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T12 3239-3244 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T13 3273-3277 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T14 3336-3341 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T15 3376-3380 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T16 3464-3468 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T17 3516-3520 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T18 3607-3611 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T19 3682-3686 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T20 3745-3749 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T21 3827-3832 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T22 3876-3880 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T23 4331-4336 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T24 4387-4391 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T25 4518-4522 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T26 4576-4580 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T27 5218-5223 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T28 5766-5770 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T29 5930-5934 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T30 5979-5983 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T31 6391-6397 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T32 6526-6532 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T33 6556-6560 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T34 7073-7078 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T35 7401-7406 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T36 7618-7624 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T37 7807-7811 Body_part denotes ball http://purl.obolibrary.org/obo/UBERON_2000006
T38 9222-9226 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T39 9286-9290 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T40 9330-9335 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T41 9379-9383 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T42 9502-9506 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T43 9749-9753 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T44 9776-9780 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T45 10373-10378 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T46 10454-10458 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T47 10907-10911 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 21-29 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 95-142 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 95-128 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T4 144-152 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 230-239 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T6 245-253 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 577-594 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T8 652-660 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 863-872 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T10 1253-1255 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T11 1408-1417 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T12 1519-1528 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T13 2067-2069 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T14 2663-2672 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T15 2775-2783 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 2855-2863 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 4629-4638 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T18 4700-4708 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 4979-4988 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T20 5113-5129 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T21 5120-5129 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T22 5406-5414 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 5481-5489 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 5514-5531 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T25 5645-5653 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 5713-5725 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T27 6234-6242 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 6418-6430 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T29 6450-6461 Disease denotes hyperplasia http://purl.obolibrary.org/obo/MONDO_0005043
T30 6550-6567 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T32 6561-6567 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T33 6746-6761 Disease denotes silver staining http://purl.obolibrary.org/obo/MONDO_0018952
T34 6980-6995 Disease denotes silver staining http://purl.obolibrary.org/obo/MONDO_0018952
T35 7020-7028 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 7346-7348 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T37 7557-7568 Disease denotes hyperplasia http://purl.obolibrary.org/obo/MONDO_0005043
T38 8045-8053 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T39 8126-8134 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 8387-8404 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T41 8473-8481 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T42 8690-8709 Disease denotes influenza infection http://purl.obolibrary.org/obo/MONDO_0005812
T43 8700-8709 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T44 8839-8847 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 9373-9390 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T47 9384-9390 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T48 9460-9468 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T49 9496-9513 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T51 9507-9513 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T52 9604-9612 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T53 9743-9760 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T55 9754-9760 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T56 9849-9857 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 9897-9905 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T58 9972-9981 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T59 10132-10140 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T60 10202-10211 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T61 10223-10231 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 10448-10465 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T64 10459-10465 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T65 10608-10617 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T66 10749-10776 Disease denotes hospital-acquired infection http://purl.obolibrary.org/obo/MONDO_0043544
T67 10767-10776 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T68 10901-10918 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T70 10912-10918 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T71 11005-11014 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T72 11055-11063 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T73 11298-11306 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T74 11504-11512 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T75 11763-11771 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T76 12392-12395 Disease denotes AHS http://purl.obolibrary.org/obo/MONDO_0008758

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 33-34 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 35-37 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T3 183-184 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 324-326 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T5 370-393 http://purl.obolibrary.org/obo/UBERON_0001558 denotes lower respiratory tract
T6 509-511 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T7 537-538 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 623-625 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T9 626-631 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T10 791-793 http://purl.obolibrary.org/obo/CLO_0009877 denotes NY
T11 801-802 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 803-805 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T13 873-874 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T14 892-894 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T15 916-917 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 1108-1109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 1277-1278 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 1369-1370 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1567-1569 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T20 1890-1893 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T21 1895-1900 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T22 1895-1900 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T23 1924-1929 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T24 1924-1929 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T25 1924-1929 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T26 1924-1929 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T27 2217-2218 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 2332-2337 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T29 2338-2342 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T30 2360-2365 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T31 2395-2397 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T32 2409-2410 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 2445-2450 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T34 2510-2514 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T35 2510-2514 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T36 2590-2591 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 2616-2620 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T38 2627-2629 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T39 2750-2752 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T40 2828-2829 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 2871-2874 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T42 2875-2876 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 2908-2911 http://purl.obolibrary.org/obo/CLO_0007203 denotes L.6
T44 2919-2927 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T45 2980-2981 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 3032-3037 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T47 3101-3106 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T48 3119-3124 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T49 3146-3147 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T50 3159-3164 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T51 3208-3212 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T52 3208-3212 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T53 3230-3231 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T54 3239-3244 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T55 3327-3328 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T56 3336-3341 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T57 3412-3413 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 3590-3591 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 3745-3749 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T60 3745-3749 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T61 3827-3832 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T62 3839-3840 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 3915-3920 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T64 4089-4090 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 4208-4209 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 4322-4323 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T67 4331-4336 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T68 4432-4433 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 4466-4467 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T70 4528-4529 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 4666-4667 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T72 4688-4690 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T73 4815-4817 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T74 4968-4978 http://purl.obolibrary.org/obo/OBI_0000245 denotes organising
T75 5035-5036 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 5216-5217 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 5490-5491 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 5681-5688 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airways
T79 5863-5870 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airways
T80 5930-5934 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T81 5930-5934 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T82 6019-6026 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airways
T83 6178-6179 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 6215-6222 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T85 6271-6272 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 6287-6289 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T87 6476-6486 http://purl.obolibrary.org/obo/OBI_0000245 denotes organising
T88 6513-6525 http://purl.obolibrary.org/obo/CL_0000057 denotes fibroblastic
T89 6556-6560 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T90 6556-6560 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T91 6580-6589 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T92 6623-6628 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T93 6770-6772 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T94 6875-6886 http://purl.obolibrary.org/obo/CL_0000235 denotes histiocytes
T95 6903-6915 http://purl.obolibrary.org/obo/CL_0000057 denotes fibroblastic
T96 7401-7406 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T97 7503-7504 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T98 7583-7593 http://purl.obolibrary.org/obo/OBI_0000245 denotes organising
T99 7605-7617 http://purl.obolibrary.org/obo/CL_0000057 denotes fibroblastic
T100 7683-7687 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T101 7759-7760 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T102 7792-7793 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 7794-7806 http://purl.obolibrary.org/obo/CL_0000057 denotes fibroblastic
T104 7983-7987 http://purl.obolibrary.org/obo/CLO_0001550 denotes a 10
T105 8030-8031 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T106 8220-8221 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 8421-8422 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T108 8438-8441 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T109 8509-8510 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 8734-8736 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T111 8947-8949 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T112 8950-8955 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T113 8981-8982 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 9222-9226 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T115 9222-9226 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T116 9330-9335 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T117 9347-9348 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 9379-9383 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T119 9379-9383 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T120 9400-9404 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T121 9400-9404 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer
T122 9502-9506 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T123 9502-9506 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T124 9545-9547 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T125 9589-9590 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 9623-9624 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T127 9655-9667 http://purl.obolibrary.org/obo/CL_0000786 denotes plasma cells
T128 9749-9753 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T129 9749-9753 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T130 9776-9780 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T131 9776-9780 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T132 9840-9844 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T133 9960-9961 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T134 10352-10354 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T135 10367-10370 http://purl.obolibrary.org/obo/CLO_0008285 denotes p 1
T136 10367-10370 http://purl.obolibrary.org/obo/CLO_0008286 denotes p 1
T137 10454-10458 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T138 10454-10458 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T139 10548-10549 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T140 10597-10607 http://purl.obolibrary.org/obo/OBI_0000245 denotes organising
T141 10747-10748 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 10907-10911 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T143 10907-10911 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T144 10932-10942 http://purl.obolibrary.org/obo/OBI_0000245 denotes organising
T145 10994-11004 http://purl.obolibrary.org/obo/OBI_0000245 denotes organising
T146 11037-11038 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 11116-11117 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T148 11248-11253 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T149 11257-11259 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T150 11321-11322 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 11724-11733 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T152 11946-11948 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T153 12282-12284 http://purl.obolibrary.org/obo/CLO_0007029 denotes JM
T154 12282-12284 http://purl.obolibrary.org/obo/CLO_0050993 denotes JM

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 324-326 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T4 429-432 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T5 495-498 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T6 509-511 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T9 623-625 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T12 702-705 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T13 791-793 Chemical denotes NY http://purl.obolibrary.org/obo/CHEBI_73427
T14 892-894 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T17 1173-1186 Chemical denotes emtricitabine http://purl.obolibrary.org/obo/CHEBI_31536
T18 1191-1212 Chemical denotes tenofovir alafenamide http://purl.obolibrary.org/obo/CHEBI_90926
T19 1191-1200 Chemical denotes tenofovir http://purl.obolibrary.org/obo/CHEBI_134504|http://purl.obolibrary.org/obo/CHEBI_63625|http://purl.obolibrary.org/obo/CHEBI_63716
T22 1316-1345 Chemical denotes tenofovir disoproxil fumarate http://purl.obolibrary.org/obo/CHEBI_63718
T23 1316-1336 Chemical denotes tenofovir disoproxil http://purl.obolibrary.org/obo/CHEBI_63717
T24 1316-1325 Chemical denotes tenofovir http://purl.obolibrary.org/obo/CHEBI_134504|http://purl.obolibrary.org/obo/CHEBI_63625|http://purl.obolibrary.org/obo/CHEBI_63716
T27 1337-1345 Chemical denotes fumarate http://purl.obolibrary.org/obo/CHEBI_29806
T28 1350-1363 Chemical denotes emtricitabine http://purl.obolibrary.org/obo/CHEBI_31536
T29 1423-1434 Chemical denotes oseltamivir http://purl.obolibrary.org/obo/CHEBI_7798
T30 1920-1922 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T32 1994-2000 Chemical denotes Oxygen http://purl.obolibrary.org/obo/CHEBI_15379
T33 2157-2167 Chemical denotes vancomycin http://purl.obolibrary.org/obo/CHEBI_28001|http://purl.obolibrary.org/obo/CHEBI_76842
T35 2195-2206 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T36 2627-2629 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T39 2750-2752 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T42 2954-2966 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T43 4044-4056 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T44 4182-4194 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T45 4238-4249 Chemical denotes clindamycin http://purl.obolibrary.org/obo/CHEBI_3745
T46 4688-4690 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T49 4790-4796 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T50 4874-4884 Chemical denotes prednisone http://purl.obolibrary.org/obo/CHEBI_8382
T51 5224-5237 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T52 5379-5382 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T53 5946-5949 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T54 6180-6183 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T55 6184-6197 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T56 6226-6229 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T57 6287-6289 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T60 6319-6322 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T61 6711-6715 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T62 6734-6745 Chemical denotes methenamine http://purl.obolibrary.org/obo/CHEBI_6824
T63 6746-6752 Chemical denotes silver http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141
T65 6807-6810 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T66 6968-6979 Chemical denotes methenamine http://purl.obolibrary.org/obo/CHEBI_6824
T67 6980-6986 Chemical denotes silver http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141
T69 7038-7041 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T70 7065-7068 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T71 7079-7092 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T72 7122-7132 Chemical denotes antibiotic http://purl.obolibrary.org/obo/CHEBI_33281
T73 7136-7146 Chemical denotes prednisone http://purl.obolibrary.org/obo/CHEBI_8382
T74 7205-7223 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T75 7489-7492 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T76 7701-7713 Chemical denotes haematoxylin http://purl.obolibrary.org/obo/CHEBI_51686
T77 7762-7765 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T78 7885-7888 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T79 8822-8834 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T80 8947-8949 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T83 9014-9017 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T84 9582-9585 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T85 9867-9870 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T86 10107-10118 Chemical denotes antibiotics http://purl.obolibrary.org/obo/CHEBI_33281
T87 10383-10386 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T88 10387-10400 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T89 11174-11185 Chemical denotes antibiotics http://purl.obolibrary.org/obo/CHEBI_33281
T90 11257-11259 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T93 12282-12284 Chemical denotes JM http://purl.obolibrary.org/obo/CHEBI_31739
T94 12322-12324 Chemical denotes CE http://purl.obolibrary.org/obo/CHEBI_3663
T95 12359-12361 Chemical denotes CE http://purl.obolibrary.org/obo/CHEBI_3663

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 5713-5725 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T2 5729-5739 http://purl.obolibrary.org/obo/GO_0046903 denotes secretions
T3 6418-6430 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T4 11162-11185 http://purl.obolibrary.org/obo/GO_0046677 denotes response to antibiotics

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 5224-5237 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 6184-6197 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 7079-7092 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 10387-10400 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 829-834 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T2 836-841 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T3 847-855 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094
T4 1687-1692 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T5 1694-1700 Phenotype denotes chills http://purl.obolibrary.org/obo/HP_0025143
T6 1702-1708 Phenotype denotes rigors http://purl.obolibrary.org/obo/HP_0025145
T7 1710-1719 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T8 1725-1744 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T9 3551-3568 Phenotype denotes reverse halo sign http://purl.obolibrary.org/obo/HP_0032983
T10 3999-4004 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T11 4009-4017 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094
T12 4080-4085 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T13 4142-4148 Phenotype denotes rigors http://purl.obolibrary.org/obo/HP_0025145
T14 4160-4168 Phenotype denotes coughing http://purl.obolibrary.org/obo/HP_0012735
T15 4629-4638 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T16 4741-4746 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T17 4748-4755 Phenotype denotes malaise http://purl.obolibrary.org/obo/HP_0012378
T18 4757-4763 Phenotype denotes rigors http://purl.obolibrary.org/obo/HP_0025145
T19 4769-4774 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T20 4979-4988 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T21 5051-5068 Phenotype denotes reverse halo sign http://purl.obolibrary.org/obo/HP_0032983
T22 5104-5129 Phenotype denotes invasive fungal infection http://purl.obolibrary.org/obo/HP_0020101
T23 6550-6567 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320
T24 6630-6640 Phenotype denotes granulomas http://purl.obolibrary.org/obo/HP_0032252
T25 7306-7311 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T26 7316-7324 Phenotype denotes myalgias http://purl.obolibrary.org/obo/HP_0003326
T27 7356-7361 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T28 8236-8250 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041
T29 8255-8275 Phenotype denotes pulmonary infiltrate http://purl.obolibrary.org/obo/HP_0002113
T30 8423-8437 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041
T31 9373-9390 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320
T32 9496-9513 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320
T33 9517-9540 Phenotype denotes diffuse alveolar damage http://purl.obolibrary.org/obo/HP_0033006
T34 9743-9760 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320
T35 10010-10016 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T36 10448-10465 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320
T37 10608-10617 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T38 10825-10831 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T39 10901-10918 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320
T40 11005-11014 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T41 11123-11137 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-77 Sentence denotes Delayed diagnosis of COVID-19 in a 34-year-old man with atypical presentation
T2 79-730 Sentence denotes The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenges clinicians with a variety of presentations of COVID-19.1, 2, 3 Infection with SARS-CoV-2 is confirmed by real-time RT-PCR, typically done on nasopharyngeal (NP) swabs or, less commonly, samples from the lower respiratory tract, including bronchoalveolar lavage (BAL).4 Some data suggest that RT-PCR might be more sensitive with BAL than with NP swabs.5 Here, we present a man who developed rapidly progressive pulmonary disease and, following two negative NP tests, was diagnosed with COVID-19 on the basis of bronchoscopic biopsy and BAL after 9 days of illness.
T3 731-980 Sentence denotes 14 days before admission to Mount Sinai Hospital (New York, NY, USA), a 34-year-old man developed fever, cough, and dyspnoea due to influenza A, confirmed by an NP swab 2 days later at a walk-in urgent care facility of the Mount Sinai Health System.
T4 981-1004 Sentence denotes No radiograph was done.
T5 1005-1148 Sentence denotes The patient was previously healthy with no past hospitalisations, and works as an anaesthesiologist in a large medical centre in New York City.
T6 1149-1388 Sentence denotes His only medication was emtricitabine and tenofovir alafenamide for HIV pre-exposure prophylaxis, which he had been taking once a day for 5 months (and prior to that, tenofovir disoproxil fumarate and emtricitabine once a day for 3 years).
T7 1389-1489 Sentence denotes He was treated for influenza with oseltamivir for 5 days; symptoms resolved after 5 days of illness.
T8 1490-1607 Sentence denotes He felt fully recovered from influenza, and returned to work in the hospital 11 days after his symptoms had resolved.
T9 1608-1745 Sentence denotes On the afternoon of his first day back at work, the patient had rapid onset of fever, chills, rigors, dry cough, and shortness of breath.
T10 1746-1993 Sentence denotes On arrival at the emergency department of Mount Sinai Hospital, on the same afternoon as symptom onset (hospital day 1), his temperature was 39·4°C, blood pressure 142/80 mm Hg, heart rate 130 beats per min, and respiratory rate20 breaths per min.
T11 1994-2050 Sentence denotes Oxygen saturation ranged from 89% to 99% at ambient air.
T12 2051-2138 Sentence denotes On examination, he appeared acutely ill and in mild distress with normal breath sounds.
T13 2139-2311 Sentence denotes Plasmalyte (2 L), vancomycin (1 g once every 12 h), and ceftriaxone (2 g once a day) were administered intravenously; all medications are detailed in the appendix (pp 1–2).
T14 2312-2444 Sentence denotes The patient's white blood cell count was 13 900 cells per μL (reference range 4500–11 000), with a lymphocyte count of 9·2% (15–50).
T15 2445-2528 Sentence denotes Chest radiograph revealed an ill-defined nodule in the right mid-lung (figure 1A ).
T16 2529-2570 Sentence denotes The patient was admitted to the hospital.
T17 2571-2673 Sentence denotes On hospital day 1, a respiratory viral panel test of an NP swab was negative, including for influenza.
T18 2674-2786 Sentence denotes On day 2, RT-PCR (Roche Cobas 6800 System, Roche, Basel, Switzerland) of an NP swab was negative for SARS-CoV-2.
T19 2787-2999 Sentence denotes This assay targets open-reading frame 1, a region that is unique to SARS-CoV-2, and has a sensitivity of 1–5 copies per μL.6 An HIV test was negative, and intravenous azithromycin (500 mg once a day) was started.
T20 3000-3078 Sentence denotes The remainder of the laboratory tests are summarised in the appendix (pp 1–2).
T21 3079-3144 Sentence denotes Figure 1 Imaging with chest radiograph, chest CT, and radial EBUS
T22 3145-3326 Sentence denotes (A) Admission chest radiograph (hospital day 1) with right mid-lung nodule (arrow). (B) First chest CT (day 2) with right lower lobe rounded opacity with possible halo sign (arrow).
T23 3327-3766 Sentence denotes A second chest CT (day 6) showed new right upper lobe nodular opacities (C; arrows), a new large ground glass opacity in the right lower lobe (D; arrow); and enlargement of the right lower lobe rounded opacity with possible reverse halo sign (E; green arrow) and a new left lower lobe rounded opacity (E; blue arrow). (F) Radial EBUS image of right lower lobe rounded opacity (arrow) used to target the transbronchial lung biopsy on day 9.
T24 3767-3797 Sentence denotes EBUS=endobronchial ultrasound.
T25 3798-3937 Sentence denotes On hospital day 2, CT of the chest found a rounded opacity in the right lower lobe (figure 1B); the remainder of the lungs appeared normal.
T26 3938-4069 Sentence denotes On day 4, the patient's peak temperature was 37·8°C, and his cough and dyspnoea had improved; intravenous azithromycin was stopped.
T27 4070-4169 Sentence denotes On day 5, fever to a peak of 38·9°C occurred, and the patient developed rigors and severe coughing.
T28 4170-4321 Sentence denotes Intravenous azithromycin (500 mg once a day) was restarted and oral clindamycin (300 mg once every 6 h) was administered, without clinical improvement.
T29 4322-4465 Sentence denotes A repeat chest CT on day 6 showed enlargement of the right lower lobe opacity, which had become surrounded by a large new ground glass opacity.
T30 4466-4595 Sentence denotes A new rounded opacity was present in the left lower lobe, and a new multilobulated opacity in the right upper lobe (figure 1C–E).
T31 4596-4665 Sentence denotes The CT report suggested atypical pneumonia of fungal or viral origin.
T32 4666-4733 Sentence denotes A repeat RT-PCR of an NP swab for SARS-CoV-2 was negative on day 7.
T33 4734-4834 Sentence denotes Severe cough, malaise, rigors, and fever continued, and oxygen saturation was 92–94% at ambient air.
T34 4835-4989 Sentence denotes Antibiotics were stopped on day 8, and prednisone 40 mg was given orally on the mornings of day 8 and day 9 for presumed cryptogenic organising pneumonia.
T35 4990-5297 Sentence denotes Consulting radiologists noted CT evidence of a halo sign and reverse halo sign (figure 1B and 1E),7 suggestive of invasive fungal infection and not characteristic of previously reported CT findings for COVID-19.1, 8 On day 8, a serum galactomannan assay was ordered and pulmonary consultation was requested.
T36 5298-5383 Sentence denotes The pulmonary consultant recommended bronchoscopy with transbronchial biopsy and BAL.
T37 5384-5532 Sentence denotes Given the epidemic of COVID-19 in New York City at the time, the pulmonary team still considered COVID-19 a possible cause of the pulmonary disease.
T38 5533-5676 Sentence denotes On hospital day 9, bronchoscopy was done with appropriate personal and environmental protection precautions for COVID-19, including intubation.
T39 5677-5740 Sentence denotes The airways appeared normal without inflammation or secretions.
T40 5741-5914 Sentence denotes The original right lower lobe opacity was targeted for biopsy, and radial endobronchial ultrasound was used to select the airways leading directly to the lesion (figure 1F).
T41 5915-6027 Sentence denotes Transbronchial lung biopsy and BAL were done in the right lower lobe lateral segment through the target airways.
T42 6028-6204 Sentence denotes Appropriate specimens were sent for histopathological and cytological examinations and for routine bacterial, fungal, and mycobacterial cultures, and a BAL galactomannan assay.
T43 6205-6352 Sentence denotes Validated testing of BAL for SARS-CoV-2 was unavailable, and thus a swab used for NP specimens was swirled in the BAL specimen and sent for RT-PCR.
T44 6353-6568 Sentence denotes On day 9, pathology reported alveolar tissue with patchy chronic inflammation, type 2 pneumocyte hyperplasia, and areas of organising intra-alveolar fibrin and fibroblastic tissue, consistent with acute lung injury.
T45 6569-6775 Sentence denotes No hyaline membranes, viral cytopathic changes, giant cells, granulomas, or malignancy were present, and no microorganisms were identified on acid-fast or Grocott's methenamine silver staining (figure 2A ).
T46 6776-7008 Sentence denotes Cytological examination of the BAL found marked reactive changes in pneumocytes, with lymphocytes, histiocytes, and occasional fibroblastic balls lined by pneumocytes, with negative Grocott's methenamine silver staining (figure 2B).
T47 7009-7107 Sentence denotes RT-PCR for SARS-CoV-2 of the BAL specimen was positive; BAL and serum galactomannan were negative.
T48 7108-7157 Sentence denotes No additional antibiotic or prednisone was given.
T49 7158-7248 Sentence denotes On day 10, the patient declined treatment with hydroxychloroquine and was discharged home.
T50 7249-7397 Sentence denotes Via follow-up phone calls, the patient reported that his cough and myalgias slowly resolved, and he had no fever higher than 37·8°C after discharge.
T51 7398-7440 Sentence denotes No chest imaging was done after discharge.
T52 7441-7501 Sentence denotes Figure 2 Pathology of transbronchial biopsy and BAL cytology
T53 7502-7625 Sentence denotes (A) Transbronchial biopsy showing prominent pneumocyte hyperplasia with areas of organising fibrin and fibroblastic tissue.
T54 7626-7884 Sentence denotes The alveolar septa showed some mild chronic inflammatory cell infiltrates (haematoxylin-eosin stain, original magnification × 200). (B) BAL cytology specimen showing a fibroblastic ball lined by pneumocytes (Papanicolaou stain, original magnification × 400).
T55 7885-7912 Sentence denotes BAL=bronchoalveolar lavage.
T56 7913-8097 Sentence denotes This patient experienced an unusual, confusing clinical course during a 10-day hospitalisation, which concluded with a diagnosis of COVID-19, confirmed only with bronchoscopic samples.
T57 8098-8405 Sentence denotes An atypical presentation of SARS-CoV-2 can explain the entire clinical course during this hospitalisation, beginning with a possible mild cytokine storm and pulmonary infiltrate on hospital day 1, with initial clinical improvement followed by rapid progression within 4 days to multifocal pulmonary disease.
T58 8406-8602 Sentence denotes Development of a cytokine storm has been reported in patients with COVID-19, but its occurrence within a few hours after onset of symptoms seems unusual,9 as does the initial clinical improvement.
T59 8603-8835 Sentence denotes The patient's clinical course might have been affected by other factors, including the influenza infection itself or its treatment 11 days earlier, chronic antiretroviral therapy, and early initiation of treatment with azithromycin.
T60 8836-8977 Sentence denotes If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives.
T61 8978-9187 Sentence denotes In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases.
T62 9188-9391 Sentence denotes The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury.
T63 9392-9722 Sentence denotes The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient.
T64 9723-9944 Sentence denotes Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course.
T65 9945-10189 Sentence denotes Alternatively, a different infection might have caused the early sepsis presentation, with clinical improvement up to day 4 related to appropriate treatment with antibiotics, after which COVID-19 manifested on day 5, causing clinical worsening.
T66 10190-10547 Sentence denotes However, no infection other than SARS-CoV-2 was identified by culture, pathology, or respiratory viral panel, procalcitonin concentration was normal in the first 48 h (appendix p 1), serum and BAL galactomannan were negative, and the pathological finding of acute lung injury in the lesion was already present on day 2, which argue against this explanation.
T67 10548-10811 Sentence denotes A third possible explanation is that cryptogenic organising pneumonia or similar inflammatory illness spontaneously worsened and improved over the hospitalisation, and the positive RT-PCR represents a hospital-acquired infection incidental to the hospital course.
T68 10812-11015 Sentence denotes However, the sepsis-like presentation and the pathology and cytology findings showing an acute lung injury pattern with organising fibrin do not support the diagnosis of cryptogenic organising pneumonia.
T69 11016-11307 Sentence denotes This case represents a presentation of COVID-19 with atypical features, including sudden onset with a mild cytokine storm profile, apparent early response to antibiotics followed by rapid clinical worsening, and two negative RT-PCR tests of NP swabs, which delayed the diagnosis of COVID-19.
T70 11308-11459 Sentence denotes However, for a disease that was unknown only 5 months ago, it might also be too early for clinicians to be certain of which manifestations are typical.
T71 11460-11610 Sentence denotes In most patients requiring hospitalisation, COVID-19 is diagnosed by positive RT-PCR,1 and bronchoscopy is rarely required to establish the diagnosis.
T72 11611-12058 Sentence denotes As noted by the American Association of Bronchology and Interventional Pulmonology, “bronchoscopy should have an extremely limited role in diagnosis of COVID-19 and only be considered in intubated patients if upper respiratory samples are negative and other diagnosis is considered that would significantly change clinical management.”18 We agree with this statement, and feel that the presentation in our patient necessitated use of bronchoscopy.
T73 12060-12082 Sentence denotes Supplementary Material
T74 12083-12105 Sentence denotes Supplementary appendix
T75 12107-12119 Sentence denotes Contributors
T76 12120-12176 Sentence denotes TJH conceived the Case Report and wrote the first draft.
T77 12177-12273 Sentence denotes TJH and KMR collected pathology, cytology, and viral specimens, and designed the appendix table.
T78 12274-12313 Sentence denotes KMR and JM collected and collated data.
T79 12314-12391 Sentence denotes TJH and CE contributed radiology images, and CE interpreted radiology images.
T80 12392-12444 Sentence denotes AHS interpreted and photographed cytology specimens.
T81 12445-12495 Sentence denotes MBB reviewed and photographed pathology specimens.
T82 12496-12585 Sentence denotes All authors participated in the construction and editing of the manuscript and revisions.
T83 12586-12648 Sentence denotes Written consent for publication was obtained from the patient.
T84 12650-12674 Sentence denotes Declaration of interests
T85 12675-12709 Sentence denotes We declare no competing interests.