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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T13 301-319 Body_part denotes respiratory system http://purl.org/sig/ont/fma/fma7158
T14 386-390 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T15 532-538 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T16 743-746 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T17 867-870 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 871-877 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T19 933-941 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T20 958-966 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T21 988-996 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T22 1064-1071 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T23 1149-1156 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T24 1232-1237 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T25 1586-1596 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T26 1615-1619 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T27 2582-2589 Body_part denotes trachea http://purl.org/sig/ont/fma/fma7394
T28 3307-3313 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T29 3314-3319 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T30 3502-3508 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T31 3617-3620 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T32 3713-3717 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T33 5184-5192 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T34 5232-5236 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 301-319 Body_part denotes respiratory system http://purl.obolibrary.org/obo/UBERON_0001004
T3 386-390 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033
T4 532-538 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T5 571-574 Body_part denotes egg http://purl.obolibrary.org/obo/UBERON_0007379
T6 591-594 Body_part denotes egg http://purl.obolibrary.org/obo/UBERON_0007379
T7 2517-2520 Body_part denotes egg http://purl.obolibrary.org/obo/UBERON_0007379
T8 2582-2589 Body_part denotes trachea http://purl.obolibrary.org/obo/UBERON_0003126
T9 3307-3313 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T10 3502-3508 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T7 16-26 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T8 27-37 Disease denotes bronchitis http://purl.obolibrary.org/obo/MONDO_0003781
T9 68-87 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T10 157-170 Disease denotes viral disease http://purl.obolibrary.org/obo/MONDO_0005108
T11 364-374 Disease denotes depression http://purl.obolibrary.org/obo/MONDO_0002050
T12 552-561 Disease denotes nephritis http://purl.obolibrary.org/obo/MONDO_0001166
T13 659-669 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T14 670-680 Disease denotes bronchitis http://purl.obolibrary.org/obo/MONDO_0003781
T15 1435-1445 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T16 2056-2065 Disease denotes nephritis http://purl.obolibrary.org/obo/MONDO_0001166
T17 2371-2387 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T18 3031-3040 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T19 3321-3323 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T20 3529-3552 Disease denotes bacterial infections in http://purl.obolibrary.org/obo/MONDO_0005113

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T32 66-67 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 271-272 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 301-319 http://purl.obolibrary.org/obo/UBERON_0001004 denotes respiratory system
T35 386-390 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T36 386-390 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T37 453-458 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T38 505-515 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T39 532-538 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T40 532-538 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T41 532-538 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T42 543-549 http://purl.obolibrary.org/obo/UBERON_0000991 denotes gonads
T43 681-686 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T44 694-695 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 747-752 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T46 1088-1090 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T47 1095-1097 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T48 1095-1097 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T49 1121-1123 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T50 1124-1126 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T51 1124-1126 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T52 1146-1148 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T53 1232-1237 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T54 1247-1249 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T55 1247-1249 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T56 1269-1277 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T57 1475-1478 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T58 1612-1614 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T59 1615-1619 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T60 1946-1950 http://purl.obolibrary.org/obo/CLO_0054064 denotes 4/91
T61 2032-2034 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T62 2124-2132 http://purl.obolibrary.org/obo/NCBITaxon_9031 denotes chickens
T63 2185-2186 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 2255-2256 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 2566-2574 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T66 2641-2642 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 2835-2839 http://purl.obolibrary.org/obo/CLO_0054064 denotes 4/91
T68 3044-3052 http://purl.obolibrary.org/obo/NCBITaxon_9031 denotes chickens
T69 3094-3096 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T70 3121-3124 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T71 3299-3306 http://purl.obolibrary.org/obo/NCBITaxon_9031 denotes chicken
T72 3307-3313 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T73 3307-3313 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T74 3307-3313 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T75 3314-3319 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T76 3453-3455 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T77 3621-3628 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T78 3721-3722 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 3868-3873 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T80 3875-3877 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T81 3902-3903 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 3942-3943 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T83 4516-4521 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T84 4741-4743 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T85 4763-4768 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T86 4813-4815 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T87 4902-4904 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T88 4910-4915 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T89 5047-5054 http://purl.obolibrary.org/obo/CLO_0001409 denotes 5], [28
T90 5100-5101 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T91 5162-5164 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T92 5229-5231 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T93 5232-5236 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T94 5450-5458 http://purl.obolibrary.org/obo/NCBITaxon_9031 denotes chickens

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T5 933-941 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T6 958-966 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T7 988-996 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T8 1064-1071 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T9 1095-1097 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T10 1124-1126 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T11 1149-1156 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T12 1247-1249 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T13 1586-1596 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T14 1586-1591 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T15 1592-1596 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 1207-1237 http://purl.obolibrary.org/obo/GO_0019062 denotes viral attachment to host cells
T3 1269-1284 http://purl.obolibrary.org/obo/GO_0061025 denotes membrane fusion
T4 2371-2387 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T5 4522-4531 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T6 4522-4531 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence
T7 4685-4698 http://purl.obolibrary.org/obo/GO_0044409 denotes host invasion

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T16 0-15 Sentence denotes 1 Introduction
T17 16-267 Sentence denotes Infectious bronchitis (IB) was first described as a respiratory disease affecting chicks in the US in 1931 as an acute and highly contagious viral disease, and continues to cause major economic loss within the poultry industry worldwide [1], [2], [3].
T18 268-442 Sentence denotes As a result of the damage to the respiratory system, the clinical signs of this disease include depression, coughing, head-shaking, as well as nasal and ocular discharge [1].
T19 443-629 Sentence denotes Since the virus causing IB replicates in many non-respiratory epithelial surfaces (e.g., kidney and gonads), nephritis, reduced egg production, and egg quality is also observed [2], [3].
T20 630-850 Sentence denotes The causative agent of IB is infectious bronchitis virus (IBV), a non-segmented, positive-sense, single-stranded RNA virus, which belongs to the genus Gammacoronavirus, family Coronaviridae, in the order Nidovirales [4].
T21 851-1057 Sentence denotes The full length RNA genome of IBV is 27.6 kb in length and encodes non-structural proteins, four accessory proteins, and four structural proteins (spike [S], matrix [M], nucleocapsid [N], and envelope [E]).
T22 1058-1141 Sentence denotes The S protein is cleaved into S1 and S2 as two subunits at the S1/S2 cleavage site.
T23 1142-1294 Sentence denotes The S1 protein contains the receptor-binding domain and mediates viral attachment to host cells, whereas S2 is responsible for membrane fusion [5], [6].
T24 1295-1534 Sentence denotes Errors generated during the genomic replication of IBV and the selective pressure following the use of live attenuated vaccines or multiple infections with different IBV serotypes has led to the emergence of numerous IBV variants [7], [8].
T25 1535-1699 Sentence denotes In particular, small change as little as 5% in the amino acid composition of S1 gene may lead to alteration in cross protection among closely related serotypes [9].
T26 1700-1811 Sentence denotes In China, IBV was first observed during the early 1980s, and outbreaks have since been frequently reported [7].
T27 1812-2048 Sentence denotes The QX-like genotype is thought to have originated during the mid-1990s and continues to be the predominant strain, whereas the LDT3, 4/91, and Taiwan subtypes have also recently been frequently isolated in China [10], [11], [12], [13].
T28 2049-2248 Sentence denotes Severe nephritis, false layer syndrome, and high mortality are observed in chickens infected with this viral genotype, which represents a major problem in the poultry industry, particularly in China.
T29 2249-2393 Sentence denotes Using a live attenuated or inactivated vaccine is typically considered to be the most cost-effective means of controlling viral infections [14].
T30 2394-2744 Sentence denotes Unfortunately, inactivated IB vaccines are not effective if used alone, which could induce little or no protection against egg loss [15], [16], as well as impaired ciliary activity in the trachea [17]; thus, birds must continue to be given one or a series of vaccinations with live attenuated IB vaccines to provide broad heterologous protection [1].
T31 2745-3104 Sentence denotes Commercial attenuated live vaccines used against IBV in China include the H120, LDT3, and 4/91 strains [7]; however, phylogenetic analysis indicates that the QX-like genotype is genetically distant from the strains described above, which may explain the poor cross-protectivity against infection in chickens immunized with these classical vaccines [18], [19].
T32 3105-3210 Sentence denotes Recently, there has been increasing research on live attenuated vaccines against the QX-like IBV strains.
T33 3211-3469 Sentence denotes Different strains of QX-like IBVs were serially passaged in embryonated eggs or primary chicken kidney cells (CK) to obtain vaccines that are less virulent and exhibit high immunogenicity against the QX-like epidemic IBV strains [20], [21], [22], [23], [24].
T34 3470-3747 Sentence denotes However, in addition to causing tissue damage or secondary bacterial infections in young vaccinated chicks [25], [26], live attenuated vaccines of RNA viruses may not be genetically stable or they may be associated with the tendency to revert back to a virulent form [9], [14].
T35 3748-3879 Sentence denotes Moreover, the potential for recombination between vaccine and virulent strains can lead to the creation of new virulent virus [27].
T36 3880-4128 Sentence denotes Furthermore, it takes a substantial amount of time to prepare a extensively passaged attenuated vaccine strain, which may not be able to effectively solved the loss problem caused by the rapid variation exhibited by prevalent strains on the flocks.
T37 4129-4341 Sentence denotes In considering the limitations of the live attenuated and inactivated IBV vaccines, reverse genetic IBV vaccines have been developed in recent years as they display increased safety and efficacy [28], [29], [30].
T38 4342-4653 Sentence denotes As reverse genetic technology is primarily based on the H120 and Beaudette strains [31], [32], [33], both of which are passage-generated attenuated strains, the mechanism of virus virulence attenuation remains unclear, thereby posing difficulties in the development of attenuated vaccines using this technology.
T39 4654-4817 Sentence denotes In addition to the function of host invasion and increasing genetic diversity, the IBV S1 subunit can induce virus neutralizing and cross-reactive antibodies [34].
T40 4818-5062 Sentence denotes Therefore, some researchers have created an attenuated IBV vaccine by replacing the S1 or S genes from other virulent strains using reverse genetic technology to generate protection against strains of the corresponding serotype [5], [28], [30].
T41 5063-5345 Sentence denotes In the present study, we constructed a recombinant strain, using the reverse genetic system. rH120-S1/YZ is based on the backbone of the vaccine strain H120, and the S1 gene was replaced with that of the QX-like nephropathogenic strain, ck/CH/IBYZ/2011, which was isolated in China.
T42 5346-5489 Sentence denotes Our results demonstrate that this recombinant strain is safe and provides effective protection in young chickens against QX-like IBV challenge.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T3 27-37 Phenotype denotes bronchitis http://purl.obolibrary.org/obo/HP_0012387
T4 364-374 Phenotype denotes depression http://purl.obolibrary.org/obo/HP_0000716
T5 376-384 Phenotype denotes coughing http://purl.obolibrary.org/obo/HP_0012735
T6 552-561 Phenotype denotes nephritis http://purl.obolibrary.org/obo/HP_0000123
T7 670-680 Phenotype denotes bronchitis http://purl.obolibrary.org/obo/HP_0012387
T8 2056-2065 Phenotype denotes nephritis http://purl.obolibrary.org/obo/HP_0000123

2_test

Id Subject Object Predicate Lexical cue
32057575-22702451-143294022 254-255 22702451 denotes 1
32057575-16537157-143294023 259-260 16537157 denotes 2
32057575-23397833-143294024 264-265 23397833 denotes 3
32057575-22702451-143294025 439-440 22702451 denotes 1
32057575-16537157-143294026 621-622 16537157 denotes 2
32057575-23397833-143294027 626-627 23397833 denotes 3
32057575-14676007-143294028 847-848 14676007 denotes 4
32057575-12885925-143294029 1286-1287 12885925 denotes 5
32057575-17296157-143294030 1291-1292 17296157 denotes 6
32057575-1708184-143294031 1531-1532 1708184 denotes 8
32057575-25954763-143294032 1696-1697 25954763 denotes 9
32057575-15223561-143294033 2026-2028 15223561 denotes 10
32057575-22545524-143294034 2032-2034 22545524 denotes 11
32057575-25000989-143294035 2038-2040 25000989 denotes 12
32057575-20556502-143294036 2044-2046 20556502 denotes 13
32057575-6246669-143294037 2527-2529 6246669 denotes 15
32057575-5388980-143294038 2533-2535 5388980 denotes 16
32057575-1659365-143294039 2591-2593 1659365 denotes 17
32057575-22702451-143294040 2741-2742 22702451 denotes 1
32057575-19590226-143294041 3094-3096 19590226 denotes 18
32057575-25168045-143294042 3100-3102 25168045 denotes 19
32057575-26277655-143294043 3441-3443 26277655 denotes 20
32057575-29496346-143294044 3447-3449 29496346 denotes 21
32057575-29859801-143294045 3453-3455 29859801 denotes 22
32057575-29891352-143294046 3459-3461 29891352 denotes 23
32057575-21331953-143294047 3465-3467 21331953 denotes 24
32057575-16860445-143294048 3578-3580 16860445 denotes 25
32057575-8719209-143294049 3584-3586 8719209 denotes 26
32057575-25954763-143294050 3738-3739 25954763 denotes 9
32057575-22798607-143294051 3875-3877 22798607 denotes 27
32057575-29366709-143294052 4331-4333 29366709 denotes 29
32057575-30355423-143294053 4337-4339 30355423 denotes 30
32057575-11711626-143294054 4426-4428 11711626 denotes 31
32057575-22999521-143294055 4432-4434 22999521 denotes 32
32057575-23840781-143294056 4438-4440 23840781 denotes 33
32057575-7980002-143294057 4813-4815 7980002 denotes 34
32057575-12885925-143294058 5047-5048 12885925 denotes 5
32057575-30355423-143294059 5058-5060 30355423 denotes 30

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
44 16-37 Disease denotes Infectious bronchitis MESH:D001991
45 68-87 Disease denotes respiratory disease MESH:D012140
46 157-170 Disease denotes viral disease MESH:D001102
47 364-374 Disease denotes depression MESH:D000275
48 376-384 Disease denotes coughing MESH:D003371
49 552-561 Disease denotes nephritis MESH:D009393
54 659-686 Species denotes infectious bronchitis virus Tax:11120
55 806-819 Species denotes Coronaviridae Tax:11118
56 688-691 Species denotes IBV Tax:11120
57 881-884 Species denotes IBV Tax:11120
67 2124-2132 Species denotes chickens Tax:9031
68 1346-1349 Species denotes IBV Tax:11120
69 1461-1464 Species denotes IBV Tax:11120
70 1512-1515 Species denotes IBV Tax:11120
71 1710-1713 Species denotes IBV Tax:11120
72 1435-1445 Disease denotes infections MESH:D007239
73 2056-2065 Disease denotes nephritis MESH:D009393
74 2098-2107 Disease denotes mortality MESH:D003643
75 2133-2141 Disease denotes infected MESH:D007239
84 3044-3052 Species denotes chickens Tax:9031
85 3299-3306 Species denotes chicken Tax:9031
86 2794-2797 Species denotes IBV Tax:11120
87 3198-3201 Species denotes IBV Tax:11120
88 3428-3431 Species denotes IBV Tax:11120
89 2371-2387 Disease denotes viral infections MESH:D001102
90 3031-3040 Disease denotes infection MESH:D007239
91 3529-3549 Disease denotes bacterial infections MESH:D001424
99 5450-5458 Species denotes chickens Tax:9031
100 4199-4202 Species denotes IBV Tax:11120
101 4229-4232 Species denotes IBV Tax:11120
102 4737-4740 Species denotes IBV Tax:11120
103 4873-4876 Species denotes IBV Tax:11120
104 5475-5478 Species denotes IBV Tax:11120
105 5275-5291 Disease denotes nephropathogenic