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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T981 35-37 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T982 66-71 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T983 140-153 Body_part denotes immune system http://purl.org/sig/ont/fma/fma9825
T984 178-198 Body_part denotes natural killer cells http://purl.org/sig/ont/fma/fma63147
T985 193-198 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T986 200-223 Body_part denotes cytotoxic T lymphocytes http://purl.org/sig/ont/fma/fma70573
T987 291-295 Body_part denotes IL-2 http://purl.org/sig/ont/fma/fma84051
T988 291-293 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T989 303-312 Body_part denotes cytokines http://purl.org/sig/ont/fma/fma84050
T990 318-320 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T991 324-326 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T992 330-334 Body_part denotes IL-2 http://purl.org/sig/ont/fma/fma84051
T993 330-332 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T994 336-338 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T995 372-377 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T996 419-443 Body_part denotes antigen-presenting cells http://purl.org/sig/ont/fma/fma273565
T997 438-443 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T998 517-522 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T999 566-569 Body_part denotes CSF http://purl.org/sig/ont/fma/fma20935
T1000 580-591 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T1001 615-620 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T1002 657-662 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T1003 671-679 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T1004 718-722 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T1005 869-877 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T1006 902-906 Body_part denotes IL-1 http://purl.org/sig/ont/fma/fma86583
T1007 902-904 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1008 909-911 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1009 916-918 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1010 986-989 Body_part denotes CSF http://purl.org/sig/ont/fma/fma20935
T1011 1027-1032 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T1012 1071-1079 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T1013 1084-1093 Body_part denotes chemokine http://purl.org/sig/ont/fma/fma241981
T1014 1150-1157 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T1015 1196-1213 Body_part denotes endothelial cells http://purl.org/sig/ont/fma/fma66772
T1016 1208-1213 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T1017 1215-1225 Body_part denotes mast cells http://purl.org/sig/ont/fma/fma66784
T1018 1220-1225 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T1019 1227-1235 Body_part denotes monocyte http://purl.org/sig/ont/fma/fma62864
T1020 1244-1255 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T1021 1290-1301 Body_part denotes neutrophils http://purl.org/sig/ont/fma/fma62860
T1022 1326-1332 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T1023 1351-1353 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1024 1372-1377 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T1025 1383-1393 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T1026 1502-1504 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1027 1564-1575 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T1028 1587-1597 Body_part denotes mast cells http://purl.org/sig/ont/fma/fma66784
T1029 1592-1597 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T1030 1618-1620 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1031 1646-1657 Body_part denotes fibroblasts http://purl.org/sig/ont/fma/fma63877
T1032 1662-1680 Body_part denotes type 2 pneumocytes http://purl.org/sig/ont/fma/fma62501
T1033 1899-1901 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1034 2087-2089 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1035 2150-2152 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1036 2188-2192 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T1037 2208-2212 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T1038 2245-2247 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T1039 2255-2259 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T58 140-153 Body_part denotes immune system http://purl.obolibrary.org/obo/UBERON_0002405
T59 718-722 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T60 1162-1169 Body_part denotes vessels http://purl.obolibrary.org/obo/UBERON_0000055
T61 1326-1332 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T62 2208-2212 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T272 718-730 Disease denotes lung disease http://purl.obolibrary.org/obo/MONDO_0005275
T273 754-762 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T274 1492-1500 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T275 1528-1546 Disease denotes pulmonary fibrosis http://purl.obolibrary.org/obo/MONDO_0002771
T276 1776-1784 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T277 2051-2059 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T278 2208-2220 Disease denotes lung disease http://purl.obolibrary.org/obo/MONDO_0005275
T279 2395-2403 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T666 66-71 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T667 140-153 http://purl.obolibrary.org/obo/UBERON_0002405 denotes immune system
T668 178-198 http://purl.obolibrary.org/obo/CL_0000623 denotes natural killer cells
T669 291-295 http://purl.obolibrary.org/obo/PR_000001379 denotes IL-2
T670 330-334 http://purl.obolibrary.org/obo/PR_000001379 denotes IL-2
T671 360-365 http://purl.obolibrary.org/obo/CLO_0053477 denotes GATA3
T672 367-371 http://purl.obolibrary.org/obo/CL_0000792 denotes Treg
T673 372-377 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T674 438-443 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T675 515-522 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T676 615-620 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T677 657-662 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T678 718-722 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T679 718-722 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T680 772-782 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T681 813-817 http://purl.obolibrary.org/obo/CLO_0050768 denotes TLR2
T682 828-829 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T683 867-868 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T684 1006-1009 http://purl.obolibrary.org/obo/CLO_0050389 denotes T17
T685 1021-1024 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T686 1025-1032 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T687 1162-1169 http://purl.obolibrary.org/obo/UBERON_0000055 denotes vessels
T688 1196-1213 http://purl.obolibrary.org/obo/CL_0000115 denotes endothelial cells
T689 1220-1225 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T690 1227-1235 http://purl.obolibrary.org/obo/CL_0000576 denotes monocyte
T691 1358-1367 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T692 1370-1377 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T693 1550-1560 http://purl.obolibrary.org/obo/CLO_0001658 denotes activating
T694 1592-1597 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T695 1646-1657 http://purl.obolibrary.org/obo/CL_0000057 denotes fibroblasts
T696 1694-1704 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T697 1746-1747 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T698 1911-1912 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T699 1972-1973 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T700 2062-2069 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T701 2126-2131 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T702 2186-2192 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T703 2193-2203 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T704 2208-2212 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T705 2208-2212 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T706 2251-2254 http://purl.obolibrary.org/obo/CLO_0051025 denotes ST2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T743 35-37 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T745 88-98 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999
T746 233-242 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T747 291-293 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T749 318-320 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T751 324-326 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T753 330-332 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T755 336-338 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T757 419-426 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T758 563-565 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T759 824-826 Chemical denotes NF http://purl.obolibrary.org/obo/CHEBI_141424|http://purl.obolibrary.org/obo/CHEBI_25573|http://purl.obolibrary.org/obo/CHEBI_1224
T762 902-904 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T764 909-911 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T766 916-918 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T768 983-985 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T769 1351-1353 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T771 1502-1504 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T773 1561-1563 Chemical denotes M2 http://purl.obolibrary.org/obo/CHEBI_34827|http://purl.obolibrary.org/obo/CHEBI_51112
T775 1618-1620 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T777 1899-1901 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T779 2062-2069 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T780 2087-2089 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T782 2150-2152 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T784 2245-2247 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T786 2314-2322 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T787 2323-2333 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T93 718-730 Phenotype denotes lung disease http://purl.obolibrary.org/obo/HP_0002088
T94 1528-1546 Phenotype denotes pulmonary fibrosis http://purl.obolibrary.org/obo/HP_0002206
T95 2208-2220 Phenotype denotes lung disease http://purl.obolibrary.org/obo/HP_0002088

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T136 233-252 http://purl.obolibrary.org/obo/GO_0051607 denotes antiviral responses
T137 278-287 http://purl.obolibrary.org/obo/GO_0046903 denotes secretion
T138 983-1000 http://purl.obolibrary.org/obo/GO_0032604 denotes GM-CSF production
T139 1694-1730 http://purl.obolibrary.org/obo/GO_0001837 denotes epithelial-to-mesenchymal transition
T140 2150-2166 http://purl.obolibrary.org/obo/GO_0072639 denotes IL-33 production
T141 2186-2203 http://purl.obolibrary.org/obo/GO_0042110 denotes T-cell activation
T142 2188-2203 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T218 0-317 Sentence denotes Upon increasing release of alarmin IL-33 from injured respiratory cells, in the lack of interferon expression, and alongside efforts of the immune system to overcome inefficient natural killer cells, cytotoxic T lymphocytes, and Th1 antiviral responses, sequential compensatory secretion of IL-2 family cytokines (ie.
T219 318-650 Sentence denotes IL-4, IL-9, IL-2, IL-7) from dysregulated GATA3+ Treg cells, differentiated ILC2, and overstimulated antigen-presenting cells might account for the early expansion of polyfunctional (CXCR3+)Vγ9Vδ2 T cells and the later expansion of (CCR2+CCR5+) GM-CSF-producing lymphocytes, both recruited to the lungs by specific chemoattractants.
T220 651-731 Sentence denotes These cells amplify alveolar damage and establish autoinflammatory lung disease.
T221 732-1044 Sentence denotes At advanced stages of COVID-19, intense activation of the NLRP3 inflammasome and TLR2–MyD88–NF-κB mediated pathways most likely create a cytokine environment enriched in IL-1β, IL-23, IL-6, and TNF, which would further elicit Th17 differentiation and GM-CSF production by γδT17, Th17, and CD8 T cells (figure 1).
T222 1045-1302 Sentence denotes Ultimately, the resulting cytokine and chemokine milieu could account for the hyperinflammatory state of tissues and vessels mediated by dysfunctional endothelial cells, mast cells, monocyte-derived macrophages, and extracellular trap-producing neutrophils.
T223 1303-1461 Sentence denotes Endothelial release of tissue factor induced by IL-33, activated γδT cells, and neutrophil extracellular traps might act to promote thrombotic manifestations.
T224 1462-1742 Sentence denotes In patients who survive acute COVID-19, IL-33 might finally drive pulmonary fibrosis by activating M2 macrophages, ILC2, and mast cells to release TGFβ and IL-13, which act in turn on fibroblasts and type 2 pneumocytes to elicit an epithelial-to-mesenchymal transition (figure 2).
T225 1743-1971 Sentence denotes As a result, different stages of COVID-19 disease can be distinguished (ie, mild-to-moderate, severe-to-critical, chronic-to-fibrotic), and we suggest that IL-33 plays a central role in all of these pathogenic phases (figure 3).
T226 1972-2230 Sentence denotes A preprint101 that recently appeared online supports our model, revealing that SARS-CoV-2 peptide exposure elicits IL-33 expression from patients who are virus seropositive, and IL-33 production is correlated with T-cell activation and lung disease severity.
T227 2231-2413 Sentence denotes Targeting the IL-33–ST2 axis using monoclonal antibodies (or, alternatively, small-molecule inhibitors) could prove to be an effective strategy for controlling the COVID-19 pandemic.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1942 35-40 Gene denotes IL-33 Gene:90865
1943 318-322 Gene denotes IL-4 Gene:3565
1944 324-328 Gene denotes IL-9 Gene:3578
1945 330-334 Gene denotes IL-2 Gene:3558
1946 336-340 Gene denotes IL-7 Gene:3574
1947 360-365 Gene denotes GATA3 Gene:2625
1948 501-506 Gene denotes CXCR3 Gene:2833
1949 551-555 Gene denotes CCR2 Gene:729230
1950 556-560 Gene denotes CCR5 Gene:1234
1951 563-569 Gene denotes GM-CSF Gene:1437
1952 790-795 Gene denotes NLRP3 Gene:114548
1953 813-817 Gene denotes TLR2 Gene:7097
1954 818-823 Gene denotes MyD88 Gene:4615
1955 824-829 Gene denotes NF-κB Gene:4790
1956 902-907 Gene denotes IL-1β Gene:3552
1957 909-914 Gene denotes IL-23 Gene:51561
1958 916-920 Gene denotes IL-6 Gene:3569
1959 926-929 Gene denotes TNF Gene:7124
1960 983-989 Gene denotes GM-CSF Gene:1437
1961 1351-1356 Gene denotes IL-33 Gene:90865
1962 1502-1507 Gene denotes IL-33 Gene:90865
1963 1609-1613 Gene denotes TGFβ Gene:7039
1964 1618-1623 Gene denotes IL-13 Gene:3596
1965 1899-1904 Gene denotes IL-33 Gene:90865
1966 2087-2092 Gene denotes IL-33 Gene:90865
1967 2150-2155 Gene denotes IL-33 Gene:90865
1968 2245-2250 Gene denotes IL-33 Gene:90865
1969 2251-2254 Gene denotes ST2 Gene:6761
1970 1021-1024 Gene denotes CD8 Gene:925
1971 1465-1473 Species denotes patients Tax:9606
1972 2051-2061 Species denotes SARS-CoV-2 Tax:2697049
1973 2109-2117 Species denotes patients Tax:9606
1974 291-295 Gene denotes IL-2 Gene:3558
1975 1326-1339 Gene denotes tissue factor Gene:2152
1976 701-730 Disease denotes autoinflammatory lung disease MESH:D008171
1977 754-762 Disease denotes COVID-19 MESH:C000657245
1978 1492-1500 Disease denotes COVID-19 MESH:C000657245
1979 1528-1546 Disease denotes pulmonary fibrosis MESH:D011658
1980 1776-1784 Disease denotes COVID-19 MESH:C000657245
1981 2208-2220 Disease denotes lung disease MESH:D008171
1982 2395-2403 Disease denotes COVID-19 MESH:C000657245
1983 508-516 CellLine denotes Vγ9Vδ2 T CVCL:M092