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PMC:7228307 / 21350-24962 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
405 127-131 Gene denotes FcγR Gene:2213
410 469-473 Gene denotes FcγR Gene:2213
411 1158-1162 Gene denotes FcγR Gene:2213
412 725-729 Gene denotes FcγR Gene:2213
413 595-599 Gene denotes FcγR Gene:2213
418 2058-2063 Disease denotes flush MESH:D005483
419 2298-2310 Disease denotes cytotoxicity MESH:D064420
420 2361-2373 Disease denotes cytotoxicity MESH:D064420
421 2480-2485 Disease denotes flush MESH:D005483
426 2976-2980 Gene denotes FcγR Gene:2213
427 2867-2871 Gene denotes FcγR Gene:2213
428 2817-2821 Chemical denotes ADCP
429 2800-2812 Disease denotes cytotoxicity MESH:D064420
432 3130-3134 Gene denotes FcγR Gene:2213
433 3378-3384 Chemical denotes glycan MESH:D011134

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T233 323-326 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T234 381-386 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T235 551-554 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T236 1234-1239 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T237 1268-1286 Body_part denotes actin cytoskeleton http://purl.org/sig/ont/fma/fma84684
T238 1309-1326 Body_part denotes glycosaminoglycan http://purl.org/sig/ont/fma/fma63011
T239 1327-1337 Body_part denotes glycocalyx http://purl.org/sig/ont/fma/fma66838
T240 1382-1395 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T241 1568-1572 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T242 1821-1825 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T243 2209-2217 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T244 2344-2352 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T245 2501-2514 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T246 2501-2505 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T247 2873-2878 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T248 3155-3168 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T249 3155-3159 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T15 2196-2200 Body_part denotes pore http://purl.obolibrary.org/obo/UBERON_0008915
T16 2331-2335 Body_part denotes pore http://purl.obolibrary.org/obo/UBERON_0008915

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T31 1064-1068 Disease denotes ADCC http://purl.obolibrary.org/obo/MONDO_0008734
T32 1978-1982 Disease denotes ADCC http://purl.obolibrary.org/obo/MONDO_0008734
T33 1987-1991 Disease denotes ADCP http://purl.obolibrary.org/obo/MONDO_0022697
T34 1995-1999 Disease denotes ADCC http://purl.obolibrary.org/obo/MONDO_0008734
T35 2256-2260 Disease denotes ADCC http://purl.obolibrary.org/obo/MONDO_0008734
T36 2421-2425 Disease denotes ADCP http://purl.obolibrary.org/obo/MONDO_0022697
T37 2536-2540 Disease denotes ADCP http://purl.obolibrary.org/obo/MONDO_0022697
T38 2685-2689 Disease denotes ADCC http://purl.obolibrary.org/obo/MONDO_0008734
T39 2694-2698 Disease denotes ADCP http://purl.obolibrary.org/obo/MONDO_0022697
T40 2817-2821 Disease denotes ADCP http://purl.obolibrary.org/obo/MONDO_0022697
T41 3005-3008 Disease denotes MOA http://purl.obolibrary.org/obo/MONDO_0016702

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T428 65-67 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T429 127-129 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T430 381-386 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T431 420-421 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T432 469-471 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T433 489-490 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T434 555-557 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T435 595-597 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T436 610-611 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T437 725-727 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T438 803-805 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T439 815-817 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T440 858-860 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T441 918-920 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T442 934-935 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T443 1149-1151 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T444 1158-1160 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T445 1234-1239 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T446 1405-1409 http://purl.obolibrary.org/obo/PR_000001307 denotes CD44
T447 1501-1503 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T448 1504-1506 http://purl.obolibrary.org/obo/CLO_0008882 denotes Rs
T449 1568-1572 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T450 1573-1583 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T451 1671-1673 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T452 1674-1676 http://purl.obolibrary.org/obo/CLO_0008882 denotes Rs
T453 1743-1749 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T454 1821-1825 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T455 1929-1931 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T456 1955-1956 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T457 2090-2098 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T458 2232-2240 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T459 2374-2377 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T460 2501-2505 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T461 2506-2514 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T462 2541-2549 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T463 2609-2617 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T464 2867-2869 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T465 2873-2878 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T466 2910-2918 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T467 2976-2978 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T468 3078-3080 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T469 3130-3132 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T470 3135-3147 http://purl.obolibrary.org/obo/OBI_0000245 denotes organization
T471 3155-3159 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T472 3160-3168 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T473 3356-3358 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc
T474 3392-3393 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T475 3559-3561 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T476 3574-3576 http://purl.obolibrary.org/obo/CLO_0052676 denotes Fc

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T103 132-140 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T104 263-271 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T105 372-380 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T106 513-521 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T107 665-672 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T108 730-738 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T109 964-971 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T110 1014-1021 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T111 1037-1045 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T112 1225-1233 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T113 1309-1326 Chemical denotes glycosaminoglycan http://purl.obolibrary.org/obo/CHEBI_18085
T114 1382-1395 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T115 1554-1561 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T116 1723-1729 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T117 1812-1820 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T118 1870-1877 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T119 2021-2028 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T120 2126-2134 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T121 2209-2217 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T122 2344-2352 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T123 2572-2579 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T124 2651-2658 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T125 3359-3370 Chemical denotes polypeptide http://purl.obolibrary.org/obo/CHEBI_15841
T126 3482-3493 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232
T127 3542-3550 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T132 235-242 http://purl.obolibrary.org/obo/BFO_0000019 denotes quality
T133 381-386 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T134 1234-1239 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T135 1347-1355 http://purl.obolibrary.org/obo/BFO_0000034 denotes function
T136 1568-1572 http://purl.obolibrary.org/obo/CL_0000000 denotes cell
T137 1821-1825 http://purl.obolibrary.org/obo/CL_0000000 denotes cell
T138 1826-1834 http://purl.obolibrary.org/obo/BFO_0000034 denotes function
T139 1916-1924 http://purl.obolibrary.org/obo/BFO_0000034 denotes function
T140 2501-2505 http://purl.obolibrary.org/obo/CL_0000000 denotes cell
T141 2873-2878 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T142 2981-2989 http://purl.obolibrary.org/obo/BFO_0000034 denotes function
T143 3135-3147 http://purl.obolibrary.org/obo/OBI_0100026 denotes organization
T144 3155-3159 http://purl.obolibrary.org/obo/CL_0000000 denotes cell
T145 3399-3407 http://purl.obolibrary.org/obo/BFO_0000034 denotes function
T146 3601-3611 http://purl.obolibrary.org/obo/IDO_0000607 denotes productive

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T23 1309-1326 Chemical denotes glycosaminoglycan http://purl.obolibrary.org/obo/CHEBI_18085
T24 1382-1395 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T25 2209-2217 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T26 2344-2352 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T27 3359-3370 Chemical denotes polypeptide http://purl.obolibrary.org/obo/CHEBI_15841

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
405 127-131 Gene denotes FcγR Gene:2213
410 469-473 Gene denotes FcγR Gene:2213
411 1158-1162 Gene denotes FcγR Gene:2213
412 725-729 Gene denotes FcγR Gene:2213
413 595-599 Gene denotes FcγR Gene:2213
418 2058-2063 Disease denotes flush MESH:D005483
419 2298-2310 Disease denotes cytotoxicity MESH:D064420
420 2361-2373 Disease denotes cytotoxicity MESH:D064420
421 2480-2485 Disease denotes flush MESH:D005483
426 2976-2980 Gene denotes FcγR Gene:2213
427 2867-2871 Gene denotes FcγR Gene:2213
428 2817-2821 Chemical denotes ADCP
429 2800-2812 Disease denotes cytotoxicity MESH:D064420
432 3130-3134 Gene denotes FcγR Gene:2213
433 3378-3384 Chemical denotes glycan MESH:D011134

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T131 0-91 Sentence denotes Not all opsonized targets are equal: size, distance, valency and Fc geometry affect potency
T132 92-387 Sentence denotes To understand the immunobiology of FcγR effector responses particularly in the therapeutic mAb context, it is important to appreciate that the quality and potency of such effector responses is greatly affected by the nature of the IgG immune complex and/or the state of potential effector cells.
T133 388-531 Sentence denotes First, opsonization, per se, of a target is not necessarily sufficient to ensure FcγR interaction in a way that initiates an effector response.
T134 532-1206 Sentence denotes Although it is the IgG Fc that interacts with and clusters the FcγR to induce a response, the nature of the Fab interaction with its epitope can strongly influence the likelihood or potency of FcγR effector responses by influencing the density of appropriately presented Fc portions.35 and also the size of the immune complex.36 Furthermore, the display/orientation and geometry of the Fc portions, as a consequence of the fragment antigen‐binding (Fab) interaction with the target epitope, can result in effector responses such as ADCC that differ substantially in potency, presumably because the orientation of the Fc makes FcγR engagement more, or less, accessible.37, 38
T135 1207-1562 Sentence denotes Second, in innate effector cells at rest, the largely linear actin cytoskeleton and the extracellular glycosaminoglycan glycocalyx regulate function by interacting with large glycoproteins, such as CD44, arranging these into ordered “picket” fences.39, 40 These corral receptors, including the FcγRs, and sterically inhibit their interaction with ligands.
T136 1563-2261 Sentence denotes Upon cell activation, cytoskeletal remodeling is associated with the loss of the receptor corrals, allowing FcγRs and other receptors to freely diffuse, engage ligand, cluster and signal.39 The influence of such surface constraints on receptors and effector cell function helps explain some of the observed epitope distance requirements for optimal mAb function,39, 41 which were apparent in a comparative study of ADCC and ADCP.42 ADCC was optimal when the epitope was displayed close, 0.3 nm “flush” or 1.5 nm, to the target membrane where close conjugation of effector and target by the mAb presumably facilitates the delivery of pore‐forming proteins to the target membrane as required by ADCC.
T137 2262-2407 Sentence denotes Interestingly, complement‐dependent cytotoxicity which also utilizes pore‐forming proteins for its cytotoxicity has similar distance constraints.
T138 2408-2701 Sentence denotes By contrast, ADCP was poor  when targeting epitopes displayed close or "flush" to the target cell membrane (within ~0.3 nm) but ADCP activity was restored when the epitope was displayed 1.5 nm off the membrane, demonstrating different optimal epitope distance requirements for ADCC and ADCP.42
T139 2702-2897 Sentence denotes Although the action of agonistic/antagonistic mAbs is mechanistically distinct to those eliciting cytotoxicity and ADCP, the distance segregation between target and FcγR+ cells is also important.
T140 2898-3029 Sentence denotes Indeed, the membrane proximal epitopes of CD28 and CD40 are important for the FcγR function in the complex MOA of these mAbs.43, 44
T141 3030-3274 Sentence denotes Clearly, the effects of immune complex valency, Fc density, presentation and geometry together with FcγR organization in the cell membrane suggest that the development of mAbs to certain targets will be heavily influenced by the context of use.
T142 3275-3391 Sentence denotes Thus, improved mAb potency may not necessarily be achieved by engineering of the Fc polypeptide or its glycan alone.
T143 3392-3612 Sentence denotes A more function‐oriented approach early in mAb selection and development by, for example, application of rapid screening technologies that select for effector potency,34 followed by Fc engineering may be more productive.

LitCovid-sample-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T15 2196-2200 Body_part denotes pore http://purl.obolibrary.org/obo/UBERON_0008915
T16 2331-2335 Body_part denotes pore http://purl.obolibrary.org/obo/UBERON_0008915

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T97 1268-1273 Protein denotes actin https://www.uniprot.org/uniprot/Q92193|https://www.uniprot.org/uniprot/Q92192|https://www.uniprot.org/uniprot/Q24733|https://www.uniprot.org/uniprot/Q11212|https://www.uniprot.org/uniprot/P91754|https://www.uniprot.org/uniprot/P90689|https://www.uniprot.org/uniprot/P80709|https://www.uniprot.org/uniprot/P68555|https://www.uniprot.org/uniprot/P45521|https://www.uniprot.org/uniprot/P38136|https://www.uniprot.org/uniprot/P14227|https://www.uniprot.org/uniprot/O17320|https://www.uniprot.org/uniprot/O16808
T110 1382-1395 Protein denotes glycoproteins https://www.uniprot.org/uniprot/Q9QSP1|https://www.uniprot.org/uniprot/Q9QJT6|https://www.uniprot.org/uniprot/Q9JGT4|https://www.uniprot.org/uniprot/Q9IPJ6|https://www.uniprot.org/uniprot/Q9DIC6|https://www.uniprot.org/uniprot/Q91DS0|https://www.uniprot.org/uniprot/Q91C28|https://www.uniprot.org/uniprot/Q8QQA2|https://www.uniprot.org/uniprot/Q8QPE5|https://www.uniprot.org/uniprot/Q8QPE4|https://www.uniprot.org/uniprot/Q8QPE3|https://www.uniprot.org/uniprot/Q8JTH0|https://www.uniprot.org/uniprot/Q8BDV6|https://www.uniprot.org/uniprot/Q8B6J6|https://www.uniprot.org/uniprot/Q8B0I1|https://www.uniprot.org/uniprot/Q8B0H6|https://www.uniprot.org/uniprot/Q8B0H1|https://www.uniprot.org/uniprot/Q89669|https://www.uniprot.org/uniprot/Q85213|https://www.uniprot.org/uniprot/Q82706|https://www.uniprot.org/uniprot/Q82683|https://www.uniprot.org/uniprot/Q82020|https://www.uniprot.org/uniprot/Q787B5|https://www.uniprot.org/uniprot/Q77SK0|https://www.uniprot.org/uniprot/Q77N36|https://www.uniprot.org/uniprot/Q76G52|https://www.uniprot.org/uniprot/Q75T09|https://www.uniprot.org/uniprot/Q6X1D5|https://www.uniprot.org/uniprot/Q6X1D1|https://www.uniprot.org/uniprot/Q6TYA0|https://www.uniprot.org/uniprot/Q6E0W7|https://www.uniprot.org/uniprot/Q66T62|https://www.uniprot.org/uniprot/Q5VKP3|https://www.uniprot.org/uniprot/Q5VKN9|https://www.uniprot.org/uniprot/Q5K2K4|https://www.uniprot.org/uniprot/Q5IX93|https://www.uniprot.org/uniprot/Q5IX92|https://www.uniprot.org/uniprot/Q5IX91|https://www.uniprot.org/uniprot/Q5IX90|https://www.uniprot.org/uniprot/Q5IX89|https://www.uniprot.org/uniprot/Q5IX88|https://www.uniprot.org/uniprot/Q5IX87|https://www.uniprot.org/uniprot/Q5GA86|https://www.uniprot.org/uniprot/Q58FH1|https://www.uniprot.org/uniprot/Q4VKV3|https://www.uniprot.org/uniprot/Q4F900|https://www.uniprot.org/uniprot/Q49LL3|https://www.uniprot.org/uniprot/Q49IU2|https://www.uniprot.org/uniprot/Q49IU1|https://www.uniprot.org/uniprot/Q49IT9|https://www.uniprot.org/uniprot/Q49IT8|https://www.uniprot.org/uniprot/Q49AV0|https://www.uniprot.org/uniprot/Q0GBY1|https://www.uniprot.org/uniprot/Q0GBX6|https://www.uniprot.org/uniprot/Q08089|https://www.uniprot.org/uniprot/P32595|https://www.uniprot.org/uniprot/P32550|https://www.uniprot.org/uniprot/P19462|https://www.uniprot.org/uniprot/P16288|https://www.uniprot.org/uniprot/P15199|https://www.uniprot.org/uniprot/P13180|https://www.uniprot.org/uniprot/P0C572|https://www.uniprot.org/uniprot/P08667|https://www.uniprot.org/uniprot/P08163|https://www.uniprot.org/uniprot/P07923|https://www.uniprot.org/uniprot/P04884|https://www.uniprot.org/uniprot/P04883|https://www.uniprot.org/uniprot/P04882|https://www.uniprot.org/uniprot/P03524|https://www.uniprot.org/uniprot/P03522|https://www.uniprot.org/uniprot/O92284|https://www.uniprot.org/uniprot/O56677|https://www.uniprot.org/uniprot/O10236|https://www.uniprot.org/uniprot/J7HBH4|https://www.uniprot.org/uniprot/D8V075|https://www.uniprot.org/uniprot/A7WNB3|https://www.uniprot.org/uniprot/A4UHQ6|https://www.uniprot.org/uniprot/A4UHQ1|https://www.uniprot.org/uniprot/A3RM22|https://www.uniprot.org/uniprot/A3F5R8|https://www.uniprot.org/uniprot/A3F5R3|https://www.uniprot.org/uniprot/A3F5Q8|https://www.uniprot.org/uniprot/A3F5N3|https://www.uniprot.org/uniprot/A3F5M3|https://www.uniprot.org/uniprot/A3F5L8
T195 1405-1409 Protein denotes CD44 https://www.uniprot.org/uniprot/Q9UJ36|https://www.uniprot.org/uniprot/Q9UCB0|https://www.uniprot.org/uniprot/Q9UC30|https://www.uniprot.org/uniprot/Q9UC29|https://www.uniprot.org/uniprot/Q9UC28|https://www.uniprot.org/uniprot/Q9QYX8|https://www.uniprot.org/uniprot/Q9H5A5|https://www.uniprot.org/uniprot/Q99J14|https://www.uniprot.org/uniprot/Q99021|https://www.uniprot.org/uniprot/Q96J24|https://www.uniprot.org/uniprot/Q92493|https://www.uniprot.org/uniprot/Q8N694|https://www.uniprot.org/uniprot/Q86Z27|https://www.uniprot.org/uniprot/Q86T72|https://www.uniprot.org/uniprot/Q64296|https://www.uniprot.org/uniprot/Q62409|https://www.uniprot.org/uniprot/Q62408|https://www.uniprot.org/uniprot/Q62063|https://www.uniprot.org/uniprot/Q62062|https://www.uniprot.org/uniprot/Q62061|https://www.uniprot.org/uniprot/Q62060|https://www.uniprot.org/uniprot/Q61395|https://www.uniprot.org/uniprot/Q60523|https://www.uniprot.org/uniprot/Q60522|https://www.uniprot.org/uniprot/Q29423|https://www.uniprot.org/uniprot/Q28284|https://www.uniprot.org/uniprot/Q16522|https://www.uniprot.org/uniprot/Q16208|https://www.uniprot.org/uniprot/Q16066|https://www.uniprot.org/uniprot/Q16065|https://www.uniprot.org/uniprot/Q16064|https://www.uniprot.org/uniprot/Q15861|https://www.uniprot.org/uniprot/Q13980|https://www.uniprot.org/uniprot/Q13968|https://www.uniprot.org/uniprot/Q13967|https://www.uniprot.org/uniprot/Q13961|https://www.uniprot.org/uniprot/Q13960|https://www.uniprot.org/uniprot/Q13959|https://www.uniprot.org/uniprot/Q13958|https://www.uniprot.org/uniprot/Q13957|https://www.uniprot.org/uniprot/Q13419|https://www.uniprot.org/uniprot/Q05732|https://www.uniprot.org/uniprot/Q05078|https://www.uniprot.org/uniprot/Q04858|https://www.uniprot.org/uniprot/P26051|https://www.uniprot.org/uniprot/P22511|https://www.uniprot.org/uniprot/P20944|https://www.uniprot.org/uniprot/P16070|https://www.uniprot.org/uniprot/P15379|https://www.uniprot.org/uniprot/P14745|https://www.uniprot.org/uniprot/O95370|https://www.uniprot.org/uniprot/D3DR13|https://www.uniprot.org/uniprot/D3DR12|https://www.uniprot.org/uniprot/B6EAT9|https://www.uniprot.org/uniprot/A5YRN9
T250 2940-2944 Protein denotes CD28 https://www.uniprot.org/uniprot/Q9BYV0|https://www.uniprot.org/uniprot/Q8WXJ2|https://www.uniprot.org/uniprot/Q8NI56|https://www.uniprot.org/uniprot/Q8NI55|https://www.uniprot.org/uniprot/Q8NI54|https://www.uniprot.org/uniprot/Q70WG0|https://www.uniprot.org/uniprot/Q6GSH7|https://www.uniprot.org/uniprot/Q52M23|https://www.uniprot.org/uniprot/Q28071|https://www.uniprot.org/uniprot/Q13964|https://www.uniprot.org/uniprot/P42069|https://www.uniprot.org/uniprot/P31042|https://www.uniprot.org/uniprot/P31041|https://www.uniprot.org/uniprot/P10747|https://www.uniprot.org/uniprot/O02757|https://www.uniprot.org/uniprot/A8KAC1
T266 2949-2953 Protein denotes CD40 https://www.uniprot.org/uniprot/Q9BYU0|https://www.uniprot.org/uniprot/Q99NE3|https://www.uniprot.org/uniprot/Q99NE2|https://www.uniprot.org/uniprot/Q99NE1|https://www.uniprot.org/uniprot/Q99NE0|https://www.uniprot.org/uniprot/Q8SQ34|https://www.uniprot.org/uniprot/Q8K2X6|https://www.uniprot.org/uniprot/Q86YK5|https://www.uniprot.org/uniprot/Q7YRL5|https://www.uniprot.org/uniprot/Q7M4Q8|https://www.uniprot.org/uniprot/Q5U007|https://www.uniprot.org/uniprot/Q5JY15|https://www.uniprot.org/uniprot/Q542B1|https://www.uniprot.org/uniprot/Q53GN5|https://www.uniprot.org/uniprot/Q3ZTK5|https://www.uniprot.org/uniprot/Q3UBH3|https://www.uniprot.org/uniprot/Q3U7C9|https://www.uniprot.org/uniprot/Q3U799|https://www.uniprot.org/uniprot/Q3TSL2|https://www.uniprot.org/uniprot/Q3TS33|https://www.uniprot.org/uniprot/Q3LRP1|https://www.uniprot.org/uniprot/Q28203|https://www.uniprot.org/uniprot/P27512|https://www.uniprot.org/uniprot/P25942|https://www.uniprot.org/uniprot/E1P5S9|https://www.uniprot.org/uniprot/A7YWS9

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T232 323-326 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T233 381-386 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T234 551-554 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T235 1234-1239 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T236 1268-1286 Body_part denotes actin cytoskeleton http://purl.org/sig/ont/fma/fma84684
T237 1309-1326 Body_part denotes glycosaminoglycan http://purl.org/sig/ont/fma/fma63011
T238 1327-1337 Body_part denotes glycocalyx http://purl.org/sig/ont/fma/fma66838
T239 1382-1395 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T240 1568-1572 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T241 1821-1825 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T242 2209-2217 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T243 2344-2352 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T244 2501-2514 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T245 2501-2505 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T246 2873-2878 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T247 3155-3168 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T248 3155-3159 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-sample-PD-MAT

Id Subject Object Predicate Lexical cue
T10 2919-2927 http://purl.obolibrary.org/obo/MAT_0000491 denotes proximal

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T53 395-407 http://purl.obolibrary.org/obo/GO_0008228 denotes opsonization
T54 1064-1068 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T55 1568-1583 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T56 1723-1738 http://purl.obolibrary.org/obo/GO_1990256 denotes ligand, cluster
T57 1978-1982 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T58 1995-1999 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T59 2111-2122 http://purl.obolibrary.org/obo/GO_0000746 denotes conjugation
T60 2256-2260 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T61 2277-2310 http://purl.obolibrary.org/obo/GO_0097278 denotes complement‐dependent cytotoxicity
T62 2685-2689 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T53 395-407 http://purl.obolibrary.org/obo/GO_0008228 denotes opsonization
T54 1064-1068 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T55 1568-1583 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T56 1723-1738 http://purl.obolibrary.org/obo/GO_1990256 denotes ligand, cluster
T57 1978-1982 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T58 1995-1999 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T59 2111-2122 http://purl.obolibrary.org/obo/GO_0000746 denotes conjugation
T60 2256-2260 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T61 2277-2310 http://purl.obolibrary.org/obo/GO_0097278 denotes complement‐dependent cytotoxicity
T62 2685-2689 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T53 395-407 http://purl.obolibrary.org/obo/GO_0008228 denotes opsonization
T54 1064-1068 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T55 1568-1583 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T56 1723-1738 http://purl.obolibrary.org/obo/GO_1990256 denotes ligand, cluster
T57 1978-1982 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T58 1995-1999 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T59 2111-2122 http://purl.obolibrary.org/obo/GO_0000746 denotes conjugation
T60 2256-2260 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC
T61 2277-2310 http://purl.obolibrary.org/obo/GO_0097278 denotes complement‐dependent cytotoxicity
T62 2685-2689 http://purl.obolibrary.org/obo/GO_0001788 denotes ADCC

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T131 0-91 Sentence denotes Not all opsonized targets are equal: size, distance, valency and Fc geometry affect potency
T132 92-387 Sentence denotes To understand the immunobiology of FcγR effector responses particularly in the therapeutic mAb context, it is important to appreciate that the quality and potency of such effector responses is greatly affected by the nature of the IgG immune complex and/or the state of potential effector cells.
T133 388-531 Sentence denotes First, opsonization, per se, of a target is not necessarily sufficient to ensure FcγR interaction in a way that initiates an effector response.
T134 532-1206 Sentence denotes Although it is the IgG Fc that interacts with and clusters the FcγR to induce a response, the nature of the Fab interaction with its epitope can strongly influence the likelihood or potency of FcγR effector responses by influencing the density of appropriately presented Fc portions.35 and also the size of the immune complex.36 Furthermore, the display/orientation and geometry of the Fc portions, as a consequence of the fragment antigen‐binding (Fab) interaction with the target epitope, can result in effector responses such as ADCC that differ substantially in potency, presumably because the orientation of the Fc makes FcγR engagement more, or less, accessible.37, 38
T135 1207-1562 Sentence denotes Second, in innate effector cells at rest, the largely linear actin cytoskeleton and the extracellular glycosaminoglycan glycocalyx regulate function by interacting with large glycoproteins, such as CD44, arranging these into ordered “picket” fences.39, 40 These corral receptors, including the FcγRs, and sterically inhibit their interaction with ligands.
T136 1563-2261 Sentence denotes Upon cell activation, cytoskeletal remodeling is associated with the loss of the receptor corrals, allowing FcγRs and other receptors to freely diffuse, engage ligand, cluster and signal.39 The influence of such surface constraints on receptors and effector cell function helps explain some of the observed epitope distance requirements for optimal mAb function,39, 41 which were apparent in a comparative study of ADCC and ADCP.42 ADCC was optimal when the epitope was displayed close, 0.3 nm “flush” or 1.5 nm, to the target membrane where close conjugation of effector and target by the mAb presumably facilitates the delivery of pore‐forming proteins to the target membrane as required by ADCC.
T137 2262-2407 Sentence denotes Interestingly, complement‐dependent cytotoxicity which also utilizes pore‐forming proteins for its cytotoxicity has similar distance constraints.
T138 2408-2701 Sentence denotes By contrast, ADCP was poor  when targeting epitopes displayed close or "flush" to the target cell membrane (within ~0.3 nm) but ADCP activity was restored when the epitope was displayed 1.5 nm off the membrane, demonstrating different optimal epitope distance requirements for ADCC and ADCP.42
T139 2702-2897 Sentence denotes Although the action of agonistic/antagonistic mAbs is mechanistically distinct to those eliciting cytotoxicity and ADCP, the distance segregation between target and FcγR+ cells is also important.
T140 2898-3029 Sentence denotes Indeed, the membrane proximal epitopes of CD28 and CD40 are important for the FcγR function in the complex MOA of these mAbs.43, 44
T141 3030-3274 Sentence denotes Clearly, the effects of immune complex valency, Fc density, presentation and geometry together with FcγR organization in the cell membrane suggest that the development of mAbs to certain targets will be heavily influenced by the context of use.
T142 3275-3391 Sentence denotes Thus, improved mAb potency may not necessarily be achieved by engineering of the Fc polypeptide or its glycan alone.
T143 3392-3612 Sentence denotes A more function‐oriented approach early in mAb selection and development by, for example, application of rapid screening technologies that select for effector potency,34 followed by Fc engineering may be more productive.