> top > docs > PMC:6988269 > spans > 15919-20325 > annotations

PMC:6988269 / 15919-20325 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T78 377-381 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T79 646-649 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T80 749-752 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T81 857-861 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T82 971-977 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T83 1151-1155 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T84 1235-1239 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T85 2128-2134 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T86 2146-2149 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T87 2260-2263 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T88 2405-2411 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T89 2423-2426 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T90 2489-2492 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T91 2630-2636 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T92 2648-2651 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T93 2840-2844 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T5 971-977 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T6 2128-2134 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T7 2405-2411 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T8 2630-2636 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T55 1417-1434 Disease denotes Influenza A(H1N1) http://purl.obolibrary.org/obo/MONDO_0005460
T56 1447-1456 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T57 1472-1481 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T58 1503-1512 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T59 1527-1536 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T60 1551-1560 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T61 1857-1867 Disease denotes Legionella http://purl.obolibrary.org/obo/MONDO_0005824
T62 2914-2933 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T142 12-19 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T143 144-151 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T144 169-175 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T145 317-323 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T146 377-381 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T147 426-431 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T148 507-513 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T149 609-614 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T150 615-621 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airway
T151 857-861 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T152 888-894 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T153 965-970 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T154 999-1005 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T155 1006-1013 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T156 1017-1022 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T157 1079-1084 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T158 1106-1113 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T159 1118-1126 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T160 1151-1155 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T161 1235-1239 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T162 1285-1292 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T163 1313-1318 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T164 1394-1396 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T165 1427-1428 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T166 1457-1458 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T167 1482-1483 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T168 1495-1497 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T169 1513-1514 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T170 1522-1526 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T171 1537-1538 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T172 1561-1562 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T173 1587-1592 http://purl.obolibrary.org/obo/CLO_0001006 denotes 31 1
T174 1646-1651 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T175 1653-1654 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T176 1655-1656 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T177 1682-1687 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T178 1712-1717 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T179 1719-1721 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T180 1742-1747 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T181 1772-1777 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T182 1779-1781 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T183 1786-1791 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T184 1834-1839 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T185 1936-1937 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T186 1964-1971 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T187 1986-1991 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T188 2070-2071 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T189 2105-2110 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T190 2120-2127 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T191 2216-2221 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T192 2222-2228 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airway
T193 2229-2239 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T194 2382-2387 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T195 2397-2404 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T196 2607-2612 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T197 2622-2629 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T198 2773-2779 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T199 2811-2818 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T200 2840-2844 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T201 2856-2862 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T202 2863-2864 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T203 3573-3578 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T204 3678-3685 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T205 3741-3745 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T206 3855-3862 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T207 3903-3908 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T208 3923-3928 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T209 4027-4032 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T210 4036-4037 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 4071-4075 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T212 4358-4363 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T48 78-94 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T49 203-208 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T50 222-234 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T51 230-234 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T52 255-271 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T53 1500-1502 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T54 1621-1623 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T55 1663-1665 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T56 1693-1695 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T57 1723-1725 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T58 1753-1755 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T59 1783-1785 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T60 1813-1815 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T61 1854-1856 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T62 1877-1879 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T63 1900-1902 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T64 1933-1935 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T65 3409-3412 Chemical denotes PHE http://purl.obolibrary.org/obo/CHEBI_28044

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T134 0-19 Sentence denotes Specificity testing
T135 21-39 Sentence denotes Chemical stability
T136 40-272 Sentence denotes To exclude non-specific reactivity of oligonucleotides among each other, causing artificial fluorescent signals, all assays were tested 120 times in parallel with water and no other nucleic acid except the provided oligonucleotides.
T137 273-333 Sentence denotes In none of these reactions was any positive signal detected.
T138 335-376 Sentence denotes Cross-reactivity with other coronaviruses
T139 377-557 Sentence denotes Cell culture supernatants containing all endemic human coronaviruses (HCoV)‑229E, ‑NL63, ‑OC43 and ‑HKU1 as well as MERS-CoV were tested in duplicate in all three assays (Table 2).
T140 558-639 Sentence denotes For the non-cultivable HCoV-HKU1, supernatant from human airway culture was used.
T141 640-814 Sentence denotes Viral RNA concentration in all samples was determined by specific real-time RT-PCRs and in vitro-transcribed RNA standards designed for absolute quantification of viral load.
T142 815-920 Sentence denotes Additional undiluted (but not quantified) cell culture supernatants were tested as summarised in Table 2.
T143 921-986 Sentence denotes These were additionally mixed into negative human sputum samples.
T144 987-1069 Sentence denotes None of the tested viruses or virus preparations showed reactivity with any assay.
T145 1070-1256 Sentence denotes Table 2 Tests of known respiratory viruses and bacteria in clinical samples and cell culture preparations for cross-reactivity in 2019 novel coronavirus E and RdRp gene assays (n = 310)
T146 1257-1328 Sentence denotes Clinical samples with known viruses Clinical samplesa Virus isolatesb
T147 1329-1346 Sentence denotes HCoV-HKU1 14 1c
T148 1347-1364 Sentence denotes HCoV-OC43 16 2d
T149 1365-1382 Sentence denotes HCoV-NL63 14 1e
T150 1383-1400 Sentence denotes HCoV-229E 18 2f
T151 1401-1416 Sentence denotes MERS-CoV 5 1g
T152 1417-1446 Sentence denotes Influenza A(H1N1)pdm09 17 1
T153 1447-1471 Sentence denotes Influenza A(H3N2) 16 1
T154 1472-1502 Sentence denotes Influenza A (untyped) 11 NA
T155 1503-1526 Sentence denotes Influenza A(H5N1) 1 1
T156 1527-1550 Sentence denotes Influenza A(H7N9) 0 1
T157 1551-1592 Sentence denotes Influenza B (Victoria or Yamagata) 31 1
T158 1593-1623 Sentence denotes Rhinovirus/enterovirus 31 NA
T159 1624-1665 Sentence denotes Respiratory syncytial virus (A/B) 33 NA
T160 1666-1695 Sentence denotes Parainfluenza 1 virus 12 NA
T161 1696-1725 Sentence denotes Parainfluenza 2 virus 11 NA
T162 1726-1755 Sentence denotes Parainfluenza 3 virus 14 NA
T163 1756-1785 Sentence denotes Parainfluenza 4 virus 11 NA
T164 1786-1815 Sentence denotes Human metapneumovirus 16 NA
T165 1816-1833 Sentence denotes Adenovirus 13 1
T166 1834-1856 Sentence denotes Human bocavirus 6 NA
T167 1857-1872 Sentence denotes Legionella spp.
T168 1874-1879 Sentence denotes 3 NA
T169 1880-1895 Sentence denotes Mycoplasma spp.
T170 1897-1902 Sentence denotes 4 NA
T171 1903-1935 Sentence denotes Total clinical samples 297 NA
T172 1936-2069 Sentence denotes a For samples with multiple viruses detected, the virus with highest concentration is listed, as indicated by real-time PCR Ct value.
T173 2070-2135 Sentence denotes b Directly quantified or spiked in human negative-testing sputum.
T174 2136-2201 Sentence denotes c 1 × 105 RNA copies/mL, determined by specific real-time RT-PCR.
T175 2202-2248 Sentence denotes Isolated from human airway epithelial culture.
T176 2249-2330 Sentence denotes d 1 × 1010 RNA copies/mL, determined by specific real-time RT-PCR of one isolate.
T177 2331-2412 Sentence denotes The other isolate was not quantified but spiked in human negative-testing sputum.
T178 2413-2478 Sentence denotes e 4 × 109 RNA copies/mL, determined by specific real-time RT-PCR.
T179 2479-2559 Sentence denotes f 3 × 109 RNA copies/mL, determined by specific real-time RT-PCR of one isolate.
T180 2560-2637 Sentence denotes The other isolate was not quantified spiked in human negative-testing sputum.
T181 2638-2703 Sentence denotes g 1 × 108 RNA copies/mL, determined by specific real-time RT-PCR.
T182 2705-2818 Sentence denotes Exclusivity of 2019 novel coronavirus based on clinical samples pre-tested positive for other respiratory viruses
T183 2819-3080 Sentence denotes Using the E and RdRp gene assays, we tested a total of 297 clinical samples from patients with respiratory disease from the biobanks of five laboratories that provide diagnostic services (one in Germany, two in the Netherlands, one in Hong Kong, one in the UK).
T184 3081-3295 Sentence denotes We selected 198 samples from three university medical centres where patients from general and intensive care wards as well as mainly paediatric outpatient departments are seen (Germany, the Netherlands, Hong Kong).
T185 3296-3462 Sentence denotes The remaining samples were contributed by national public health services performing surveillance studies (RIVM, PHE), with samples mainly submitted by practitioners.
T186 3463-3662 Sentence denotes The samples contained the broadest range of respiratory agents possible and reflected the general spectrum of virus concentrations encountered in diagnostic laboratories in these countries (Table 2).
T187 3663-3721 Sentence denotes In total, this testing yielded no false positive outcomes.
T188 3722-3848 Sentence denotes In four individual test reactions, weak initial reactivity was seen but they were negative upon retesting with the same assay.
T189 3849-4085 Sentence denotes These signals were not associated with any particular virus, and for each virus with which initial positive reactivity occurred, there were other samples that contained the same virus at a higher concentration but did not test positive.
T190 4086-4406 Sentence denotes Given the results from the extensive technical qualification described above, it was concluded that this initial reactivity was not due to chemical instability of real-time PCR probes but most probably to handling issues caused by the rapid introduction of new diagnostic tests and controls during this evaluation study.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
274 121-131 Species denotes artificial Tax:81077
275 78-94 Chemical denotes oligonucleotides MESH:D009841
276 203-208 Chemical denotes water MESH:D014867
277 255-271 Chemical denotes oligonucleotides MESH:D009841
287 466-481 Gene denotes ‑OC43 and ‑HKU1
288 426-431 Species denotes human Tax:9606
289 432-445 Species denotes coronaviruses Tax:11118
290 447-457 Species denotes HCoV)‑229E Tax:11137
291 493-501 Species denotes MERS-CoV Tax:1335626
292 581-590 Species denotes HCoV-HKU1 Tax:290028
293 609-614 Species denotes human Tax:9606
294 965-970 Species denotes human Tax:9606
295 460-464 Species denotes NL63 Tax:277944
309 1329-1338 Species denotes HCoV-HKU1 Tax:290028
310 1347-1356 Species denotes HCoV-OC43 Tax:31631
311 1365-1374 Species denotes HCoV-NL63 Tax:277944
312 1383-1392 Species denotes HCoV-229E Tax:11137
313 1401-1409 Species denotes MERS-CoV Tax:1335626
314 1429-1433 Species denotes H1N1 Tax:114727
315 1459-1463 Species denotes H3N2 Tax:119210
316 1593-1603 Species denotes Rhinovirus Tax:12059
317 1624-1654 Species denotes Respiratory syncytial virus (A Tax:1439707
318 1786-1807 Species denotes Human metapneumovirus Tax:162145
319 1816-1826 Species denotes Adenovirus Tax:10508
320 1834-1849 Species denotes Human bocavirus Tax:329641
321 1539-1543 CellLine denotes H7N9 CVCL:0452
325 1230-1234 Gene denotes RdRp Gene:43740578
326 1201-1223 Species denotes 2019 novel coronavirus Tax:2697049
327 1094-1105 Species denotes respiratory Tax:1439707
329 2105-2110 Species denotes human Tax:9606
332 2157-2159 Gene denotes mL Gene:21832
333 2216-2221 Species denotes human Tax:9606
336 2271-2273 Gene denotes mL Gene:21832
337 2382-2387 Species denotes human Tax:9606
339 2434-2436 Gene denotes mL Gene:21832
342 2500-2502 Gene denotes mL Gene:21832
343 2607-2612 Species denotes human Tax:9606
345 2659-2661 Gene denotes mL Gene:21832
348 2720-2742 Species denotes 2019 novel coronavirus Tax:2697049
349 2799-2810 Species denotes respiratory Tax:1439707
356 2835-2839 Gene denotes RdRp Gene:43740578
357 2900-2908 Species denotes patients Tax:9606
358 3149-3157 Species denotes patients Tax:9606
359 3225-3235 Species denotes outpatient Tax:9606
360 3507-3518 Species denotes respiratory Tax:1439707
361 2914-2933 Disease denotes respiratory disease MESH:D012140