
PMC:7519301 / 3845-5853
Annnotations
LitCovid-PD-FMA-UBERON
Id | Subject | Object | Predicate | Lexical cue | fma_id |
---|---|---|---|---|---|
T16 | 438-444 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
T17 | 470-480 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
T18 | 669-680 | Body_part | denotes | amino acids | http://purl.org/sig/ont/fma/fma82739 |
T19 | 742-749 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
T20 | 964-971 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
T21 | 1208-1212 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
LitCovid-PD-UBERON
Id | Subject | Object | Predicate | Lexical cue | uberon_id |
---|---|---|---|---|---|
T1 | 1677-1682 | Body_part | denotes | scale | http://purl.obolibrary.org/obo/UBERON_0002542 |
LitCovid-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T35 | 29-37 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
T36 | 342-350 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T37 | 342-346 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T38 | 495-503 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T39 | 495-499 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T40 | 571-579 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T41 | 571-575 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T42 | 803-811 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T43 | 803-807 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T44 | 1091-1099 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T45 | 1091-1095 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T46 | 1492-1500 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T47 | 1492-1496 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T48 | 1622-1630 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T49 | 1622-1626 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T50 | 1739-1747 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T51 | 1739-1743 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T52 | 1924-1932 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T53 | 1924-1928 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T33 | 47-50 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
T34 | 58-59 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T35 | 376-377 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T36 | 387-394 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
T37 | 414-418 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bats |
T38 | 434-437 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
T39 | 452-455 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
T40 | 714-716 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
T41 | 721-723 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
T42 | 721-723 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
T43 | 756-758 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
T44 | 759-761 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
T45 | 759-761 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
T46 | 775-776 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T47 | 913-915 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
T48 | 1051-1054 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
T49 | 1139-1141 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
T50 | 1142-1144 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
T51 | 1142-1144 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
T52 | 1208-1212 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T53 | 1393-1396 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
T54 | 1397-1404 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
T55 | 1416-1417 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T56 | 1443-1444 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T57 | 1454-1459 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
T58 | 1545-1550 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
T59 | 1560-1566 | http://purl.obolibrary.org/obo/NCBITaxon_33208 | denotes | animal |
T60 | 1581-1588 | http://purl.obolibrary.org/obo/CLO_0009985 | denotes | focused |
T61 | 1659-1665 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | humans |
T62 | 1758-1764 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | humans |
T63 | 1771-1772 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T11 | 470-480 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
T12 | 470-475 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
T13 | 476-480 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
T14 | 669-680 | Chemical | denotes | amino acids | http://purl.obolibrary.org/obo/CHEBI_33709 |
T15 | 669-674 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
T16 | 675-680 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
T17 | 721-723 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
T18 | 742-749 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
T19 | 759-761 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
T20 | 1142-1144 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
---|---|---|---|---|---|
113 | 594-600 | Gene | denotes | ORF1ab | Gene:43740578 |
114 | 633-634 | Gene | denotes | S | Gene:43740568 |
115 | 427-428 | Gene | denotes | S | Gene:43740568 |
116 | 276-287 | Species | denotes | coronavirus | Tax:11118 |
117 | 342-352 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
118 | 404-418 | Species | denotes | horseshoe bats | Tax:49442 |
119 | 495-505 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
120 | 571-581 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
121 | 803-813 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
122 | 894-911 | Species | denotes | Malayan pangolins | Tax:9974 |
123 | 952-963 | Species | denotes | coronavirus | Tax:11118 |
124 | 1091-1101 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
125 | 1492-1502 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
126 | 1622-1632 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
127 | 1659-1665 | Species | denotes | humans | Tax:9606 |
128 | 1739-1749 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
129 | 1758-1764 | Species | denotes | humans | Tax:9606 |
130 | 1924-1934 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
131 | 29-37 | Disease | denotes | COVID-19 | MESH:C000657245 |
132 | 110-119 | Disease | denotes | mortality | MESH:D003643 |
133 | 225-231 | Disease | denotes | deaths | MESH:D003643 |
LitCovid-PD-GO-BP
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T2 | 1779-1791 | http://purl.obolibrary.org/obo/GO_0000003 | denotes | reproduction |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T30 | 0-151 | Sentence | denotes | In the span of 7 months, the COVID-19 pandemic has caused a devastating global health crisis with significant mortality and socioeconomic implications. |
T31 | 152-306 | Sentence | denotes | As of July 23, 2020, more than 15 million cases and 622,000 attributable deaths have been reported worldwide (5–8) (https://coronavirus.jhu.edu/map.html). |
T32 | 307-423 | Sentence | denotes | Phylogenetic analyses suggest that SARS-CoV-2 is likely derived from a clade of viruses found in horseshoe bats (9). |
T33 | 424-510 | Sentence | denotes | In S, the bat genome RaTG13 has more than 97% amino acid identity with SARS-CoV-2 (6). |
T34 | 511-820 | Sentence | denotes | Interestingly, the RmYN02 sequence, which is the closest to SARS-CoV-2 in the long ORF1ab but more distant than RaTG13 in S, showed the insertion of multiple amino acids at the cleavage site between the S1 and S2 subunits of the S protein (this S1/S2 insertion is a characteristic feature of SARS-CoV-2) (10). |
T35 | 821-1009 | Sentence | denotes | Highly similar sequences, especially in the RBD, were also identified in Malayan pangolins (11, 12), emphasizing the plasticity of coronavirus genomes and their propensity to switch hosts. |
T36 | 1010-1503 | Sentence | denotes | Although the closest currently available bat sequences are fairly divergent from SARS-CoV-2, their characteristics (insertion at S1/S2 cleavage site, high diversity, and similarity between specific gene fragments and particular strains) together with their known adaptive properties (high recombination and host-switching rates and evidence of positive selection) support that these bat viruses constitute a generalist lineage where a specific virus is likely the natural origin of SARS-CoV-2. |
T37 | 1504-1666 | Sentence | denotes | We did not study the transmission of the virus from its animal reservoir and focused our analysis on the evolution of SARS-CoV-2 since its introduction in humans. |
T38 | 1667-2008 | Sentence | denotes | While the scale of the pandemic attests to the high transmissibility of SARS-CoV-2 between humans, with a basic reproduction number R0 estimated to be 2.2 (95% CI, 1.4 to 3.9) in Wuhan, China (13), we wanted to investigate evidence of further adaptation of SARS-CoV-2 to its host, as adaptive processes could interfere with vaccine efficacy. |