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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T279 41-46 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T280 129-133 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T281 258-262 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T282 308-311 Body_part denotes IgD http://purl.org/sig/ont/fma/fma62876
T283 326-331 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T284 379-381 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T285 544-546 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T286 612-628 Body_part denotes germinal centers http://purl.org/sig/ont/fma/fma55224
T287 749-753 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T288 885-888 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T289 1136-1140 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T290 1369-1385 Body_part denotes cell compartment http://purl.org/sig/ont/fma/fma223408
T291 1369-1373 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T292 1508-1511 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T293 1577-1580 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T294 1665-1670 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T295 1672-1675 Body_part denotes IgD http://purl.org/sig/ont/fma/fma62876
T296 1705-1708 Body_part denotes IgD http://purl.org/sig/ont/fma/fma62876
T297 1911-1916 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T298 2111-2116 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T299 2179-2181 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T300 2300-2305 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T301 2375-2377 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T302 2465-2477 Body_part denotes cell Cluster http://purl.org/sig/ont/fma/fma62807
T303 2465-2469 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T304 2530-2534 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T305 2635-2637 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T306 2661-2665 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T307 2700-2704 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T308 2781-2797 Body_part denotes cell compartment http://purl.org/sig/ont/fma/fma223408
T309 2781-2785 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T310 2891-2895 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T311 2980-2984 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T312 3061-3065 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T15 612-628 Body_part denotes germinal centers http://purl.obolibrary.org/obo/UBERON_0010754
T16 2465-2477 Body_part denotes cell Cluster http://purl.obolibrary.org/obo/UBERON_0034922

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1189 298-303 Gene denotes CXCR5 Gene:643
1190 447-451 Gene denotes CD27 Gene:939
1191 453-457 Gene denotes CD38 Gene:952
1192 459-464 Gene denotes CD138 Gene:6382
1193 513-517 Gene denotes CD95 Gene:355
1194 527-531 Gene denotes CD27 Gene:939
1195 532-536 Gene denotes CD38 Gene:952
1196 537-542 Gene denotes CD138 Gene:6382
1197 1676-1680 Gene denotes CD27 Gene:939
1198 1699-1704 Gene denotes CXCR5 Gene:643
1199 2095-2100 Gene denotes T-bet Gene:30009
1200 2157-2161 Gene denotes CD27 Gene:939
1201 2162-2166 Gene denotes CD38 Gene:952
1202 2167-2172 Gene denotes CD138 Gene:6382
1203 2449-2454 Gene denotes T-bet Gene:30009
1204 2691-2696 Gene denotes T-bet Gene:30009
1205 2725-2730 Gene denotes CXCR5 Gene:643
1206 73-81 Species denotes patients Tax:9606
1207 248-255 Species denotes patient Tax:9606
1208 692-700 Species denotes patients Tax:9606
1209 1022-1030 Species denotes patients Tax:9606
1210 1181-1189 Species denotes patients Tax:9606
1211 1454-1462 Species denotes patients Tax:9606
1212 1813-1821 Species denotes patients Tax:9606
1213 2041-2049 Species denotes patients Tax:9606
1214 2222-2230 Species denotes patients Tax:9606
1215 2320-2328 Species denotes patients Tax:9606
1216 2588-2596 Species denotes patients Tax:9606
1217 2916-2924 Species denotes patients Tax:9606
1218 3016-3024 Species denotes patients Tax:9606
1219 1683-1690 Species denotes Cluster Tax:100569
1220 1732-1739 Species denotes Cluster Tax:100569
1221 2133-2140 Species denotes Cluster Tax:100569
1222 2386-2393 Species denotes Cluster Tax:100569
1223 2470-2477 Species denotes Cluster Tax:100569
1224 379-381 Chemical denotes PB
1225 52-54 Disease denotes HD MESH:D006816
1226 64-72 Disease denotes COVID-19 MESH:C000657245
1227 149-157 Disease denotes COVID-19 MESH:C000657245
1228 195-197 Disease denotes HD MESH:D006816
1229 239-247 Disease denotes COVID-19 MESH:C000657245
1230 337-339 Disease denotes HD MESH:D006816
1231 683-691 Disease denotes COVID-19 MESH:C000657245
1232 705-707 Disease denotes HD MESH:D006816
1233 1013-1021 Disease denotes COVID-19 MESH:C000657245
1234 1172-1180 Disease denotes COVID-19 MESH:C000657245
1235 1232-1234 Disease denotes HD MESH:D006816
1236 1348-1357 Disease denotes infection MESH:D007239
1237 1434-1436 Disease denotes HD MESH:D006816
1238 1445-1453 Disease denotes COVID-19 MESH:C000657245
1239 1630-1632 Disease denotes HD MESH:D006816
1240 1804-1812 Disease denotes COVID-19 MESH:C000657245
1241 2032-2040 Disease denotes COVID-19 MESH:C000657245
1242 2213-2221 Disease denotes COVID-19 MESH:C000657245
1243 2311-2319 Disease denotes COVID-19 MESH:C000657245
1244 2579-2587 Disease denotes COVID-19 MESH:C000657245
1245 2907-2915 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T249 52-54 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T250 56-58 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T251 64-72 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T252 149-157 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T253 188-190 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T254 195-197 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T255 239-247 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T256 337-339 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T257 344-346 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T258 379-381 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T259 544-546 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T260 683-691 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T261 705-707 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T262 712-714 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T263 1013-1021 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T264 1172-1180 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T265 1232-1234 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T266 1250-1252 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T267 1348-1357 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T268 1434-1436 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T269 1438-1440 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T270 1445-1453 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T271 1630-1632 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T272 1637-1639 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T273 1804-1812 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T274 2032-2040 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T275 2179-2181 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T276 2213-2221 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T277 2311-2319 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T278 2375-2377 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T279 2579-2587 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T280 2635-2637 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T281 2907-2915 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T534 39-46 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T535 56-58 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T536 105-106 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T537 127-133 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T538 188-190 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T539 256-262 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T540 324-331 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T541 344-346 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T542 447-451 http://purl.obolibrary.org/obo/PR_000001963 denotes CD27
T543 453-457 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T544 527-531 http://purl.obolibrary.org/obo/PR_000001963 denotes CD27
T545 532-536 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T546 712-714 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T547 747-753 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T548 801-803 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T549 1134-1140 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T550 1250-1252 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T551 1367-1373 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T552 1438-1440 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T553 1637-1639 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T554 1663-1670 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T555 1676-1680 http://purl.obolibrary.org/obo/PR_000001963 denotes CD27
T556 1709-1713 http://purl.obolibrary.org/obo/PR_000001963 denotes CD27
T557 1909-1916 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T558 2109-2116 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T559 2157-2161 http://purl.obolibrary.org/obo/PR_000001963 denotes CD27
T560 2162-2166 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T561 2298-2305 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T562 2463-2469 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T563 2528-2534 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T564 2659-2665 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T565 2689-2690 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T566 2698-2704 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T567 2779-2785 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T568 2889-2895 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T569 2968-2977 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T570 2978-2984 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T571 2999-3000 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T572 3052-3058 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T573 3059-3065 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T229 52-54 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T230 56-58 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T231 188-190 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T232 195-197 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T233 337-339 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T234 344-346 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T235 379-381 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T237 544-546 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T239 705-707 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T240 712-714 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T241 1232-1234 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T242 1250-1252 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T243 1434-1436 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T244 1438-1440 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T245 1551-1556 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T246 1630-1632 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T247 1637-1639 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T248 2179-2181 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T250 2375-2377 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T252 2635-2637 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T254 2817-2826 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T255 3007-3012 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T68 1724-1730 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T69 2102-2108 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T70 2456-2462 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T71 2652-2658 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T72 2817-2836 http://purl.obolibrary.org/obo/GO_0051607 denotes antiviral responses

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T183 0-234 Sentence denotes Projecting the flow cytometry data for B cells from HD, RD, and COVID-19 patients in tSNE space revealed a distinct picture of B cell populations in COVID-19 compared to controls, whereas RD and HD were similar (Fig. 4J and fig. S5J).
T184 235-357 Sentence denotes The COVID-19 patient B cell phenotype was dominated by loss of CXCR5 and IgD compared to B cells from HD and RD (Fig. 4J).
T185 358-485 Sentence denotes Moreover, the robust PB response was apparent in the upper right section, highlighted by CD27, CD38, CD138, and KI67 (Fig. 4J).
T186 486-629 Sentence denotes The expression of KI67 and CD95 in these CD27+CD38+CD138+ PB (Fig. 4J) could suggest recent generation and/or emigration from germinal centers.
T187 630-763 Sentence denotes We next asked whether there were different groups of COVID-19 patients (or HD and RD) with global differences in the B cell response.
T188 764-996 Sentence denotes We used Earth Movers Distance (EMD) (45) to calculate similarities between the probability distributions within the tSNE map (Fig. 4J) and clustered so that individuals with the most similar distributions grouped together (Fig. 4K).
T189 997-1150 Sentence denotes The majority of COVID-19 patients fell into two distinct groups (EMD Groups 1 and 3, Fig. 4L), suggesting two major “immunotypes” of the B cell response.
T190 1151-1386 Sentence denotes The remainder of the COVID-19 patients (~25%) clustered with the majority of the HD and all of the RD controls, supporting the observation that some individuals had limited evidence of response to infection in their B cell compartment.
T191 1387-1599 Sentence denotes To identify the population differences between HD, RD and COVID-19 patients, we performed FlowSOM clustering on the tSNE map, and also overlaid each individual EMD group onto this same tSNE map (Fig. 4, M and N).
T192 1600-1832 Sentence denotes EMD Group 2 containing mostly HD and RD was enriched for naive B cells (IgD+CD27−, Cluster 10) and CXCR5+IgD−CD27+ switched memory (Cluster 2) and, indeed, Clusters 2 and 10 were statistically reduced in COVID-19 patients (Fig. 4P).
T193 1833-1908 Sentence denotes EMD Groups 1 and 3 displayed distinct patterns across the FlowSOM clusters.
T194 1909-2060 Sentence denotes B cells from individuals in EMD Group 1 were enriched for the FlowSOM Clusters 1, 5, and 6, all of which were increased in COVID-19 patients (Fig. 4P).
T195 2061-2284 Sentence denotes FlowSOM Clusters 1 and 6 captured T-bet+ memory B cells whereas FlowSOM Cluster 5 contained the CD27+CD38+CD138+KI67+ PB, all of which were enriched in COVID-19 patients compared to controls (Fig. 4, O and P, and fig. S5K).
T196 2285-2521 Sentence denotes In contrast, B cells from COVID-19 patients in EMD Group 3 also showed enrichment for the PB FlowSOM Cluster 5, though less prominent than for EMD Group 1, but the T-bet+ memory B cell Cluster 1 was substantially reduced in EMD Group 3.
T197 2522-2742 Sentence denotes Thus, B cell responses were evident in many hospitalized COVID-19 patients, most often characterized by elevated PB, decreases in memory B cell subsets, enrichment in a T-bet+ B cell subset, and loss of CXCR5 expression.
T198 2743-2848 Sentence denotes Whether all of these changes in the B cell compartment were due to direct antiviral responses is unclear.
T199 2849-3075 Sentence denotes Although there was heterogeneity in the B cell responses, COVID-19 patients fell into two distinct patterns containing activated B cell responses and a third group of patients with little evidence of an active B cell response.

2_test

Id Subject Object Predicate Lexical cue
32669297-27008164-135105211 801-803 27008164 denotes 45