> top > docs > PMC:7200337 > spans > 39807-43902 > annotations

PMC:7200337 / 39807-43902 JSONTXT

Annnotations TAB JSON ListView MergeView

2_test

Id Subject Object Predicate Lexical cue
32505227-32284614-46575327 462-466 32284614 denotes 2020
32505227-32284614-46575329 656-660 32284614 denotes 2020
32505227-18832706-46575330 774-778 18832706 denotes 2008
32505227-29654146-46575331 1171-1175 29654146 denotes 2018
32505227-18832706-46575337 2845-2849 18832706 denotes 2008
32505227-32284614-46575338 3813-3817 32284614 denotes 2020
T4570 462-466 32284614 denotes 2020
T63291 656-660 32284614 denotes 2020
T22882 774-778 18832706 denotes 2008
T81493 1171-1175 29654146 denotes 2018
T22604 2845-2849 18832706 denotes 2008
T87043 3813-3817 32284614 denotes 2020

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T405 28-32 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T406 128-132 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T407 278-283 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T408 326-329 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T409 569-574 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T410 612-617 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T411 729-733 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T412 1003-1007 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T413 1152-1157 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T414 1435-1440 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T415 1511-1516 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T416 1654-1659 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T417 1838-1843 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T418 1917-1922 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T419 1948-1956 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T420 2195-2200 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T421 2439-2444 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T422 2701-2706 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T423 2719-2724 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T424 2758-2762 Body_part denotes IL-2 http://purl.org/sig/ont/fma/fma84051
T425 2773-2778 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T426 2900-2904 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T427 3057-3060 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T428 3073-3076 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T429 3120-3125 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T430 3325-3330 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T431 3647-3652 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T432 3920-3924 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T263 44-52 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T264 157-165 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T265 536-544 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T266 751-759 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T267 816-824 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T268 2068-2071 Disease denotes PMA http://purl.obolibrary.org/obo/MONDO_0016692|http://purl.obolibrary.org/obo/MONDO_0018687
T270 2211-2219 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T271 2623-2631 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T272 2634-2643 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T273 3153-3161 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T274 3341-3349 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T275 3943-3951 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T276 3954-3963 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T498 26-32 http://purl.obolibrary.org/obo/CL_0000084 denotes T Cell
T499 126-132 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T500 200-204 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T501 200-204 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer
T502 266-275 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T503 276-283 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T504 334-338 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T505 340-344 http://purl.obolibrary.org/obo/PR_000001343 denotes CD69
T506 346-350 http://purl.obolibrary.org/obo/PR_000001380 denotes CD25
T507 352-356 http://purl.obolibrary.org/obo/PR_000001307 denotes CD44
T508 563-566 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T509 567-574 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T510 591-600 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T511 606-609 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T512 610-617 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T513 683-684 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T514 714-717 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T515 723-726 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T516 727-733 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T517 763-765 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T518 763-765 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T519 797-798 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T520 1001-1007 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T521 1091-1100 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T522 1131-1140 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T523 1141-1157 http://purl.obolibrary.org/obo/CL_0000911 denotes effector T cells
T524 1171-1175 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T525 1331-1337 http://purl.obolibrary.org/obo/PR_000001852 denotes CTLA-4
T526 1429-1432 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T527 1433-1440 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T528 1505-1508 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T529 1509-1516 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T530 1636-1639 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T531 1648-1651 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T532 1652-1659 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T533 1824-1827 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T534 1832-1835 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T535 1836-1843 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T536 1915-1922 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T537 2189-2192 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T538 2193-2200 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T539 2307-2308 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T540 2363-2364 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T541 2433-2436 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T542 2437-2444 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T543 2554-2555 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T544 2699-2706 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T545 2713-2716 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T546 2717-2724 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T547 2758-2762 http://purl.obolibrary.org/obo/PR_000001379 denotes IL-2
T548 2767-2770 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T549 2771-2778 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T550 2834-2836 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T551 2834-2836 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T552 2898-2904 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T553 3114-3117 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T554 3118-3125 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T555 3189-3194 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T556 3323-3330 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T557 3366-3375 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T558 3392-3393 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T559 3641-3644 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T560 3645-3652 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T561 3771-3772 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T562 3897-3898 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T563 3918-3924 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T203 330-332 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T204 389-391 Chemical denotes Ni http://purl.obolibrary.org/obo/CHEBI_28112
T205 406-409 Chemical denotes Guo http://purl.obolibrary.org/obo/CHEBI_16750
T206 763-765 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T207 869-871 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T208 957-959 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T209 1058-1060 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T210 1141-1149 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T211 1275-1284 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T212 1493-1495 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T213 2041-2048 Chemical denotes phorbol http://purl.obolibrary.org/obo/CHEBI_8116
T214 2049-2058 Chemical denotes myristate http://purl.obolibrary.org/obo/CHEBI_30807
T215 2059-2066 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T217 2068-2071 Chemical denotes PMA http://purl.obolibrary.org/obo/CHEBI_37537|http://purl.obolibrary.org/obo/CHEBI_53780|http://purl.obolibrary.org/obo/CHEBI_60755
T220 2077-2086 Chemical denotes ionomycin http://purl.obolibrary.org/obo/CHEBI_63954
T221 2246-2254 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T222 2573-2578 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T223 2758-2760 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T225 2834-2836 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T226 3133-3136 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T227 3479-3481 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T228 3740-3748 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T229 3749-3758 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T138 1091-1100 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1315 44-52 Disease denotes COVID-19 MESH:C000657245
1328 563-566 Gene denotes CD8 Gene:925
1329 606-609 Gene denotes CD4 Gene:920
1330 714-717 Gene denotes CD8 Gene:925
1331 723-726 Gene denotes CD4 Gene:920
1332 1040-1042 Gene denotes to Gene:6999
1333 899-901 Gene denotes to Gene:6999
1334 580-582 Gene denotes to Gene:6999
1335 751-759 Species denotes SARS-CoV Tax:694009
1336 825-833 Species denotes patients Tax:9606
1337 157-165 Disease denotes COVID-19 MESH:C000657245
1338 536-544 Disease denotes COVID-19 MESH:C000657245
1339 816-824 Disease denotes COVID-19 MESH:C000657245
1390 1293-1298 Gene denotes OX-40 Gene:7293
1391 1303-1308 Gene denotes CD137 Gene:3604
1395 1429-1432 Gene denotes CD8 Gene:925
1396 1499-1503 Gene denotes TIM3 Gene:84868
1397 1505-1508 Gene denotes CD8 Gene:925
1398 1636-1639 Gene denotes CD8 Gene:925
1399 1824-1827 Gene denotes CD4 Gene:920
1400 1832-1835 Gene denotes CD8 Gene:925
1401 1985-1990 Gene denotes IFN-γ Gene:3458
1402 1995-2000 Gene denotes TNF-α Gene:7124
1403 2189-2192 Gene denotes CD8 Gene:925
1404 2273-2279 Gene denotes CD107a Gene:3916
1405 2298-2308 Gene denotes granzyme B Gene:3002
1406 2310-2314 Gene denotes GzmB Gene:3002
1407 2397-2401 Gene denotes GzmB Gene:3002
1408 2713-2716 Gene denotes CD4 Gene:920
1409 2740-2745 Gene denotes IFN-γ Gene:3458
1410 2747-2752 Gene denotes TNF-α Gene:7124
1411 2758-2762 Gene denotes IL-2 Gene:3558
1412 2767-2770 Gene denotes CD8 Gene:925
1413 2794-2799 Gene denotes IFN-γ Gene:3458
1414 2801-2806 Gene denotes TNF-α Gene:7124
1415 2812-2818 Gene denotes CD107a Gene:3916
1416 3114-3117 Gene denotes CD8 Gene:925
1417 3203-3207 Gene denotes GZMA Gene:3001
1418 3209-3213 Gene denotes GZMB Gene:3002
1419 3219-3223 Gene denotes GZMK Gene:3003
1420 3248-3253 Gene denotes KLRC1 Gene:3821
1421 3258-3262 Gene denotes XCL1 Gene:6375
1422 2433-2436 Gene denotes CD8 Gene:925
1423 1806-1808 Gene denotes to Gene:6999
1424 1743-1745 Gene denotes to Gene:6999
1425 1679-1681 Gene denotes to Gene:6999
1426 1620-1622 Gene denotes to Gene:6999
1427 1648-1651 Gene denotes CD4 Gene:920
1428 1524-1532 Species denotes patients Tax:9606
1429 1862-1870 Species denotes patients Tax:9606
1430 2462-2470 Species denotes patients Tax:9606
1431 2593-2601 Species denotes patients Tax:9606
1432 3162-3170 Species denotes patients Tax:9606
1433 2041-2066 Chemical denotes phorbol myristate acetate MESH:D013755
1434 2068-2071 Chemical denotes PMA MESH:D013755
1435 2077-2086 Chemical denotes ionomycin MESH:D015759
1436 1847-1861 Disease denotes critically ill MESH:D016638
1437 2211-2219 Disease denotes COVID-19 MESH:C000657245
1438 2623-2643 Disease denotes SARS-CoV-1 infection MESH:C000657245
1439 3153-3161 Disease denotes COVID-19 MESH:C000657245
1451 3488-3493 Gene denotes TIM-3 Gene:84868
1452 3641-3644 Gene denotes CD4 Gene:920
1453 3774-3778 Gene denotes GzmB Gene:3002
1454 3767-3772 Gene denotes Gzm A Gene:3001
1455 3990-3992 Gene denotes to Gene:6999
1456 3600-3602 Gene denotes to Gene:6999
1457 3355-3357 Gene denotes to Gene:6999
1458 3580-3588 Species denotes patients Tax:9606
1459 3341-3349 Disease denotes COVID-19 MESH:C000657245
1460 3543-3555 Disease denotes cytotoxicity MESH:D064420
1461 3943-3963 Disease denotes SARS-CoV-2 infection MESH:C000657245

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T216 0-52 Sentence denotes Phenotype and Function of T Cell Subsets in COVID-19
T217 53-166 Sentence denotes Currently, little is known about specific phenotypical and/or functional T cell changes associated with COVID-19.
T218 167-509 Sentence denotes In the majority of preprints and peer-reviewed studies, there are reports of increased presence of activated T cells (Figure 3) characterized by expression of HLA-DR, CD38, CD69, CD25, CD44, and Ki-67 (Braun et al., 2020, Ni et al., 2020, Guo et al., 2020, Liao et al., 2020, Thevarajan et al., 2020, Yang et al., 2020a, Zheng et al., 2020a).
T219 510-780 Sentence denotes Generally, independent of COVID-19 disease severity, CD8 T cells seem to be more activated than CD4 T cells (Qin et al., 2020, Thevarajan et al., 2020, Yang et al., 2020a), a finding that echoes stronger CD8 than CD4 T cell responses during SARS-CoV-1 (Li et al., 2008).
T220 781-956 Sentence denotes Furthermore, in a case study of 10 COVID-19 patients, Diao et al. showed that levels of PD-1 increased from prodromal to symptomatic stages of the disease (Diao et al., 2020).
T221 957-1177 Sentence denotes PD-1 expression is commonly associated with T cell exhaustion, but it is important to emphasize that PD-1 is primarily induced by TCR signaling; it is thus also expressed by activated effector T cells (Ahn et al., 2018).
T222 1178-1403 Sentence denotes In addition, several studies reported higher expression of various co-stimulatory and inhibitory molecules such as OX-40 and CD137 (Zhou et al., 2020c), CTLA-4 and TIGIT (Zheng et al., 2020a), and NKG2a (Zheng et al., 2020b).
T223 1404-1573 Sentence denotes Reduced numbers of CD28+ CD8 T cells (Qin et al., 2020) as well as larger frequencies of PD-1+ TIM3+ CD8 T cells in ICU patients were also reported (Zhou et al., 2020c).
T224 1574-1772 Sentence denotes Expression of most of these markers was found to be higher in CD8 than in CD4 T cells, and levels tended to increase in severe versus non-severe cases, which may be due to differences in viral load.
T225 1773-2150 Sentence denotes Cellular functionality was shown to be impaired in CD4 and CD8 T cells of critically ill patients, with reduced frequencies of polyfunctional T cells (producing more than one cytokine) as well as generally lower IFN-γ and TNF-α production following restimulation with phorbol myristate acetate (PMA) and ionomycin (Chen et al., 2020c, Zheng et al., 2020a, Zheng et al., 2020b).
T226 2151-2349 Sentence denotes Similarly, Zheng et al. reported that CD8 T cells in severe COVID-19 appear less cytotoxic and effector-like with reduced CD107a degranulation and granzyme B (GzmB) production (Zheng et al., 2020b).
T227 2350-2493 Sentence denotes In contrast, a different study found that both GzmB and perforin were increased in CD8 T cells of severely sick patients (Zheng et al., 2020a).
T228 2494-2851 Sentence denotes In accordance with the latter observation, when compared to a moderate disease group, convalescent patients with resolved severe SARS-CoV-1 infection had significantly higher frequencies of polyfunctional T cells, with CD4 T cells producing more IFN-γ, TNF-α, and IL-2 and CD8 T cells producing more IFN-γ, TNF-α, and CD107a, respectively (Li et al., 2008).
T229 2852-3043 Sentence denotes However, given the vigorous dynamics of acute T cell responses and potential differences in sample timing throughout disease course, these observations are not necessarily mutually exclusive.
T230 3044-3310 Sentence denotes Accordingly, RNA sequencing (RNA-seq) data by Liao et al. showed that CD8 T cells in the BAL fluid of severe COVID-19 patients express cytotoxic genes such as GZMA, GZMB, and GZMK at higher levels, while KLRC1 and XCL1 are enriched in mild cases (Liao et al., 2020).
T231 3311-3556 Sentence denotes In summary, T cells in severe COVID-19 seem to be more activated and may exhibit a trend toward exhaustion based on continuous expression of inhibitory markers such as PD-1 and TIM-3 as well as overall reduced polyfunctionality and cytotoxicity.
T232 3557-3860 Sentence denotes Conversely, recovering patients were shown to have an increase in follicular helper CD4 T cells (TFH) as well as decreasing levels of inhibitory markers along with enhanced levels of effector molecules such as Gzm A, GzmB, and perforin (Thevarajan et al., 2020, Yang et al., 2020a, Zheng et al., 2020b).
T233 3861-4095 Sentence denotes Collectively, these studies provide a first glimpse into T cell dynamics in acute SARS-CoV-2 infection, but any conclusions have to be tempered at this stage on account of significant limitations in many of the current investigations.