> top > docs > PMC:7170415 > spans > 1962-28855 > annotations

PMC:7170415 / 1962-28855 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
35 23-31 Disease denotes COVID-19 MESH:C000657245
39 177-187 Species denotes SARS–CoV-2 Tax:2697049
40 191-202 Species denotes respiratory Tax:12814
41 252-260 Disease denotes COVID-19 MESH:C000657245
43 381-391 Species denotes SARS–CoV-2 Tax:2697049
54 611-619 Species denotes patients Tax:9606
55 740-793 Species denotes severe acute respiratory syndrome–related coronavirus Tax:694009
56 797-807 Species denotes SARS–CoV-2 Tax:2697049
57 832-847 Species denotes betacoronavirus Tax:694002
58 941-952 Species denotes coronavirus Tax:11118
59 963-969 Species denotes humans Tax:9606
60 625-634 Disease denotes pneumonia MESH:D011014
61 902-910 Disease denotes COVID-19 MESH:C000657245
62 1000-1008 Disease denotes COVID-19 MESH:C000657245
63 1436-1452 Disease denotes viral infections MESH:D001102
74 1583-1590 Species denotes persons Tax:9606
75 1658-1666 Species denotes children Tax:9606
76 2093-2100 Species denotes persons Tax:9606
77 1571-1576 Disease denotes death MESH:D003643
78 1596-1604 Disease denotes COVID-19 MESH:C000657245
79 1646-1654 Disease denotes COVID-19 MESH:C000657245
80 1764-1780 Disease denotes critical illness MESH:D016638
81 1908-1917 Disease denotes mortality MESH:D003643
82 1989-1997 Disease denotes COVID-19 MESH:C000657245
83 2149-2154 Disease denotes death MESH:D003643
87 2414-2424 Species denotes SARS–CoV-2 Tax:2697049
88 2648-2658 Species denotes SARS–CoV-2 Tax:2697049
89 2441-2450 Disease denotes infection MESH:D007239
99 2797-2807 Species denotes SARS–CoV-2 Tax:2697049
100 2885-2896 Species denotes Coronavirus Tax:11118
101 2981-2996 Species denotes Betacoronavirus Tax:694002
102 3006-3016 Species denotes SARS Virus Tax:694009
103 3497-3505 Species denotes SARS-CoV Tax:694009
104 3692-3697 Species denotes human Tax:9606
105 2906-2928 Disease denotes Coronavirus Infections MESH:D018352
106 2938-2971 Disease denotes Severe Acute Respiratory Syndrome MESH:D045169
107 3484-3489 Disease denotes covid MESH:C000657245
109 4325-4335 Species denotes SARS–CoV-2 Tax:2697049
115 4458-4465 Species denotes persons Tax:9606
116 4703-4710 Species denotes persons Tax:9606
117 4819-4829 Species denotes SARS–CoV-2 Tax:2697049
118 4870-4877 Species denotes persons Tax:9606
119 4678-4686 Disease denotes infected MESH:D007239
128 4912-4922 Species denotes SARS–CoV-2 Tax:2697049
129 5287-5294 Species denotes persons Tax:9606
130 5476-5483 Species denotes persons Tax:9606
131 5536-5544 Species denotes patients Tax:9606
132 5642-5650 Species denotes patients Tax:9606
133 5467-5475 Disease denotes infected MESH:D007239
134 5550-5559 Disease denotes pneumonia MESH:D011014
135 5674-5680 Disease denotes deaths MESH:D003643
137 6161-6169 Species denotes patients Tax:9606
144 6587-6597 Species denotes SARS–CoV-2 Tax:2697049
145 6745-6752 Species denotes persons Tax:9606
146 8073-8080 Species denotes persons Tax:9606
147 6778-6786 Disease denotes COVID-19 MESH:C000657245
148 6983-6992 Disease denotes infection MESH:D007239
149 8124-8134 Disease denotes infections MESH:D007239
152 8361-8368 Species denotes persons Tax:9606
153 8394-8402 Disease denotes COVID-19 MESH:C000657245
159 8558-8566 Species denotes patients Tax:9606
160 9032-9042 Species denotes SARS–CoV-2 Tax:2697049
161 9120-9130 Species denotes SARS–CoV-2 Tax:2697049
162 9141-9151 Species denotes SARS–CoV-2 Tax:2697049
163 9154-9207 Species denotes severe acute respiratory syndrome–related coronavirus Tax:694009
172 10188-10196 Species denotes patients Tax:9606
173 10260-10267 Species denotes persons Tax:9606
174 10299-10306 Species denotes persons Tax:9606
175 10471-10479 Species denotes patients Tax:9606
176 10602-10609 Species denotes persons Tax:9606
177 9317-9325 Disease denotes COVID-19 MESH:C000657245
178 10232-10240 Disease denotes COVID-19 MESH:C000657245
179 10370-10378 Disease denotes COVID-19 MESH:C000657245
188 11069-11077 Species denotes patients Tax:9606
189 10789-10800 Species denotes respiratory Tax:12814
190 11315-11326 Species denotes respiratory Tax:12814
191 10834-10842 Disease denotes COVID-19 MESH:C000657245
192 11033-11041 Disease denotes COVID-19 MESH:C000657245
193 11093-11101 Disease denotes COVID-19 MESH:C000657245
194 11133-11149 Disease denotes viral infections MESH:D001102
195 11266-11286 Disease denotes SARS–CoV-2 infection MESH:C000657245
199 11785-11792 Species denotes persons Tax:9606
200 11599-11615 Disease denotes acute infections MESH:D007239
201 11832-11841 Disease denotes infection MESH:D007239
210 11980-11988 Species denotes patients Tax:9606
211 12131-12141 Species denotes SARS–CoV-2 Tax:2697049
212 12213-12223 Species denotes SARS–CoV-2 Tax:2697049
213 12037-12048 Species denotes respiratory Tax:12814
214 12970-12981 Species denotes respiratory Tax:12814
215 12463-12471 Chemical denotes aluminum MESH:D000535
216 12523-12539 Chemical denotes calcium alginate MESH:D000464
217 11994-12002 Disease denotes COVID-19 MESH:C000657245
225 13568-13572 Gene denotes RdRP Gene:43740578
226 13330-13342 Gene denotes nucleocapsid Gene:43740575
227 13246-13256 Species denotes SARS–CoV-2 Tax:2697049
228 13373-13378 Species denotes human Tax:9606
229 13527-13537 Species denotes SARS–CoV-2 Tax:2697049
230 13666-13676 Species denotes SARS–CoV-2 Tax:2697049
231 13742-13755 Species denotes coronaviruses Tax:11118
239 15115-15122 Species denotes patient Tax:9606
240 15313-15323 Species denotes SARS–CoV-2 Tax:2697049
241 15020-15031 Species denotes respiratory Tax:12814
242 15228-15239 Species denotes respiratory Tax:12814
243 14795-14805 Species denotes SARS–CoV-2 Tax:2697049
244 14702-14711 Disease denotes infection MESH:D007239
245 14989-14997 Disease denotes COVID-19 MESH:C000657245
248 15458-15486 Disease denotes respiratory viral infections
249 15642-15651 Disease denotes Abbott ID MESH:C537985
253 15804-15814 Species denotes SARS–CoV-2 Tax:2697049
254 15911-15921 Species denotes SARS–CoV-2 Tax:2697049
255 16038-16050 Disease denotes tuberculosis MESH:D014376
262 17051-17063 Gene denotes nucleocapsid Gene:43740575
263 16377-16404 Species denotes respiratory syncytial virus Tax:12814
264 16648-16675 Species denotes respiratory syncytial virus Tax:12814
265 16785-16795 Species denotes SARS–CoV-2 Tax:2697049
266 16918-16937 Species denotes novel coronaviruses Tax:2697049
267 17075-17085 Species denotes SARS–CoV-2 Tax:2697049
280 17255-17258 Gene denotes IgG
281 17263-17273 Species denotes SARS–CoV-2 Tax:2697049
282 17898-17908 Species denotes SARS–CoV-2 Tax:2697049
283 17909-17920 Species denotes coronavirus Tax:11118
284 18042-18047 Species denotes human Tax:9606
285 18048-18061 Species denotes coronaviruses Tax:11118
286 18130-18138 Species denotes patients Tax:9606
287 17524-17540 Disease denotes acute infections MESH:D007239
288 17684-17693 Disease denotes infection MESH:D007239
289 17780-17800 Disease denotes SARS–CoV-2 infection MESH:C000657245
290 18021-18030 Disease denotes infection MESH:D007239
291 18168-18197 Disease denotes late complications of disease MESH:D002493
294 18372-18382 Species denotes SARS–CoV-2 Tax:2697049
295 18346-18355 Disease denotes infection MESH:D007239
304 19148-19156 Species denotes patients Tax:9606
305 18906-18915 Disease denotes pneumonia MESH:D011014
306 19239-19247 Disease denotes COVID-19 MESH:C000657245
307 19526-19534 Disease denotes COVID-19 MESH:C000657245
308 19603-19611 Disease denotes COVID-19 MESH:C000657245
309 19662-19671 Disease denotes pneumonia MESH:D011014
310 19733-19741 Disease denotes COVID-19 MESH:C000657245
311 19763-19775 Disease denotes co-infection MESH:D060085
313 19838-19846 Disease denotes COVID-19 MESH:C000657245
329 19995-20013 Gene denotes C-reactive protein Gene:1401
330 20296-20320 Gene denotes alanine aminotransferase Gene:2875
331 19904-19912 Species denotes patients Tax:9606
332 20535-20545 Species denotes SARS–CoV-2 Tax:2697049
333 20617-20625 Species denotes patients Tax:9606
334 20326-20336 Chemical denotes creatinine MESH:D003404
335 20392-20401 Chemical denotes bilirubin MESH:D001663
336 20406-20416 Chemical denotes creatinine MESH:D003404
337 19918-19926 Disease denotes COVID-19 MESH:C000657245
338 20120-20131 Disease denotes lymphopenia MESH:D008231
339 20352-20362 Disease denotes leukopenia MESH:D007970
340 20364-20376 Disease denotes leukocytosis MESH:D007964
341 20570-20591 Disease denotes end-organ dysfunction MESH:C564816
342 20631-20637 Disease denotes sepsis MESH:D018805
343 20768-20776 Disease denotes COVID-19 MESH:C000657245
350 21807-21814 Species denotes persons Tax:9606
351 22441-22449 Species denotes patients Tax:9606
352 22601-22608 Species denotes persons Tax:9606
353 21819-21827 Disease denotes COVID-19 MESH:C000657245
354 21929-21938 Disease denotes infection MESH:D007239
355 22592-22600 Disease denotes infected MESH:D007239
358 23677-23687 Species denotes SARS–CoV-2 Tax:2697049
359 23496-23521 Chemical denotes phosphate-buffered saline
366 23908-23916 Species denotes patients Tax:9606
367 23996-24003 Species denotes persons Tax:9606
368 24100-24108 Species denotes patients Tax:9606
369 24694-24702 Species denotes patients Tax:9606
370 25320-25325 Species denotes human Tax:9606
371 25334-25349 Disease denotes trypanosomiasis MESH:D014352
374 26313-26324 Species denotes respiratory Tax:12814
375 25924-25932 Disease denotes COVID-19 MESH:C000657245
379 26719-26729 Species denotes SARS–CoV-2 Tax:2697049
380 26387-26395 Disease denotes COVID-19 MESH:C000657245
381 26787-26795 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 3134-3144 Body_part denotes Nucleotide http://purl.org/sig/ont/fma/fma82740
T2 3269-3285 Body_part denotes Immunoglobulin G http://purl.org/sig/ont/fma/fma62872
T3 3269-3283 Body_part denotes Immunoglobulin http://purl.org/sig/ont/fma/fma62871
T4 3295-3311 Body_part denotes Immunoglobulin M http://purl.org/sig/ont/fma/fma62873
T5 3295-3309 Body_part denotes Immunoglobulin http://purl.org/sig/ont/fma/fma62871
T6 3609-3623 Body_part denotes Immunoglobulin http://purl.org/sig/ont/fma/fma62871
T7 5927-5931 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T8 11353-11356 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T9 11558-11566 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T10 12037-12054 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T11 12256-12265 Body_part denotes turbinate http://purl.org/sig/ont/fma/fma57456
T12 12794-12800 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T13 12964-12987 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T14 13113-13116 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 13343-13347 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T16 13387-13391 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T17 13406-13409 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 13538-13541 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 13552-13555 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T20 14819-14824 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T21 14829-14834 Body_part denotes urine http://purl.org/sig/ont/fma/fma12274
T22 15014-15037 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T23 15222-15245 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T24 16055-16058 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T25 17064-17071 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T26 17241-17244 Body_part denotes IgA http://purl.org/sig/ont/fma/fma62874
T27 17246-17249 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T28 17255-17258 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T29 17307-17312 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T30 17316-17322 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T31 17662-17670 Body_part denotes Antibody http://purl.org/sig/ont/fma/fma62871
T32 17882-17890 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T33 17921-17929 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T34 18845-18850 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T35 18877-18882 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T36 19251-19256 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T37 19414-19419 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T38 20006-20013 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T39 20226-20237 Body_part denotes erythrocyte http://purl.org/sig/ont/fma/fma62845
T40 20296-20303 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T41 20574-20579 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T42 20921-20925 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T43 23012-23021 Body_part denotes turbinate http://purl.org/sig/ont/fma/fma57456
T44 23151-23157 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T45 23194-23200 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 2366-2371 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 5927-5931 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T4 12037-12054 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T5 12794-12800 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T6 12964-12987 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T7 12970-12987 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T8 14819-14824 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T9 14829-14834 Body_part denotes urine http://purl.obolibrary.org/obo/UBERON_0001088
T10 15014-15037 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T11 15020-15037 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T12 15222-15245 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T13 15228-15245 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T14 16149-16154 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T15 17307-17312 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T16 17316-17322 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T17 18845-18850 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T18 18877-18882 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T19 19251-19256 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T20 19414-19419 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T21 20574-20579 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T22 20921-20925 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T23 23151-23157 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T24 23194-23200 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T25 25731-25736 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T12 23-31 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 177-181 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T14 252-260 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T15 381-385 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T16 625-634 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T17 740-773 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T18 797-801 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T19 902-910 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T20 1000-1008 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 1436-1452 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T22 1596-1604 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 1646-1654 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 1935-1944 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T25 1989-1997 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 2414-2418 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T27 2441-2450 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T28 2648-2652 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T29 2797-2801 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T30 2938-2971 Disease denotes Severe Acute Respiratory Syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T31 3006-3010 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T32 3491-3495 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T33 3497-3505 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 4325-4329 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T35 4615-4629 Disease denotes infectiousness http://purl.obolibrary.org/obo/MONDO_0005550
T36 4819-4823 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T37 4912-4916 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T38 5550-5559 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T39 5564-5573 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T40 5697-5707 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T41 6587-6591 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T42 6778-6786 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T43 6983-6992 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T44 8124-8134 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T45 8394-8402 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T46 9032-9036 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T47 9120-9124 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T48 9141-9145 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T49 9154-9187 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T50 9317-9325 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 10232-10240 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T52 10370-10378 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T53 10834-10842 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T54 11033-11041 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T55 11093-11101 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T56 11133-11149 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T57 11266-11270 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T58 11277-11286 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T59 11605-11615 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T60 11832-11841 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T61 11994-12002 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T62 12131-12135 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T63 12213-12217 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T64 13246-13250 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T65 13527-13531 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 13666-13670 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 14436-14440 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T68 14702-14711 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T69 14795-14799 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T70 14989-14997 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T71 15313-15317 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T72 15470-15486 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T73 15804-15808 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T74 15911-15915 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T75 16038-16050 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T76 16408-16417 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T77 16634-16643 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T78 16785-16789 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T79 17075-17079 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T80 17263-17267 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T81 17530-17540 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T82 17684-17693 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T83 17780-17784 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T84 17791-17800 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T85 17898-17902 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T86 18021-18030 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T87 18346-18355 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T88 18372-18376 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T89 18906-18915 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T90 19239-19247 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T91 19526-19534 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T92 19603-19611 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T93 19662-19671 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T94 19733-19741 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T95 19766-19775 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T96 19838-19846 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T97 19918-19926 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T98 20120-20131 Disease denotes lymphopenia http://purl.obolibrary.org/obo/MONDO_0003783
T99 20352-20362 Disease denotes leukopenia http://purl.obolibrary.org/obo/MONDO_0003785
T100 20535-20539 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T101 20768-20776 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T102 21819-21827 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T103 21929-21938 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T104 23677-23681 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T105 25320-25349 Disease denotes human African trypanosomiasis http://purl.obolibrary.org/obo/MONDO_0005459
T106 25334-25349 Disease denotes trypanosomiasis http://purl.obolibrary.org/obo/MONDO_0000940
T107 25924-25932 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T108 26387-26395 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T109 26719-26723 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T110 26787-26795 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T19 561-568 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T20 598-599 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 806-811 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2) (2
T22 814-815 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 854-859 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T24 963-969 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T25 1016-1019 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T26 1116-1128 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T27 1283-1288 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T28 1290-1294 http://purl.obolibrary.org/obo/CLO_0053799 denotes 4, 5
T29 1606-1608 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T30 2064-2071 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T31 2264-2271 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T32 2281-2282 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 2326-2329 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T34 2575-2582 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T35 2638-2643 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T36 2845-2853 http://purl.obolibrary.org/obo/UBERON_0000033 denotes Headings
T37 2845-2853 http://www.ebi.ac.uk/efo/EFO_0000964 denotes Headings
T38 3011-3016 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T39 3216-3223 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T40 3512-3519 http://www.ebi.ac.uk/efo/EFO_0000881 denotes digital
T41 3575-3579 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T42 3692-3697 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T43 3962-3963 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 4197-4210 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizations
T45 4310-4317 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T46 4637-4645 http://purl.obolibrary.org/obo/OBI_0100026 denotes organism
T47 4637-4645 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organism
T48 4712-4714 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T49 4923-4930 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T50 4931-4934 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T51 4967-4968 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T52 5167-5174 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T53 5255-5260 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T54 5269-5274 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T55 5372-5373 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 5686-5687 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 5766-5768 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T58 5862-5869 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T59 5915-5917 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T60 5927-5931 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T61 5983-5993 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T62 6020-6027 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T63 6066-6073 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T64 6178-6179 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 6446-6453 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T66 6538-6543 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T67 6596-6602 http://purl.obolibrary.org/obo/CLO_0001196 denotes 2 (25)
T68 6731-6738 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T69 6865-6866 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 6867-6871 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T71 6900-6904 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T72 6970-6974 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T73 7015-7020 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T74 7070-7074 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T75 7120-7125 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T76 7183-7184 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 7220-7227 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T78 7280-7284 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T79 7422-7426 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T80 7506-7511 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T81 7540-7545 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T82 7628-7633 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T83 7655-7656 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 7827-7828 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 7829-7833 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T86 7959-7960 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 7971-7975 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T88 8013-8014 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T89 8087-8093 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T90 8182-8185 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T91 8196-8197 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 8260-8264 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T93 8347-8354 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T94 8404-8405 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T95 8406-8410 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T96 8621-8625 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T97 8644-8645 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T98 8674-8678 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T99 8784-8791 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T100 8817-8823 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T101 8963-8968 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T102 9219-9223 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T103 9366-9373 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T104 9398-9405 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T105 9463-9468 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T106 9520-9527 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T107 9657-9662 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T108 9684-9691 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T109 9774-9775 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 9796-9798 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T111 9861-9864 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T112 9886-9893 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T113 9973-9974 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 9975-9979 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T115 10014-10021 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T116 10051-10053 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T117 10106-10107 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 10123-10126 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T119 10157-10164 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T120 10419-10420 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T121 10505-10506 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 10528-10536 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test, as
T123 10558-10561 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T124 10581-10588 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T125 10619-10623 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T126 10636-10641 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T127 10854-10861 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T128 11150-11153 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T129 11225-11226 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 11757-11762 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T131 11772-11773 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 11905-11912 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T133 11964-11967 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T134 12009-12013 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T135 12140-12146 http://purl.obolibrary.org/obo/CLO_0001196 denotes 2 (25)
T136 12148-12149 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T137 12224-12231 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T138 12359-12360 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 12629-12636 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T140 13047-13048 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 13064-13068 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T142 13207-13210 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T143 13211-13214 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T144 13343-13347 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T145 13373-13378 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T146 13387-13391 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T147 13478-13490 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T148 13591-13596 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T149 13770-13771 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 13841-13844 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T151 14107-14114 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T152 14116-14118 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T153 14251-14253 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T154 14269-14272 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T155 14319-14321 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T156 14814-14816 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T157 15058-15059 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 15113-15114 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 15123-15126 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T160 15131-15132 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 15142-15146 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T162 15448-15453 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T163 15818-15829 http://purl.obolibrary.org/obo/OBI_0000968 denotes instruments
T164 15885-15892 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T165 15922-15926 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T166 15937-15940 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T167 16059-16066 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T168 16158-16165 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T169 16289-16296 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T170 16315-16316 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 16353-16358 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T172 16359-16364 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T173 16399-16404 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T174 16418-16423 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T175 16670-16675 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T176 16732-16734 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T177 16801-16806 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T178 16902-16907 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T179 17012-17014 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T180 17137-17138 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 17170-17174 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T182 17201-17206 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T183 17307-17312 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T184 17307-17312 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T185 17404-17409 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T186 17855-17860 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T187 17938-17939 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T188 18042-18047 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T189 18276-18278 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T190 18671-18676 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T191 18755-18760 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T192 18796-18801 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T193 18845-18850 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T194 18877-18882 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T195 19003-19004 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 19016-19021 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T197 19251-19256 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T198 19285-19286 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 19414-19419 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T200 19477-19481 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T201 19485-19486 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 19536-19538 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T203 19761-19762 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T204 20226-20237 http://purl.obolibrary.org/obo/CL_0000232 denotes erythrocyte
T205 20574-20579 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T206 20753-20754 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T207 20859-20863 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T208 20906-20913 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T209 20921-20925 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T210 20929-20930 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 20988-20995 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T212 21262-21267 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T213 21549-21560 http://purl.obolibrary.org/obo/OBI_0000968 denotes instruments
T214 21572-21575 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T215 21607-21609 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T216 21669-21673 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T217 21751-21755 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T218 21983-21990 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T219 22056-22067 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing, as
T220 22222-22229 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T221 22235-22238 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T222 22402-22409 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T223 22488-22495 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T224 22679-22686 http://purl.obolibrary.org/obo/OBI_0000968 denotes Devices
T225 22886-22889 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T226 22984-22987 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T227 23127-23136 http://purl.obolibrary.org/obo/UBERON_0001353 denotes posterior
T228 23280-23281 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T229 23288-23290 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T230 23297-23300 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T231 23301-23304 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T232 23314-23315 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T233 23569-23572 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T234 23696-23698 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T235 23735-23742 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T236 24557-24562 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T237 24969-24974 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T238 25263-25270 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T239 25320-25325 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T240 25554-25561 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T241 25773-25778 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T242 25933-25940 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T243 26084-26091 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T244 26228-26235 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T245 26267-26268 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T246 26325-26332 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T247 26405-26408 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T248 26581-26582 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T249 26730-26737 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T250 26796-26799 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T251 26885-26892 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1352-1360 Chemical denotes carriers http://purl.obolibrary.org/obo/CHEBI_78059
T2 3134-3144 Chemical denotes Nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T3 3581-3588 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T4 8936-8948 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T5 8944-8948 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T6 12098-12110 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T7 12106-12110 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T8 12463-12471 Chemical denotes aluminum http://purl.obolibrary.org/obo/CHEBI_28984
T9 12523-12530 Chemical denotes calcium http://purl.obolibrary.org/obo/CHEBI_22984|http://purl.obolibrary.org/obo/CHEBI_29320
T11 12531-12539 Chemical denotes alginate http://purl.obolibrary.org/obo/CHEBI_58187
T12 12761-12773 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T13 12769-12773 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T14 13292-13297 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T15 13356-13358 Chemical denotes N2 http://purl.obolibrary.org/obo/CHEBI_17997
T16 13498-13503 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T17 14882-14894 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T18 14890-14894 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T19 15649-15651 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T20 16424-16432 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T21 17064-17071 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T22 17152-17159 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T23 17921-17929 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T24 20006-20013 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T25 20057-20064 Chemical denotes lactate http://purl.obolibrary.org/obo/CHEBI_24996
T26 20268-20277 Chemical denotes aspartate http://purl.obolibrary.org/obo/CHEBI_132943|http://purl.obolibrary.org/obo/CHEBI_29995|http://purl.obolibrary.org/obo/CHEBI_72314
T29 20296-20303 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T30 20326-20336 Chemical denotes creatinine http://purl.obolibrary.org/obo/CHEBI_16737
T31 20392-20401 Chemical denotes bilirubin http://purl.obolibrary.org/obo/CHEBI_16990
T32 20406-20416 Chemical denotes creatinine http://purl.obolibrary.org/obo/CHEBI_16737
T33 20647-20656 Chemical denotes biomarker http://purl.obolibrary.org/obo/CHEBI_59163
T34 20885-20891 Chemical denotes Access http://purl.obolibrary.org/obo/CHEBI_34922
T35 21292-21300 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T36 21499-21511 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T37 21507-21511 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T38 23496-23505 Chemical denotes phosphate http://purl.obolibrary.org/obo/CHEBI_18367|http://purl.obolibrary.org/obo/CHEBI_26020|http://purl.obolibrary.org/obo/CHEBI_35780|http://purl.obolibrary.org/obo/CHEBI_43474
T42 24543-24550 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T43 25879-25890 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1436-1452 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T5 3069-3082 http://purl.obolibrary.org/obo/GO_0003968 denotes Transcriptase
T6 3069-3082 http://purl.obolibrary.org/obo/GO_0003899 denotes Transcriptase
T7 3388-3406 http://purl.obolibrary.org/obo/GO_0099048 denotes CRISPR-Cas Systems
T8 4595-4609 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T9 8978-8995 http://purl.obolibrary.org/obo/GO_0044405 denotes detection of host
T10 10696-10709 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T11 10696-10709 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T12 11133-11149 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T13 11680-11694 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T14 12690-12699 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T15 13379-13386 http://purl.obolibrary.org/obo/GO_0004526 denotes RNase P
T16 13568-13572 http://purl.obolibrary.org/obo/GO_0003968 denotes RdRP
T17 15470-15486 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T18 17600-17614 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T19 18244-18258 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T20 22692-22701 http://purl.obolibrary.org/obo/GO_0006810 denotes Transport
T21 22837-22852 http://purl.obolibrary.org/obo/GO_0046794 denotes viral transport
T22 22843-22852 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T23 23382-23397 http://purl.obolibrary.org/obo/GO_0046794 denotes viral transport
T24 23388-23397 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T25 23447-23462 http://purl.obolibrary.org/obo/GO_0046794 denotes viral transport
T26 23453-23462 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T27 23648-23657 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T28 24079-24093 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T17 0-18 Sentence denotes Key Summary Points
T18 19-128 Sentence denotes The COVID-19 pandemic demonstrates the essential role of diagnostics in the control of communicable diseases.
T19 129-351 Sentence denotes Laboratory-based molecular assays for detecting SARS–CoV-2 in respiratory specimens are the current reference standard for COVID-19 diagnosis, but point-of-care technologies and serologic immunoassays are rapidly emerging.
T20 352-467 Sentence denotes Early, massive deployment of SARS–CoV-2 diagnostics for case finding helped curb the epidemic in several countries.
T21 468-578 Sentence denotes Urgent clinical and public health needs now drive an unprecedented global effort to increase testing capacity.
T22 580-685 Sentence denotes In December 2019, a cluster of patients with pneumonia of unknown cause was reported in Wuhan, China (1).
T23 686-848 Sentence denotes The causative pathogen was subsequently identified as severe acute respiratory syndrome–related coronavirus-2 (SARS–CoV-2) (2), a newly described betacoronavirus.
T24 849-974 Sentence denotes This virus, now recognized as the etiologic agent of COVID-19 disease, is the seventh known coronavirus to infect humans (1).
T25 975-1078 Sentence denotes Since the recognition of COVID-19, there has been an exponential rise in the number of cases worldwide.
T26 1079-1216 Sentence denotes As of 1 April 2020, the World Health Organization reported more than 926 000 cases in more than 195 countries, areas, or territories (3).
T27 1217-1505 Sentence denotes Reasons for the rapid spread include high transmissibility of the virus (4, 5), especially among asymptomatic or minimally symptomatic carriers (6, 7); the apparent absence of any cross-protective immunity from related viral infections; and delayed public health response measures (8–10).
T28 1506-1614 Sentence denotes Age and the presence of comorbid illnesses increase the risk for death among persons with COVID-19 (11, 12).
T29 1615-1786 Sentence denotes The clinical manifestations of COVID-19 in children are less severe compared with adults, yet age younger than 1 year seems to increase the risk for critical illness (13).
T30 1787-1958 Sentence denotes Current case-fatality rate estimates range from 0.6% to 7.2% by region and seem to be substantially higher than the 0.1% mortality rate of seasonal influenza (12, 14, 15).
T31 1959-2164 Sentence denotes However, current estimates of COVID-19 case-fatality rates are probably inflated because of preferential testing in many countries of persons with severe manifestations, who are at risk for death (12, 16).
T32 2165-2322 Sentence denotes In Germany and South Korea, the case-fatality rates are less than 0.5%, probably because extensive testing revealed a large denominator of mild illness (17).
T33 2323-2490 Sentence denotes It has been estimated that before the wide-scale travel restrictions in China, undiagnosed SARS–CoV-2 represented the infection source for 79% of documented cases (7).
T34 2491-2600 Sentence denotes These observations underscore the critical importance of ample, accurate diagnostic testing in this pandemic.
T35 2601-2739 Sentence denotes Here, we review the current array of tests for SARS–CoV-2, highlight gaps in current diagnostic capacity, and propose potential solutions.
T36 2741-2748 Sentence denotes Methods
T37 2749-2824 Sentence denotes We searched the PubMed database for articles on SARS–CoV-2 and diagnostics.
T38 2825-3451 Sentence denotes The Medical Subject Headings (MeSH) search terms used were “Coronavirus”[MeSH]; “Coronavirus Infections”[MeSH]; “Severe Acute Respiratory Syndrome”[MeSH]; “Betacoronavirus”[MeSH]; “SARS Virus”[MeSH]; “Polymerase Chain Reaction”[MeSH]; “Reverse Transcriptase Polymerase Chain Reaction”[MeSH]; “High-Throughput Nucleotide Sequencing”[MeSH]; “Sensitivity and Specificity”[MeSH]; “Point-of-Care Testing”[MeSH]; “Antigens”[MeSH]; “Serology”[MeSH]; “Immunoglobulin G”[MeSH]; “Immunoglobulin M”[MeSH]; “Clustered Regularly Interspaced Short Palindromic Repeats”[MeSH]; “CRISPR-Cas Systems”[MESH]; and “Diagnosis, Differential”[MESH].
T39 3452-3667 Sentence denotes Non-MeSH search terms used were covid, SARS, SARS-CoV, pcr, digital droplet PCR, next generation sequencing, point-of-care test, antigen, analyte, serology, Immunoglobulin, CRISPR-CAS, Diagnos, and turn around time.
T40 3668-3766 Sentence denotes Only articles including human subjects and those published from 2003 to the present were included.
T41 3767-3832 Sentence denotes Articles in languages other than English or French were excluded.
T42 3833-3904 Sentence denotes We screened the results on title and abstract for relevant information.
T43 3905-4089 Sentence denotes Starting from the articles found in this search, we used a snowball search strategy, scanning useful references and similar articles and retrieving those that were considered relevant.
T44 4090-4152 Sentence denotes Furthermore, experts were consulted for additional literature.
T45 4153-4239 Sentence denotes Guidelines and resources from international organizations were used where appropriate.
T46 4240-4285 Sentence denotes This search was last updated on 1 April 2020.
T47 4287-4344 Sentence denotes The Role of Diagnostic Testing in the SARS–CoV-2 Pandemic
T48 4345-4534 Sentence denotes The primary goal of epidemic containment is to reduce disease transmission by reducing the number of susceptible persons in the population or by reducing the basic reproductive number (R0).
T49 4535-4716 Sentence denotes This number is modulated by such factors as the duration of viral shedding, the infectiousness of the organism, and the contact matrix between infected and susceptible persons (18).
T50 4717-4897 Sentence denotes Given the lack of effective vaccines or treatments (19), the only currently available lever to reduce SARS–CoV-2 transmission is to identify and isolate persons who are contagious.
T51 4898-4966 Sentence denotes Deployment of SARS–CoV-2 testing has varied widely across the globe.
T52 4967-5088 Sentence denotes A few Asian countries have illustrated the power of preparedness, flexible isolation systems, and intensive case finding.
T53 5089-5187 Sentence denotes South Korea dramatically slowed the epidemic by implementing an unprecedented testing effort (20).
T54 5188-5356 Sentence denotes Using innovative measures, South Korea performed more than 300 000 tests (5828.6 tests per million persons) in the 9 weeks after the first case was identified (20, 21).
T55 5357-5444 Sentence denotes Singapore used a broad case definition, aggressive contact tracing, and isolation (10).
T56 5445-5719 Sentence denotes Moreover, to identify infected persons not meeting the case definition, Singapore screened patients with pneumonia and influenza-like illnesses in hospitals and primary care settings, severely ill patients in intensive care, and deaths with a possible infectious cause (10).
T57 5720-5770 Sentence denotes Taiwan and Hong Kong used similar approaches (22).
T58 5771-5919 Sentence denotes These countries rapidly deployed resource-intensive strategies that prioritized aggressive testing and isolation to interrupt transmission (20, 22).
T59 5920-6102 Sentence denotes In the face of widespread transmission, the role of diagnostic testing is contingent on the type of testing available, the resources required for testing, and time to obtain results.
T60 6103-6326 Sentence denotes For example, rapidly identifying cases among hospitalized patients remains a high priority to properly allocate personal protective equipment and to prevent nosocomial spread with subsequent community transmission (23, 24).
T61 6327-6433 Sentence denotes Likewise, specific treatment decisions and enrollment in ongoing clinical trials require prompt diagnosis.
T62 6435-6454 Sentence denotes Diagnostic Testing:
T63 6455-6477 Sentence denotes Defining Key Use Cases
T64 6478-6672 Sentence denotes Despite the remarkable speed with which accurate diagnostic tests have been developed and made available for SARS–CoV-2 (25), current tools only partially meet several clinically relevant needs.
T65 6673-6787 Sentence denotes Figure 1 illustrates different indications for diagnostic testing among persons with proven or suspected COVID-19.
T66 6788-6899 Sentence denotes For each of these, the most important consideration is the clinical decision a test result will help to inform.
T67 6900-7367 Sentence denotes Test designs must account for several parameters, such as whether the test detects infection directly (such as the virus itself) or indirectly (such as host antibodies), test turnaround time, the ability to perform many tests at the same time (that is, throughput), the need to have a minimum number of specimens before testing (that is, batching), and the ability to perform the test in low-infrastructure settings (such as on cruise ships or in remote communities).
T68 7368-7438 Sentence denotes The potential for use at the point of care depends on test complexity.
T69 7439-7447 Sentence denotes The U.S.
T70 7448-7532 Sentence denotes Food and Drug Administration (FDA) categorizes diagnostic tests by their complexity:
T71 7533-7668 Sentence denotes Waived tests are available for use at the point of care, whereas moderate- and high-complexity tests must be performed in a laboratory.
T72 7669-7745 Sentence denotes The intended use also determines which specimen types are ideal or feasible.
T73 7746-7865 Sentence denotes Finally, it is important to recognize that the acceptable diagnostic accuracy of a test may vary according to use case.
T74 7866-8135 Sentence denotes For example, sensitivity and specificity requirements of an assay used to confirm results of a screening test need not be as stringent as those of a method used for standalone diagnosis, because the pool of persons being tested is already enriched with true infections.
T75 8136-8298 Sentence denotes The Foundation for Innovative New Diagnostics has published a detailed assessment of priority use cases to be considered by test developers and policymakers (26).
T76 8299-8308 Sentence denotes Figure 1.
T77 8310-8403 Sentence denotes Examples of use cases for diagnostic testing among persons with proven or suspected COVID-19.
T78 8404-8616 Sentence denotes A test well suited for one use case (such as epidemiologic surveillance) may be completely inadequate for another (such as rapid screening of symptomatic patients for allocation of personal protective equipment).
T79 8617-8852 Sentence denotes For test results to enable a specific clinical decision, test developers, policymakers, and clinicians need to consider each of these with respect to the intention of testing and the population being tested as specifically as possible.
T80 8853-9140 Sentence denotes For the moment, most use cases placed above the green and gray bar are best met by nucleic acid amplification tests, whereas detection of host-derived antibodies directed against SARS–CoV-2 will be crucial for surveillance, epidemic forecasting, and determination of SARS–CoV-2 immunity.
T81 9141-9210 Sentence denotes SARS–CoV-2 = severe acute respiratory syndrome–related coronavirus-2.
T82 9212-9224 Sentence denotes Who to Test:
T83 9225-9280 Sentence denotes Current Diagnostic Recommendations in the United States
T84 9281-9486 Sentence denotes In response to the rapidly evolving COVID-19 pandemic, countries have used different testing approaches depending on testing capacity, public health resources, and the spread of the virus in the community.
T85 9487-9663 Sentence denotes In the United States, diagnostic testing indications and capacity were limited at the beginning of the outbreak, largely because of regulatory hurdles for the use of new tests.
T86 9664-9800 Sentence denotes To expand access to testing, the FDA released policies to allow laboratories to use their validated assays in a more timely manner (27).
T87 9801-10005 Sentence denotes On 4 March, the Centers for Disease Control and Prevention (CDC) removed restrictive testing criteria, recommending that clinicians use their judgment to determine whether a test should be performed (28).
T88 10006-10118 Sentence denotes Because testing capacity remains suboptimal (27), the implementation of this recommendation remains a challenge.
T89 10119-10464 Sentence denotes The CDC still recommends priority for testing 3 groups: hospitalized patients with presentations compatible with COVID-19, other symptomatic persons at risk for poor outcomes, and persons who had close contact with someone with suspected or confirmed COVID-19 within 14 days of illness onset or have a history of travel in an affected area (28).
T90 10465-10553 Sentence denotes These patients should be evaluated with a molecular diagnostic test, as described later.
T91 10554-10610 Sentence denotes The CDC does not recommend testing asymptomatic persons.
T92 10612-10624 Sentence denotes How to Test:
T93 10625-10668 Sentence denotes Diagnostic Tests in Use or Under Evaluation
T94 10669-10952 Sentence denotes Although real-time reverse transcriptase polymerase chain reaction (RT-PCR)–based assays performed in the laboratory on respiratory specimens are the cornerstone of COVID-19 diagnostic testing, several novel or complementary diagnostic methods are being developed and evaluated (16).
T95 10953-11062 Sentence denotes Figure 2 depicts the adequacy of the principal assay types used or proposed for COVID-19 for 4 key use cases.
T96 11063-11221 Sentence denotes Among patients diagnosed with COVID-19, the occurrence of concomitant viral infections has been reported to range from below 6% (29) to greater than 60% (30).
T97 11222-11336 Sentence denotes As a result, it is not possible to rule out SARS–CoV-2 infection merely by detecting another respiratory pathogen.
T98 11337-11346 Sentence denotes Figure 2.
T99 11348-11430 Sentence denotes Heat map showing the adequacy of principal assay types (rows) for 4 key use cases.
T100 11431-11540 Sentence denotes * This assumes that assays in development or currently undergoing regulatory evaluation prove to be accurate.
T101 11541-11736 Sentence denotes † The utility of antibody detection assays for diagnosing acute infections is probably very limited around the time of symptom onset, when viral shedding and transmission risk seem to be highest.
T102 11737-11876 Sentence denotes Thus, although such tests may have a role among persons presenting late in the course of their infection, the potential for misuse is high.
T103 11878-11912 Sentence denotes Laboratory-Based Molecular Testing
T104 11913-12147 Sentence denotes The current diagnostic strategy recommended by the CDC to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of 1 or several nucleic acid targets specific to SARS–CoV-2 (25).
T105 12148-12322 Sentence denotes A nasopharyngeal specimen is the preferred choice for swab-based SARS–CoV-2 testing, but oropharyngeal, mid-turbinate, or anterior nares samples also are acceptable (31, 32).
T106 12323-12448 Sentence denotes Samples should be obtained by using a flocked swab, if available, to enhance the collection and release of cellular material.
T107 12449-12503 Sentence denotes Swabs with an aluminum or plastic shaft are preferred.
T108 12504-12637 Sentence denotes Swabs that contain calcium alginate, wood, or cotton should be avoided, because they may contain substances that inhibit PCR testing.
T109 12638-12774 Sentence denotes Ideally, swabs should be transferred into universal transport medium immediately after sample collection to preserve viral nucleic acid.
T110 12775-13003 Sentence denotes Samples taken from sputum, endotracheal aspirates, and bronchoalveolar lavage also may be sent directly to the microbiology laboratory for processing, and may have greater sensitivity than upper respiratory tract specimens (33).
T111 13004-13069 Sentence denotes Inadequate sample collection may result in a false-negative test.
T112 13070-13180 Sentence denotes After specimen collection, samples undergo RNA extraction followed by qualitative RT-PCR for target detection.
T113 13181-13263 Sentence denotes In the United States, the CDC has developed the most widely used SARS–CoV-2 assay.
T114 13264-13436 Sentence denotes The kit contains PCR primer–probe sets for 2 regions of the viral nucleocapsid gene (N1 and N2), and for the human RNase P gene to ensure the RNA extraction was successful.
T115 13437-13602 Sentence denotes This assay differs from the World Health Organization primer–probe sets, which target the SARS–CoV-2 RNA-dependent RNA polymerase (RdRP) and envelope (E) genes (25).
T116 13603-13836 Sentence denotes Both assays have high analytic sensitivity and specificity for SARS–CoV-2, with minimal cross-reactivity with other circulating strains of coronaviruses, and both use a cycle threshold of less than 40 as the criterion for positivity.
T117 13837-14120 Sentence denotes The CDC kit may be used by state public health laboratories, other laboratories determined by the state to be qualified, and clinical laboratories that meet the regulatory requirements of the Clinical Laboratories Improvement Amendment (CLIA) to perform high-complexity testing (27).
T118 14121-14255 Sentence denotes Dozens of laboratories have applied for Emergency Use Authorization (EUA) from the FDA for their own laboratory-developed assays (34).
T119 14256-14410 Sentence denotes The FDA also has granted an EUA for several commercial assays (35), further expanding the ability of clinical laboratories to use these platforms (Table).
T120 14411-14417 Sentence denotes Table.
T121 14418-14818 Sentence denotes The 28 Commercial SARS–CoV-2 in Vitro Diagnostic Assays Given an EUA From the FDA as of 4 April 2020 The lack of an established reference standard, use of differing sample collection and preparation methods, and an incomplete understanding of viral dynamics across the time course of infection hamper rigorous assessment of the diagnostic accuracy of the many newly introduced SARS–CoV-2 assays (36).
T122 14819-14932 Sentence denotes Serum and urine are usually negative for the presence of viral nucleic acid, regardless of illness severity (33).
T123 14933-15094 Sentence denotes Of importance, the ability of RT-PCR assays to rule out COVID-19 on the basis of upper respiratory tract samples obtained at a single time point remains unclear.
T124 15095-15343 Sentence denotes Conversely, after a patient has had a positive test result, several authorities have recommended obtaining at least 2 negative upper respiratory tract samples, collected at intervals of 24 hours or longer, to document SARS–CoV-2 clearance (37, 38).
T125 15345-15380 Sentence denotes Point-of-Care Molecular Diagnostics
T126 15381-15772 Sentence denotes Low-complexity, rapid (results within 1 hour) molecular diagnostic tests for respiratory viral infections that are CLIA waived (FDA approved for use outside the laboratory by nonlaboratory personnel) include cartridge-based assays on platforms that include the Abbott ID NOW (Abbott Laboratories), BioFire FilmArray (bioMérieux), cobas Liat (Roche Diagnostics), and GeneXpert (Cepheid) (39).
T127 15773-15893 Sentence denotes Rapid point-of-care assays for SARS–CoV-2 on instruments such as these will be critical to expand point-of-care testing.
T128 15894-16115 Sentence denotes The Xpert Xpress SARS–CoV-2 test (Cepheid) has received an FDA EUA and is performed on the GeneXpert platform, which is already widely used for tuberculosis and HIV testing, especially in low- and middle-income countries.
T129 16116-16333 Sentence denotes This capacity might be useful to scale up testing across the world as well as in settings where rapid results at the point of care would enable clinical decisions, although testing throughput may be a limiting factor.
T130 16335-16358 Sentence denotes Antigen Detection Tests
T131 16359-16615 Sentence denotes Tests that detect respiratory syncytial virus or influenza virus antigens by immunoassay directly from clinical specimens have been commercially available for decades, are of low complexity, and may provide results within minutes at the point of care (40).
T132 16616-16882 Sentence denotes Current tools for influenza and respiratory syncytial virus suffer from suboptimal sensitivity to rule out disease (41, 42); the same challenge would probably exist for SARS–CoV-2, and tests would need to be implemented with clear guidance on correct interpretation.
T133 16883-17016 Sentence denotes Prototypes of such tests for other novel coronaviruses have not received regulatory approval (43, 44) but are under development (45).
T134 17017-17180 Sentence denotes Monoclonal antibodies against the nucleocapsid protein of SARS–CoV-2 have been generated, which might form the basis of a future rapid antigen detection test (20).
T135 17182-17190 Sentence denotes Serology
T136 17191-17485 Sentence denotes Serologic tests that identify antibodies (such as IgA, IgM, and IgG) to SARS–CoV-2 from clinical specimens (such as blood or saliva), such as enzyme-linked immunosorbent assays, may be less complex than molecular tests and have the potential to be used for diagnosis in certain situations (46).
T137 17486-17661 Sentence denotes However, their utility for diagnosing acute infections is probably limited around the time of symptom onset, when viral shedding and transmission risk seem to be highest (32).
T138 17662-17744 Sentence denotes Antibody responses to infection take days to weeks to be reliably detectable (46).
T139 17745-17861 Sentence denotes Negative results would not exclude SARS–CoV-2 infection, particularly among those with recent exposure to the virus.
T140 17862-18067 Sentence denotes Cross-reactivity of antibody to non–SARS–CoV-2 coronavirus proteins is also a potential problem, whereby positive results may be the result of past or present infection with other human coronaviruses (47).
T141 18068-18280 Sentence denotes Serologic assays might be more relevant in scenarios in which patients present to medical care with late complications of disease, when RT-PCR may be falsely negative, because viral shedding drops over time (48).
T142 18281-18526 Sentence denotes The development of serologic assays that accurately assess prior infection and immunity to SARS–CoV-2 will be essential for epidemiologic studies, ongoing surveillance, vaccine studies, and potentially for risk assessment of health care workers.
T143 18527-18648 Sentence denotes Immunoassays are already on the market in some countries, but their diagnostic accuracy and optimal use remain undefined.
T144 18650-18676 Sentence denotes Ancillary Diagnostic Tests
T145 18677-18781 Sentence denotes The optimal use of diagnostic imaging, biomarkers, and other nonmicrobiologic tests is rapidly evolving.
T146 18783-18801 Sentence denotes Radiographic Tests
T147 18802-18873 Sentence denotes Many centers have evaluated the utility of chest imaging for diagnosis.
T148 18874-19031 Sentence denotes On chest radiography, bilateral pneumonia is the most frequently reported feature (range, 11.8% to 100%) and is more common than a unilateral focus (49, 50).
T149 19032-19200 Sentence denotes Computed tomography is regarded as more sensitive than radiography, with several cohort studies reporting that most patients (77.8% to 100%) had ground glass opacities.
T150 19201-19367 Sentence denotes Other features commonly reported with COVID-19 on chest computed tomography include a peripheral distribution, fine reticular opacities, and vascular thickening (51).
T151 19368-19544 Sentence denotes Compared with serial nasopharyngeal sampling, chest computed tomography may be more sensitive than an RT-PCR test at a single time point for the diagnosis of COVID-19 (52, 53).
T152 19545-19677 Sentence denotes In addition, artificial intelligence may help distinguish COVID-19 from other etiologic agents of community-acquired pneumonia (54).
T153 19678-19809 Sentence denotes However, these findings are not completely specific to COVID-19 and do not exclude a co-infection or an alternative diagnosis (55).
T154 19811-19855 Sentence denotes Biomarkers Associated With COVID-19 Patients
T155 19856-20166 Sentence denotes The most common laboratory features reported in patients with COVID-19 include decreased albumin (75.8% [95% CI, 30.5% to 100%]), elevated C-reactive protein (58.3% [CI, 21.8% to 94.7%]), and elevated lactate dehydrogenase levels (57.0% [CI, 38.0% to 76.0%]), and lymphopenia (43.1% [CI, 18.9% to 67.3%]) (56).
T156 20167-20432 Sentence denotes Other biomarkers that have been reported include increased erythrocyte sedimentation rates; elevated aspartate aminotransferase, alanine aminotransferase, and creatinine kinase levels; leukopenia; leukocytosis; and increased bilirubin and creatinine levels (57–59).
T157 20433-20643 Sentence denotes Such findings are not surprising, because these biomarkers represent an inflammatory host response to SARS–CoV-2 or are early markers of end-organ dysfunction, similar to that seen in patients with sepsis (60).
T158 20644-20826 Sentence denotes No biomarker or combination of biomarkers currently exists that is sensitive or specific enough to establish a diagnosis of COVID-19, or to pragmatically predict its clinical course.
T159 20828-20872 Sentence denotes Unmet Needs and the Diagnostic Test Pipeline
T160 20874-20913 Sentence denotes Scaling Up Access to Diagnostic Testing
T161 20914-21078 Sentence denotes In the face of a public health emergency, important first steps to expand testing capacity include relaxing and streamlining regulatory requirements and procedures.
T162 21079-21306 Sentence denotes Local public health laboratories and academic diagnostic laboratories in the United States are being rapidly enabled to perform EUA-granted commercial assays and laboratory-developed tests using research use–only reagents (61).
T163 21307-21476 Sentence denotes University research laboratories could also add capacity, although concerns exist regarding quality control and the absence of protocols for managing clinical specimens.
T164 21477-21611 Sentence denotes Flexibility regarding nucleic acid extraction methods and amplification instruments when using CDC protocols is being introduced (34).
T165 21612-21770 Sentence denotes National agencies are expeditiously making materials for test development and validation available to clinical laboratories and diagnostic test manufacturers.
T166 21771-21939 Sentence denotes Safely evaluating clinically stable persons for COVID-19 at traditional health care access points is resource intensive and slow, and risks exposing staff to infection.
T167 21940-22170 Sentence denotes Many jurisdictions are enabling innovative testing venues, such as external tents or drive-through or “phone booth” testing, as well as home assessment teams to expedite specimen collection while limiting potential exposures (62).
T168 22171-22258 Sentence denotes Telemedicine combined with at-home nasal swab self-testing also has been proposed (63).
T169 22259-22450 Sentence denotes Of importance, in jurisdictions without universal health care coverage, policy solutions must be introduced to eliminate financial barriers to testing for uninsured and underinsured patients.
T170 22451-22628 Sentence denotes Efforts to increase accessibility of testing for multiple use cases need to be coupled to appropriate public health interventions to isolate infected persons and their contacts.
T171 22630-22707 Sentence denotes Alternatives to Usual Specimen Types, Collection Devices, and Transport Media
T172 22708-22781 Sentence denotes Nasopharyngeal swabs are the recommended specimen for molecular analysis.
T173 22782-22959 Sentence denotes The sudden demand for flocked nasopharyngeal swabs and viral transport medium generated by the pandemic has put enormous pressures on supply chain capacities for these products.
T174 22960-23112 Sentence denotes As of 19 March 2020 the CDC made oropharyngeal, mid-turbinate, and nasal swabs acceptable specimen types if nasopharyngeal swabs are not available (31).
T175 23113-23292 Sentence denotes Early-morning posterior oropharyngeal saliva samples (coughed up by clearing the throat) also have been assessed as useful specimen types and would not require use of a swab (48).
T176 23293-23560 Sentence denotes The CDC has released a standard operating procedure for laboratories to create their own viral transport medium (64); other solutions also may be used if viral transport medium is unavailable, including phosphate-buffered saline, liquid Amies, and normal saline (65).
T177 23561-23700 Sentence denotes The FDA has provided guidance on its Web site for alternative materials to collect and transport samples for RT-PCR SARS–CoV-2 assays (34).
T178 23701-23792 Sentence denotes The diagnostic value of molecular testing of nonrespiratory specimens currently is unclear.
T179 23794-23843 Sentence denotes Diagnostics Pipeline in the Short and Medium Term
T180 23844-24180 Sentence denotes Although excellent tools exist for the diagnosis of symptomatic patients in well-equipped laboratories, important gaps remain in screening asymptomatic persons in the incubation phase, as well as for the accurate determination of live viral shedding among patients in the convalescence phase to inform de-isolation decisions (Figure 2).
T181 24181-24301 Sentence denotes Further, it is critical to advance solutions that require less well-equipped laboratories to curb the pandemic globally.
T182 24302-24535 Sentence denotes The Foundation for Innovative New Diagnostics (FIND) and others have created online resources to collate the rapidly evolving set of assays at various stages of development, from proof of concept to full regulatory approval (20, 53).
T183 24536-24745 Sentence denotes Simple antigen-based tests, if sensitive enough, might be useful in lower-resource and home settings to inform quarantine and spatial distancing measures for patients without severe illness and their contacts.
T184 24746-25075 Sentence denotes Novel technologies, such as Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)-based diagnostics are being used to develop rapid, simple, low-cost, portable, temperature-stable assays for deployment in the field in nontraditional and resource-limited settings, such as airports and border crossings (20, 51, 54).
T185 25076-25168 Sentence denotes Other technologies might be deployed to lower-resource settings if they can be standardized.
T186 25169-25368 Sentence denotes For example, it might be possible to leverage existing loop-mediated isothermal amplification testing networks established for other diseases, such as human African trypanosomiasis surveillance (66).
T187 25370-25390 Sentence denotes Other Considerations
T188 25391-25562 Sentence denotes Critical considerations for diagnostics used for epidemic diseases of public health importance include the quality assurance and regulatory frameworks surrounding testing.
T189 25563-25779 Sentence denotes Mature regulatory agencies have developed mechanisms to account for emergencies, such as the FDA's EUA stream, but pragmatic solutions must be found to facilitate wide-scale, independent evaluation of emerging tests.
T190 25780-25941 Sentence denotes Initially, the need for elaborate biosafety precautions and inconsistent recommendations for their application across regions severely hampered COVID-19 testing.
T191 25942-26370 Sentence denotes Although these continue to evolve, current recommendations in Canada and the United States acknowledge that nonpropagative work for molecular testing may be performed in containment level 2 conditions found in routine diagnostic laboratories and provide specific guidance on diagnostic testing of specimens conducted outside a biosafety level 2 laboratory, such as rapid respiratory testing performed at the point of care (67) .
T192 26372-26382 Sentence denotes Conclusion
T193 26383-26508 Sentence denotes The COVID-19 pandemic has dramatically highlighted the essential role of diagnostics in the control of communicable diseases.
T194 26509-26625 Sentence denotes Intensive diagnostics deployment probably contributed to the success of a few countries in controlling transmission.
T195 26626-26747 Sentence denotes Urgent clinical and public health needs now drive an unprecedented global effort to increase SARS–CoV-2 testing capacity.
T196 26748-26893 Sentence denotes Finally, the blinding speed with which COVID-19 has spread illustrates the need for preparedness and long-term investments in diagnostic testing.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 625-634 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 5550-5559 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 18906-18915 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T4 19662-19671 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T5 20120-20131 Phenotype denotes lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T6 20216-20257 Phenotype denotes increased erythrocyte sedimentation rates http://purl.obolibrary.org/obo/HP_0003565
T7 20352-20362 Phenotype denotes leukopenia http://purl.obolibrary.org/obo/HP_0001882
T8 20364-20376 Phenotype denotes leukocytosis http://purl.obolibrary.org/obo/HP_0001974
T9 20382-20401 Phenotype denotes increased bilirubin http://purl.obolibrary.org/obo/HP_0003573
T10 20631-20637 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806