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PMC:7029759 / 2181-6461
Annnotations
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 |