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PMC:7029759 / 2181-6461 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
67 42-51 Disease denotes pneumonia MESH:D011014
162 3817-3826 Species denotes 2019-nCoV Tax:2697049
64 197-214 Species denotes novel coronavirus Tax:2697049
65 216-225 Species denotes 2019-nCoV Tax:2697049
66 585-591 Species denotes people Tax:9606
68 133-142 Disease denotes pneumonia MESH:D011014
69 239-272 Disease denotes Severe Acute Respiratory Syndrome MESH:D045169
70 274-278 Disease denotes SARS MESH:D045169
71 286-318 Disease denotes Middle East Respiratory Syndrome MESH:D018352
72 320-324 Disease denotes MERS MESH:D018352
73 341-345 Disease denotes SARS MESH:D045169
74 350-354 Disease denotes MERS MESH:D018352
75 437-441 Disease denotes SARS MESH:D045169
76 559-572 Disease denotes SARS infected MESH:D045169
77 607-613 Disease denotes deaths MESH:D003643
91 670-687 Species denotes novel coronavirus Tax:2697049
92 689-698 Species denotes 2019-nCoV Tax:2697049
93 772-777 Species denotes Human Tax:9606
94 781-786 Species denotes human Tax:9606
95 803-812 Species denotes 2019-nCoV Tax:2697049
96 1387-1398 Species denotes coronavirus Tax:11118
97 996-1015 Disease denotes 2019-nCoV infection MESH:C000657245
98 1024-1029 Disease denotes fever MESH:D005334
99 1031-1036 Disease denotes cough MESH:D003371
100 1042-1049 Disease denotes myalgia MESH:D063806
101 1053-1060 Disease denotes fatigue MESH:D005221
102 1066-1075 Disease denotes pneumonia MESH:D011014
103 1473-1478 Disease denotes fever MESH:D005334
112 1658-1669 Species denotes Ebola virus Tax:1570291
113 1805-1812 Species denotes patient Tax:9606
114 2047-2052 Species denotes Ebola Tax:1570291
115 2186-2195 Species denotes 2019-nCoV Tax:2697049
116 1626-1630 Disease denotes SARS MESH:D045169
117 1771-1779 Disease denotes infected MESH:D007239
118 1960-1968 Disease denotes infected MESH:D007239
119 2039-2043 Disease denotes SARS MESH:D045169
138 3182-3183 Gene denotes S Gene:43740568
139 3175-3180 Gene denotes spike Gene:43740568
140 2224-2232 Species denotes patients Tax:9606
141 2475-2483 Species denotes patients Tax:9606
142 2704-2709 Species denotes Ebola Tax:1570291
143 2959-2968 Species denotes 2019-nCoV Tax:2697049
144 2970-2975 Species denotes Ebola Tax:1570291
145 3133-3142 Species denotes 2019-nCoV Tax:2697049
146 3200-3211 Species denotes coronavirus Tax:11118
147 3505-3514 Species denotes 2019-nCoV Tax:2697049
148 3560-3568 Species denotes patients Tax:9606
149 3583-3592 Species denotes 2019-nCoV Tax:2697049
150 3628-3633 Species denotes Ebola Tax:1570291
151 3634-3642 Species denotes patients Tax:9606
152 3339-3343 Disease denotes SARS MESH:D045169
153 3348-3352 Disease denotes MERS MESH:D018352
154 3569-3577 Disease denotes infected MESH:D007239
155 3222-3232 CellLine denotes MN908947.3 CVCL:U508
163 3894-3902 Species denotes patients Tax:9606
164 3979-3988 Species denotes 2019-nCoV Tax:2697049
165 4048-4057 Species denotes 2019-nCoV Tax:2697049
166 4082-4090 Species denotes patients Tax:9606
167 4265-4273 Species denotes patients Tax:9606

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T80 92-99 GO:0040007 denotes growing
T79 133-142 UBERON:0002048 denotes pneumonia
T78 203-214 NCBITaxon:11118 denotes coronavirus
T77 216-225 SP_7 denotes 2019-nCoV
T76 274-278 SP_10 denotes SARS
T75 320-324 SP_9 denotes MERS
T74 341-345 SP_10 denotes SARS
T73 350-354 SP_9 denotes MERS
T72 437-441 SP_10 denotes SARS
T71 559-563 SP_10 denotes SARS
T70 585-591 NCBITaxon:9606 denotes people
T69 607-613 GO:0016265 denotes deaths
T68 676-687 NCBITaxon:11118 denotes coronavirus
T67 689-698 SP_7 denotes 2019-nCoV
T66 772-777 SP_6;NCBITaxon:9606 denotes Human
T65 781-786 SP_6;NCBITaxon:9606 denotes human
T64 803-812 SP_7 denotes 2019-nCoV
T63 996-1005 SP_7 denotes 2019-nCoV
T62 1031-1036 UBERON:0002048 denotes cough
T61 1092-1097 UBERON:0001443 denotes chest
T60 1200-1211 NCBITaxon:1 denotes individuals
T59 1270-1275 NCBITaxon:10239 denotes virus
T58 1387-1398 NCBITaxon:11118 denotes coronavirus
T57 1626-1630 SP_10 denotes SARS
T56 1658-1669 NCBITaxon:10376 denotes Ebola virus
T55 1780-1791 NCBITaxon:1 denotes individuals
T54 2039-2043 SP_10 denotes SARS
T53 2047-2052 NCBITaxon:10376 denotes Ebola
T52 2186-2195 SP_7 denotes 2019-nCoV
T51 2390-2394 CHEBI:23888;CHEBI:23888;GO:0017144 denotes drug
T50 2395-2406 GO:0017144 denotes development
T49 2492-2497 GO:0016265 denotes dying
T48 2885-2890 NCBITaxon:10239 denotes virus
T47 2959-2968 SP_7 denotes 2019-nCoV
T46 2970-2975 NCBITaxon:10376 denotes Ebola
T45 3083-3089 NCBITaxon:33208 denotes animal
T44 3133-3142 SP_7 denotes 2019-nCoV
T43 3200-3211 NCBITaxon:11118 denotes coronavirus
T42 3263-3274 CHEBI:60816;CHEBI:60816 denotes immunogenic
T41 3339-3343 SP_10 denotes SARS
T40 3348-3352 SP_9 denotes MERS
T39 3505-3514 SP_7 denotes 2019-nCoV
T38 3583-3592 SP_7 denotes 2019-nCoV
T37 3628-3633 NCBITaxon:10376 denotes Ebola
T36 3817-3826 SP_7 denotes 2019-nCoV
T35 3827-3832 NCBITaxon:10239 denotes virus
T34 3979-3988 SP_7 denotes 2019-nCoV
T33 4048-4057 SP_7 denotes 2019-nCoV

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T10 1092-1097 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T11 3185-3192 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T12 3291-3298 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 1092-1097 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T5 42-51 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T6 133-142 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T7 239-272 Disease denotes Severe Acute Respiratory Syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T8 274-278 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T9 341-345 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 437-441 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T11 559-563 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T12 996-1015 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T13 1006-1015 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T14 1066-1075 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T15 1626-1630 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T16 1658-1663 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T17 2039-2043 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T18 2047-2052 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T19 2704-2709 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T20 2970-2975 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T21 3339-3343 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T22 3628-3633 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T21 13-14 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T22 105-106 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 195-196 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 644-656 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T25 772-777 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T26 781-786 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T27 813-816 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T28 1092-1097 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T29 1175-1178 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T30 1270-1275 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T31 1319-1320 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 1373-1375 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T33 1564-1571 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T34 1664-1669 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T35 2113-2115 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T36 2126-2127 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 2170-2180 http://purl.obolibrary.org/obo/UBERON_0001456 denotes are facing
T38 2217-2223 http://purl.obolibrary.org/obo/UBERON_0001456 denotes facing
T39 2437-2438 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 2726-2727 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 2826-2827 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 2885-2890 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T43 3061-3067 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T44 3083-3089 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T45 3408-3409 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 3435-3436 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 3803-3804 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 3827-3832 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T49 3846-3851 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T50 3884-3890 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T51 4180-4182 http://purl.obolibrary.org/obo/CLO_0050475 denotes my
T52 4254-4261 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T8 2014-2023 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T9 2390-2394 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T10 3185-3192 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T11 3291-3298 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T16 0-12 Sentence denotes Introduction
T17 13-126 Sentence denotes A mysterious illness causing pneumonia in December 2019 in Wuhan, China is now growing into a potential pandemic.
T18 127-340 Sentence denotes These pneumonia cases were eventually characterized to be caused by a novel coronavirus (2019-nCoV) 1, of which Severe Acute Respiratory Syndrome (SARS) 2 and Middle East Respiratory Syndrome (MERS) 3 are members.
T19 341-436 Sentence denotes SARS and MERS famously caused their own outbreak concerns when they were originally identified.
T20 437-546 Sentence denotes SARS caused significant economic damage to Hong Kong and Southern China, before spreading to other countries.
T21 547-665 Sentence denotes Ultimately, SARS infected up to 8,098 people and caused 774 deaths according to the World Health Organization (WHO) 4.
T22 666-771 Sentence denotes The novel coronavirus, 2019-nCoV, is now quickly spreading across the world after originating in Wuhan 1.
T23 772-974 Sentence denotes Human-to-human transmission of 2019-nCoV has been confirmed in familial case cluster reports 5, as additional cases continue to be identified in different cities in China and countries around the world.
T24 975-1116 Sentence denotes Clinical symptoms of 2019-nCoV infection include fever, cough, and myalgia or fatigue with pneumonia demonstrated on chest CT scan imaging 6.
T25 1117-1425 Sentence denotes Within China, the city of Wuhan along with several others has been shut down, with individuals not allowed to leave the city in an effort to contain the virus; such efforts are largely unprecedented in a city of this size ( https://www.nytimes.com/2020/01/22/world/asia/coronavirus-quarantines-history.html).
T26 1426-1574 Sentence denotes For now, many travelers are being screened for fever (≥38°C) and reported recent history of travel to Wuhan in order to triage diagnostic testing 7.
T27 1575-1692 Sentence denotes These efforts resemble not only what happened with SARS in 2002–2003, but also the Ebola virus outbreak in 2014–2015.
T28 1693-1832 Sentence denotes During those outbreaks, special protocols were put in place to quarantine any infected individuals and identify patient contacts at risk 8.
T29 1833-1989 Sentence denotes Healthcare workers were also at risk, and despite extensive personal protective equipment measures, clinical providers did get infected in both outbreaks 9.
T30 1990-2196 Sentence denotes There were no specific, antiviral treatments for SARS or Ebola at the time of the outbreaks beyond supportive measures 10, 11, which is a similar situation that healthcare systems are facing with 2019-nCoV.
T31 2197-2331 Sentence denotes The dire situations facing patients in outbreak scenarios demand quick responses by the healthcare community and the biotech industry.
T32 2332-2541 Sentence denotes Unfortunately, many of the traditional options that guide drug development are inadequate for outbreaks; a process that takes years can’t help patients who are dying today, and economies that are being halted.
T33 2542-2658 Sentence denotes In these situations, studies have often been conducted on compassionate use, and clinical trial approvals expedited.
T34 2659-2778 Sentence denotes This was most recently seen in the 2014–2015 Ebola outbreak, where a variety of clinical trial candidates were studied.
T35 2779-2894 Sentence denotes Many of these therapies failed, but ultimately a vaccine did emerge that was fully protective against the virus 12.
T36 2895-3128 Sentence denotes It is important to note that, unlike the current situation with 2019-nCoV, Ebola had already been studied for years and this particular neutralizing vaccine made and tested in preclinical animal models years prior to the outbreak 13.
T37 3129-3418 Sentence denotes For 2019-nCoV, beyond knowing the sequence of spike (S) protein of the coronavirus (GenBank: MN908947.3), there are no studies on how immunogenic this particular protein will be beyond surrogate comparisons to SARS and MERS, which limits the potential ability to quickly produce a vaccine.
T38 3419-3707 Sentence denotes Moreover, while a vaccine would be greatly effective in helping to stop the spread of 2019-nCoV, an effective therapy is also needed for the patients infected with 2019-nCoV today, similar to the situation of Ebola patients needing effective therapies while vaccines were being developed.
T39 3708-3989 Sentence denotes In this article, I will outline different potential treatment options that could be pursued as a therapy for 2019-nCoV virus, keeping the focus on agents that could be rapidly tested in patients today and broadly effective in spite of limited knowledge of the biology of 2019-nCoV.
T40 3990-4122 Sentence denotes Simply stated, there is limited time for basic studies of 2019-nCoV in research labs, while patients need effective therapies today.
T41 4123-4280 Sentence denotes I finally propose the best potential treatment option in my opinion, along with instructions on how to manufacture the therapy for testing in patients today.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T2 42-51 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 133-142 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T4 1024-1029 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T5 1031-1036 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T6 1042-1049 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326
T7 1053-1060 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T8 1066-1075 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T9 1473-1478 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945