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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T6 7-11 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T7 188-195 Body_part denotes capsule http://purl.org/sig/ont/fma/fma85272
T8 214-219 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T9 268-276 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T10 291-299 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T11 358-366 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T12 380-388 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T13 411-416 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737
T14 530-538 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T15 567-571 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T16 630-638 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T17 673-678 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T18 790-798 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T19 816-829 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T20 831-839 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T21 858-872 Body_part denotes polysaccharide http://purl.org/sig/ont/fma/fma82746
T22 876-891 Body_part denotes oligosaccharide http://purl.org/sig/ont/fma/fma82742
T23 941-954 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T24 1178-1191 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T25 1303-1311 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T26 1357-1362 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T27 1465-1473 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T28 1520-1525 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T29 1661-1666 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T30 1743-1756 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T31 1896-1900 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T32 1923-1936 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T33 1923-1927 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T34 1989-2002 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T35 1989-1993 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T36 2068-2082 Body_part denotes cell membranes http://purl.org/sig/ont/fma/fma63841
T37 2068-2072 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T38 2296-2306 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T39 2512-2519 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T40 2547-2562 Body_part denotes dendritic cells http://purl.org/sig/ont/fma/fma273565
T41 2557-2562 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T42 2575-2580 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T43 2648-2661 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T44 2669-2682 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T45 2699-2706 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T46 2724-2731 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T47 2755-2760 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T48 2769-2774 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T49 2912-2920 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T50 3002-3005 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T51 3484-3492 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T52 3531-3535 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T53 3636-3641 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 188-195 Body_part denotes capsule http://purl.obolibrary.org/obo/UBERON_0003893
T2 2575-2580 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T3 85-93 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T4 98-106 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 1760-1768 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 3009-3017 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T19 7-11 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T20 44-51 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Viruses
T21 65-72 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T22 109-116 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T23 212-213 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 228-236 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T25 282-290 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T26 437-438 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 567-571 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T28 673-678 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T29 693-700 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T30 960-961 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 1260-1261 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 1329-1338 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T33 1357-1362 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T34 1484-1491 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T35 1520-1525 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T36 1639-1644 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T37 1661-1666 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T38 1680-1685 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T39 1707-1708 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T40 1850-1856 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T41 1896-1900 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T42 1923-1927 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T43 1928-1936 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T44 1947-1949 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T45 1989-1993 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T46 1994-2002 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T47 2016-2018 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T48 2016-2018 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T49 2068-2072 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T50 2073-2082 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T51 2088-2090 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T52 2159-2160 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 2232-2238 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T54 2273-2274 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 2296-2315 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T56 2296-2315 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T57 2329-2331 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T58 2446-2451 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T59 2547-2562 http://purl.obolibrary.org/obo/CL_0000451 denotes dendritic cells
T60 2564-2566 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T61 2575-2580 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T62 2575-2580 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T63 2634-2637 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T64 2643-2646 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T65 2683-2688 http://purl.obolibrary.org/obo/CLO_0007225 denotes label
T66 2716-2723 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T67 2753-2760 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cells
T68 2767-2774 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cells
T69 2802-2808 http://purl.obolibrary.org/obo/CLO_0007225 denotes labels
T70 2843-2850 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T71 2873-2876 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T72 3023-3028 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T73 3356-3361 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T74 3440-3445 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T75 3469-3474 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T76 3531-3535 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T77 3582-3583 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 3618-3625 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T79 3636-3641 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T14 214-219 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T15 268-276 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T16 291-299 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T17 358-366 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T18 380-388 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T19 417-426 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T20 530-538 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T21 630-638 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T22 790-798 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T23 816-829 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T24 831-839 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T25 858-872 Chemical denotes polysaccharide http://purl.obolibrary.org/obo/CHEBI_18154
T26 876-891 Chemical denotes oligosaccharide http://purl.obolibrary.org/obo/CHEBI_50699
T27 920-927 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T28 941-954 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T29 1041-1046 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T30 1178-1191 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T31 1303-1311 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T32 1378-1385 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T33 1465-1473 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T34 1743-1756 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T35 2016-2018 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T36 2189-2200 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T37 2296-2306 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T38 2296-2301 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T39 2302-2306 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T40 2479-2486 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T41 2512-2519 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T42 2648-2661 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396
T43 2669-2682 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396
T44 2683-2688 Chemical denotes label http://purl.obolibrary.org/obo/CHEBI_35209
T45 2699-2706 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T46 2724-2731 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T47 2828-2835 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T48 2912-2920 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T49 3121-3129 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T50 3149-3152 Chemical denotes GNA http://purl.obolibrary.org/obo/CHEBI_48015
T51 3227-3236 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T52 3229-3236 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T53 3484-3492 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 473-486 http://purl.obolibrary.org/obo/GO_0006493 denotes O-glycosylate
T2 657-672 http://purl.obolibrary.org/obo/GO_0044409 denotes entry into host
T3 1639-1666 http://purl.obolibrary.org/obo/GO_0046718 denotes virus entry into host cells
T4 1645-1660 http://purl.obolibrary.org/obo/GO_0044409 denotes entry into host
T5 2457-2473 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
40 784-789 Gene denotes Spike Gene:43740568
41 624-629 Gene denotes spike Gene:43740568
42 85-93 Species denotes SARS-CoV Tax:694009
43 98-108 Species denotes SARS-CoV-2 Tax:2697049
44 713-726 Species denotes coronaviruses Tax:11118
45 348-353 Gene denotes spike Gene:43740568
46 411-416 Chemical denotes sugar MESH:D000073893
47 449-455 Chemical denotes glycan MESH:D011134
48 467-486 Chemical denotes N- or O-glycosylate
49 858-872 Chemical denotes polysaccharide MESH:D011134
50 876-891 Chemical denotes oligosaccharide MESH:D009844
51 920-927 Chemical denotes glycans MESH:D011134
55 1041-1046 Chemical denotes water MESH:D014867
56 1288-1294 Chemical denotes glycan MESH:D011134
57 1378-1385 Chemical denotes glycans MESH:D011134
65 2189-2220 Gene denotes angiotensin-converting-enzyme 2 Gene:59272
66 2222-2227 Gene denotes ACE-2 Gene:59272
67 1760-1770 Species denotes SARS-CoV-2 Tax:2697049
68 2129-2142 Species denotes coronaviruses Tax:11118
69 2232-2238 Species denotes humans Tax:9606
70 2380-2393 Species denotes coronaviruses Tax:11118
71 1737-1742 Gene denotes spike Gene:43740568
88 2693-2698 Gene denotes spike Gene:43740568
89 2506-2511 Gene denotes spike Gene:43740568
90 2446-2451 Species denotes human Tax:9606
91 2494-2505 Species denotes coronavirus Tax:11118
92 3002-3007 Species denotes HIV-1 Tax:11676
93 3009-3017 Species denotes SARS-CoV Tax:694009
94 3023-3044 Species denotes human cytomegalovirus Tax:10359
95 3154-3171 Species denotes Galanthus nivalis Tax:4670
96 3545-3558 Species denotes coronaviruses Tax:11118
97 2479-2486 Chemical denotes glycans MESH:D011134
98 2600-2606 Chemical denotes glycan MESH:D011134
99 2648-2661 Chemical denotes glycopeptides MESH:D006020
100 2669-2682 Chemical denotes glycopeptides MESH:D006020
101 2897-2903 Chemical denotes glycan MESH:D011134
102 3227-3236 Chemical denotes N-glycans
103 3344-3350 Chemical denotes glycan MESH:D011134

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T23 0-2 Sentence denotes 2.
T24 3-51 Sentence denotes The Cell Entry Mechanism of Encapsulated Viruses
T25 52-163 Sentence denotes Encapsulated viruses such as the SARS-CoV and SARS-CoV-2 viruses comprise of some general surface constituents.
T26 164-371 Sentence denotes The surface envelope or capsule is presented as a lipid bilayer membrane that contains various envelope proteins (E), membrane proteins (M), and an outer layer that presents so-called spike (S) proteins [1].
T27 372-466 Sentence denotes M and S proteins are generally rich in sugar molecules that form a so-called glycan structure.
T28 467-617 Sentence denotes N- or O-glycosylate moieties are commonly found in the viral S proteins and they can recognize some cell receptors to which the virion can bind [2,3].
T29 618-679 Sentence denotes These spike proteins facilitate virion entry into host cells.
T30 680-783 Sentence denotes Encapsulated viruses such as the coronaviruses present approximately 200 of these spiky structures [4].
T31 784-936 Sentence denotes Spike proteins are comprised of glycoproteins, proteins that also contain polysaccharide or oligosaccharide moieties otherwise known as glycans [5,6,7].
T32 937-1133 Sentence denotes The glycoproteins have a variety of functions that maintain the virion structure and properties such as water solubility, creation of diffusion barriers, and antiadhesive actions among others [6].
T33 1134-1367 Sentence denotes In addition to the intrinsic functions that glycoproteins afford to the maintenance of the virion structure, they also act as a structure that recognizes glycan-binding proteins presented on the membranes of potential host cells [1].
T34 1368-1474 Sentence denotes The viral glycans may be recognized by bacterial, fungal, and parasite-associated glycan-binding proteins.
T35 1475-1549 Sentence denotes However, viruses are also recognized by host cells via the same mechanism.
T36 1550-1706 Sentence denotes It is this form of intercellular recognition interactions that prove vital to effect the virus entry into host cells in which the virus could replicate [7].
T37 1707-1827 Sentence denotes A detailed description of the spike glycoproteins of SARS-CoV-2 reported that two binding subunits can be distinguished.
T38 1828-1937 Sentence denotes These subunits become active when the two units are cleaved by host cell proteases on the host cell membrane.
T39 1938-2083 Sentence denotes Subunit, S1 is responsible for binding to the host cell membrane and subunit, S2 is responsible for fusion of the virion and host cell membranes.
T40 2084-2178 Sentence denotes The S1 unit is the factor that makes various coronaviruses specific toward a certain host [8].
T41 2179-2430 Sentence denotes Pulmonary angiotensin-converting-enzyme 2 (ACE-2) in humans exhibit the appropriate receptor, a specific sequence of amino acid residues [9], towards S1 and partly explains the effective spread of the coronaviruses via droplets in the atmosphere [10].
T42 2431-2662 Sentence denotes As part of the human host immune responses, the glycans of the coronavirus spike protein subunits are recognized by dendritic cells [11] in the blood which binds to the glycan and subsequently expresses CD4+ and CD8+ glycopeptides.
T43 2663-2766 Sentence denotes These glycopeptides label the spike protein and this labeled protein is then presented to T-cells [12].
T44 2767-2869 Sentence denotes T-cells subsequently recognize the labels, phagocytose these antigen-marked viruses, and degrade them.
T45 2870-3045 Sentence denotes It has been found that the glycan-binding proteins, also known as lectins [5], can impart broad-spectrum binding properties against HIV-1, SARS-CoV, and human cytomegalovirus.
T46 3046-3184 Sentence denotes The lectin which is capable of showing broad interaction via oligomannosyl antigens is known as lectin GNA (Galanthus nivalis agglutinin).
T47 3185-3314 Sentence denotes The N-oligomannosyl cores are embedded in N-glycans which are commonly expressed on the surface of numerous viral pathogens [13].
T48 3315-3481 Sentence denotes Once the lectin binds to the glycan, the virus structure may undergo conformational changes that result in the fusion of the virus and host to facilitate virus entry.
T49 3482-3564 Sentence denotes S-proteins are specifically responsible for host cell entry by coronaviruses [14].
T50 3565-3642 Sentence denotes Figure 1 depicts a simplified entry mechanism of the viruses into host cells.

2_test

Id Subject Object Predicate Lexical cue
32731428-26925438-71421239 368-369 26925438 denotes 1
32731428-10799570-71421240 612-613 10799570 denotes 2
32731428-24736006-71421241 614-615 24736006 denotes 3
32731428-24188132-71421242 929-930 24188132 denotes 5
32731428-27558841-71421243 931-932 27558841 denotes 6
32731428-31121217-71421244 933-934 31121217 denotes 7
32731428-27558841-71421245 1130-1131 27558841 denotes 6
32731428-26925438-71421246 1364-1365 26925438 denotes 1
32731428-31121217-71421247 1703-1704 31121217 denotes 7
32731428-32155444-71421248 2175-2176 32155444 denotes 8
32731428-14651994-71421249 2317-2318 14651994 denotes 9
32731428-18931070-71421250 2426-2428 18931070 denotes 10
32731428-18799140-71421251 2564-2566 18799140 denotes 11
32731428-32328406-71421252 2762-2764 32328406 denotes 12
32731428-24188132-71421253 2945-2946 24188132 denotes 5
32731428-25774492-71421254 3310-3312 25774492 denotes 13
32731428-16258152-71421255 3560-3562 16258152 denotes 14