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PMC:7402624 / 65890-67795 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T525 234-239 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T526 551-557 Body_part denotes Plasma http://purl.org/sig/ont/fma/fma62970
T527 759-767 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T528 854-861 Body_part denotes Eotaxin http://purl.org/sig/ont/fma/fma241992
T529 874-877 Body_part denotes CSF http://purl.org/sig/ont/fma/fma20935
T530 882-885 Body_part denotes CSF http://purl.org/sig/ont/fma/fma20935
T531 964-968 Body_part denotes IL-1 http://purl.org/sig/ont/fma/fma86583
T532 982-986 Body_part denotes IL-2 http://purl.org/sig/ont/fma/fma84051

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2033 328-332 Gene denotes CD28 Gene:940
2034 333-338 Gene denotes CD49d Gene:3676
2035 842-845 Gene denotes EGF Gene:1950
2036 847-852 Gene denotes FGF-2 Gene:2247
2037 854-861 Gene denotes Eotaxin Gene:6356
2038 872-877 Gene denotes G-CSF Gene:1440
2039 879-885 Gene denotes GM-CSF Gene:1437
2040 887-893 Gene denotes IFN-α2 Gene:3440
2041 895-900 Gene denotes IFN-γ Gene:3458
2042 902-907 Gene denotes IL-10 Gene:3586
2043 929-934 Gene denotes IL-13 Gene:3596
2044 936-941 Gene denotes IL-15 Gene:3600
2045 943-949 Gene denotes IL-17A Gene:3605
2046 951-957 Gene denotes IL-1Ra Gene:3557
2047 959-962 Gene denotes HGF Gene:3082
2048 964-969 Gene denotes IL-1β Gene:3552
2049 971-976 Gene denotes CXCL9 Gene:4283
2050 977-980 Gene denotes MIG Gene:4283
2051 982-986 Gene denotes IL-2 Gene:3558
2052 988-992 Gene denotes IL-4 Gene:3565
2053 994-998 Gene denotes IL-5 Gene:3567
2054 1000-1004 Gene denotes IL-6 Gene:3569
2055 1006-1010 Gene denotes IL-7 Gene:3574
2056 1012-1017 Gene denotes CXCL8 Gene:3576
2057 1018-1022 Gene denotes IL-8 Gene:3576
2058 1024-1030 Gene denotes CXCL10 Gene:3627
2059 1031-1036 Gene denotes IP-10 Gene:3627
2060 1038-1042 Gene denotes CCL2 Gene:6347
2061 1043-1048 Gene denotes MCP-1 Gene:6347
2062 1063-1067 Gene denotes CCL4 Gene:6351
2063 1068-1074 Gene denotes MIP-1β Gene:6351
2064 1076-1082 Gene denotes RANTES Gene:6352
2065 1084-1089 Gene denotes TNF-α Gene:7124
2066 1095-1099 Gene denotes VEGF Gene:7422
2067 19-27 Species denotes patients Tax:9606
2068 753-758 Species denotes human Tax:9606
2069 322-327 Species denotes human Tax:9606
2070 198-201 Chemical denotes PBS MESH:D007854
2071 401-405 CellLine denotes L293 CVCL:M775
2073 1425-1430 Species denotes minor Tax:53258

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T431 415-417 Disease denotes BD http://purl.obolibrary.org/obo/MONDO_0007191
T432 1393-1395 Disease denotes R2 http://purl.obolibrary.org/obo/MONDO_0019903

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T959 165-168 http://purl.obolibrary.org/obo/CLO_0052882 denotes CD3
T960 165-168 http://purl.obolibrary.org/obo/CLO_0053434 denotes CD3
T961 205-208 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T962 234-239 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T963 266-276 http://purl.obolibrary.org/obo/CLO_0001040 denotes at 1 × 105
T964 322-327 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T965 390-393 http://purl.obolibrary.org/obo/CLO_0052882 denotes CD3
T966 390-393 http://purl.obolibrary.org/obo/CLO_0053434 denotes CD3
T967 551-557 http://purl.obolibrary.org/obo/UBERON_0001969 denotes Plasma
T968 744-745 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T969 753-758 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T970 872-877 http://purl.obolibrary.org/obo/PR_000005932 denotes G-CSF
T971 959-962 http://purl.obolibrary.org/obo/CLO_0003740 denotes HGF
T972 982-986 http://purl.obolibrary.org/obo/PR_000001379 denotes IL-2
T973 1018-1022 http://purl.obolibrary.org/obo/CLO_0053704 denotes IL-8
T974 1134-1135 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T975 1155-1165 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrument
T976 1384-1387 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T977 1388-1389 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T978 1638-1644 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T979 1666-1671 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T980 1837-1839 http://purl.obolibrary.org/obo/CLO_0008954 denotes SC
T981 1854-1860 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T94021 842-845 Chemical denotes EGF http://purl.obolibrary.org/obo/CHEBI_140739
T65282 879-881 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T7701 902-904 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T70736 909-911 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T87965 919-921 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T48479 929-931 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T16150 936-938 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T29560 943-945 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T21327 951-953 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T47948 964-966 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T94087 971-976 Chemical denotes CXCL9 http://purl.obolibrary.org/obo/CHEBI_138154
T89357 982-984 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T78875 988-990 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T30910 994-996 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T92516 1000-1002 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T24109 1006-1008 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T31035 1018-1020 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T89429 1024-1030 Chemical denotes CXCL10 http://purl.obolibrary.org/obo/CHEBI_138157
T61718 1031-1036 Chemical denotes IP-10 http://purl.obolibrary.org/obo/CHEBI_138157
T96412 1031-1033 Chemical denotes IP http://purl.obolibrary.org/obo/CHEBI_74076
T85413 1043-1046 Chemical denotes MCP http://purl.obolibrary.org/obo/CHEBI_132592|http://purl.obolibrary.org/obo/CHEBI_50099

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T135 951-957 http://purl.obolibrary.org/obo/GO_0005152 denotes IL-1Ra

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T399 0-7 Sentence denotes Luminex
T400 8-104 Sentence denotes PBMCs from patients were thawed and rested overnight at 37°C in complete RPMI (cRPMI, table S7).
T401 105-219 Sentence denotes 96-well flat bottom plates were coated with 1 μg/mL of anti-CD3 (UCHT1, #BE0231, BioXell) in PBS at 4°C overnight.
T402 220-305 Sentence denotes The next day, cells were collected and plated at 1 × 105/well in 100 μl in duplicate.
T403 306-419 Sentence denotes 2 μg/mL of anti-human CD28/CD49d was added to the wells containing plate-bound anti-CD3 (Clone L293, 347690, BD).
T404 420-550 Sentence denotes PBMCs were stimulated or left unstimulated for 16 hours, spun down (1200 rpm, 10 min) and 85 μL/well of supernatant was collected.
T405 551-673 Sentence denotes Plasma from matched subjects was thawed on ice, spun (3000 rpm, 1 min) to remove debris, and 85 μl collected in duplicate.
T406 674-821 Sentence denotes Luminex assay was run according to manufacturer’s instructions, using a custom human cytokine 31-plex panel (EMD Millipore Corporation, SPRCUS707).
T407 822-1100 Sentence denotes The panel included: EGF, FGF-2, Eotaxin, sIL-2Ra, G-CSF, GM-CSF, IFN-α2, IFN-γ, IL-10, IL-12P40, IL-12P70, IL-13, IL-15, IL-17A, IL-1Ra, HGF, IL-1β, CXCL9/MIG, IL-2, IL-4, IL-5, IL-6, IL-7, CXCL8/IL-8, CXCL10/IP-10, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, RANTES, TNF-α, and VEGF.
T408 1101-1194 Sentence denotes Assay plates were measured using a Luminex FlexMAP 3D instrument (Thermofisher, Cat#APX1342).
T409 1195-1288 Sentence denotes Data acquisition and analysis were done using xPONENT software www.luminexcorp.com/xponent/).
T410 1289-1347 Sentence denotes Data quality was examined based on the following criteria:
T411 1348-1462 Sentence denotes The standard curve for each analyte has a 5P R2 value > 0.95 with or without minor fitting using xPONENT software.
T412 1463-1654 Sentence denotes To pass assay technical quality control, the results for two controls in the kit needed to be within the 95% of CI (confidence interval) provided by the vendor for >25 of the tested analytes.
T413 1655-1730 Sentence denotes No further tests were done on samples with results out of range low (<OOR).
T414 1731-1905 Sentence denotes Samples with results that were out of range high (>OOR) or greater than the standard curve maximum value (SC max) were not tested at higher dilutions without further request.