PMC:7106203 / 2883-6937
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 60 | 1381-1386 | Species | denotes | CoV-2 | Tax:2697049 |
| 61 | 3097-3108 | CellLine | denotes | HBCDC-HB-01 | CVCL:3694 |
| 63 | 1223-1233 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 67 | 318-336 | Gene | denotes | ORF1ab polyprotein | Gene:43740578 |
| 68 | 121-131 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 69 | 1003-1013 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32092483-31226023-47573170 | 698-702 | 31226023 | denotes | 2019 |
| T3166 | 698-702 | 31226023 | denotes | 2019 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T23 | 27-37 | Body_part | denotes | nucleotide | http://purl.org/sig/ont/fma/fma82740 |
| T24 | 110-117 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T25 | 236-244 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T26 | 266-273 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T27 | 365-377 | Body_part | denotes | glycoprotein | http://purl.org/sig/ont/fma/fma62925 |
| T28 | 397-404 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T29 | 435-442 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T30 | 521-533 | Body_part | denotes | glycoprotein | http://purl.org/sig/ont/fma/fma62925 |
| T31 | 577-589 | Body_part | denotes | glycoprotein | http://purl.org/sig/ont/fma/fma62925 |
| T32 | 650-654 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T33 | 810-822 | Body_part | denotes | glycoprotein | http://purl.org/sig/ont/fma/fma62925 |
| T34 | 949-960 | Body_part | denotes | amino acids | http://purl.org/sig/ont/fma/fma82739 |
| T35 | 1028-1040 | Body_part | denotes | glycoprotein | http://purl.org/sig/ont/fma/fma62925 |
| T36 | 1097-1108 | Body_part | denotes | amino acids | http://purl.org/sig/ont/fma/fma82739 |
| T37 | 1213-1219 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T38 | 1299-1309 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T39 | 1317-1324 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T40 | 3611-3618 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T41 | 3630-3637 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T42 | 3723-3730 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T43 | 4042-4048 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
LitCovid_AGAC
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| p63588s9 | 840-862 | MPA | denotes | conformational changes |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T17 | 121-129 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T18 | 1003-1011 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T19 | 1223-1231 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T21 | 650-654 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T22 | 922-923 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T23 | 1405-1406 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T24 | 1426-1428 | http://purl.obolibrary.org/obo/CLO_0001382 | denotes | 48 |
| T25 | 1432-1433 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T26 | 1531-1534 | http://purl.obolibrary.org/obo/CLO_0002941 | denotes | EPI |
| T27 | 1626-1627 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T28 | 1982-1983 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T29 | 2100-2101 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T30 | 2889-2891 | http://purl.obolibrary.org/obo/CLO_0008954 | denotes | SC |
| T31 | 3075-3079 | http://purl.obolibrary.org/obo/CLO_0001079 | denotes | 14 8 |
| T32 | 3103-3105 | http://purl.obolibrary.org/obo/CLO_0003622 | denotes | HB |
| T33 | 3600-3601 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T34 | 3708-3709 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T35 | 3738-3741 | http://purl.obolibrary.org/obo/CLO_0001079 | denotes | 148 |
| T36 | 4031-4032 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T13 | 27-37 | Chemical | denotes | nucleotide | http://purl.obolibrary.org/obo/CHEBI_36976 |
| T14 | 236-244 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T15 | 266-273 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T16 | 365-377 | Chemical | denotes | glycoprotein | http://purl.obolibrary.org/obo/CHEBI_17089 |
| T17 | 397-404 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T18 | 435-442 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T19 | 521-533 | Chemical | denotes | glycoprotein | http://purl.obolibrary.org/obo/CHEBI_17089 |
| T20 | 577-589 | Chemical | denotes | glycoprotein | http://purl.obolibrary.org/obo/CHEBI_17089 |
| T21 | 810-822 | Chemical | denotes | glycoprotein | http://purl.obolibrary.org/obo/CHEBI_17089 |
| T22 | 949-960 | Chemical | denotes | amino acids | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T23 | 949-954 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T24 | 955-960 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T25 | 1028-1040 | Chemical | denotes | glycoprotein | http://purl.obolibrary.org/obo/CHEBI_17089 |
| T26 | 1097-1108 | Chemical | denotes | amino acids | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T27 | 1097-1102 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T28 | 1103-1108 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T29 | 1299-1309 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T30 | 1299-1304 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T31 | 1305-1309 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T32 | 1317-1324 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T33 | 1645-1647 | Chemical | denotes | TY | http://purl.obolibrary.org/obo/CHEBI_73667 |
| T34 | 1648-1650 | Chemical | denotes | WK | http://purl.obolibrary.org/obo/CHEBI_74872 |
| T35 | 2009-2011 | Chemical | denotes | SD | http://purl.obolibrary.org/obo/CHEBI_74807 |
| T36 | 2366-2368 | Chemical | denotes | YN | http://purl.obolibrary.org/obo/CHEBI_141452 |
| T37 | 2406-2408 | Chemical | denotes | SD | http://purl.obolibrary.org/obo/CHEBI_74807 |
| T38 | 2585-2587 | Chemical | denotes | KY | http://purl.obolibrary.org/obo/CHEBI_73608 |
| T39 | 2834-2836 | Chemical | denotes | AI | http://purl.obolibrary.org/obo/CHEBI_73805|http://purl.obolibrary.org/obo/CHEBI_74007|http://purl.obolibrary.org/obo/CHEBI_74088 |
| T42 | 3611-3618 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T43 | 3630-3637 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T44 | 3723-3730 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 675-682 | http://purl.obolibrary.org/obo/GO_0009606 | denotes | tropism |
| T2 | 933-945 | http://purl.obolibrary.org/obo/GO_0051179 | denotes | localization |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T26 | 0-143 | Sentence | denotes | It is interesting that our nucleotide sequence alignment also revealed ninety-three mutations over the entire genomes of SARS-CoV-2 (Table 1 ). |
| T27 | 144-274 | Sentence | denotes | Forty-two missense mutations were identified in all the major non-structural and structural proteins, except the envelope protein. |
| T28 | 275-443 | Sentence | denotes | Twenty-nine missense mutations were in the ORF1ab polyprotein, eight in the spike surface glycoprotein, one in the matrix protein, and four in the nucleocapsid protein. |
| T29 | 444-558 | Sentence | denotes | Of note, three mutations (D354, Y364, and F367) located in the spike surface glycoprotein receptor-binding domain. |
| T30 | 559-704 | Sentence | denotes | The spike surface glycoprotein plays an essential role in binding to receptors on the host cell and determines host tropism (Fung and Liu, 2019). |
| T31 | 705-778 | Sentence | denotes | It is also the major target of neutralizing antibodies (Yu et al., 2020). |
| T32 | 779-912 | Sentence | denotes | Mutations in the spike surface glycoprotein might induce its conformational changes, which probably led to the changing antigenicity. |
| T33 | 913-1068 | Sentence | denotes | To date, a study on localization of amino acids involved in conformational changes of the SARS-CoV-2 spike surface glycoprotein structure is not available. |
| T34 | 1069-1174 | Sentence | denotes | The identification of these amino acids is of significance and should be investigated by further studies. |
| T35 | 1175-1242 | Sentence | denotes | Table 1 Mutations found in the entire genome of SARS-CoV-2 strains. |
| T36 | 1243-1325 | Sentence | denotes | The number in the parentheses indicated the location of amino acid in its protein. |
| T37 | 1326-1393 | Sentence | denotes | Genomic region No. nt mutations Missense mutation SARV-CoV-2 strain |
| T38 | 1394-1406 | Sentence | denotes | 5′ UTR 8 N/A |
| T39 | 1407-1431 | Sentence | denotes | ORF1ab polyprotein 48 29 |
| T40 | 1432-1498 | Sentence | denotes | A (117) → T USA/CA3/2020/EPI_ISL_408008USA/CA4/2020/EPI_ISL_408009 |
| T41 | 1499-1545 | Sentence | denotes | P (309) → S France/IDF0515/2020/EPI ISL_408430 |
| T42 | 1546-1585 | Sentence | denotes | S (428) → N USA/CA1/2020/EPI_ISL_406034 |
| T43 | 1586-1625 | Sentence | denotes | T (609) → I USA/CA5/2020/EPI_ISL_408010 |
| T44 | 1626-1674 | Sentence | denotes | A (1176) → V Japan/TY-WK-012/2020/EPI_ISL_408665 |
| T45 | 1675-1720 | Sentence | denotes | L (1599) → F Korea/KCDC03/2020/EPI_ISL_407193 |
| T46 | 1721-1788 | Sentence | denotes | I (1607) → V USA/CA3/2020/EPI_ISL_408008USA/CA4/2020/EPI_ISL_408009 |
| T47 | 1789-1839 | Sentence | denotes | M (2194) → T Shenzhen/SZTH-004/2020/EPI_ISL_406595 |
| T48 | 1840-1883 | Sentence | denotes | L (2235) → I Wuhan/WH01/2019/EPI_ISL_406798 |
| T49 | 1884-1936 | Sentence | denotes | I (2244) → T Wuhan/IPBCAMS-WH-03/2019/EPI_ISL_403930 |
| T50 | 1937-1981 | Sentence | denotes | G (2251) → S Wuhan/WIV05/2019/EPI_ISL_402128 |
| T51 | 1982-2035 | Sentence | denotes | A (2345) → V Shandong/IVDC-SD-001/2020/EPI_ISL_408482 |
| T52 | 2036-2088 | Sentence | denotes | G (2534) → V Wuhan/IPBCAMS-WH-05/2020/EPI_ISL_403928 |
| T53 | 2089-2133 | Sentence | denotes | D (2579) → A Wuhan/WIV07/2019/EPI_ISL_402130 |
| T54 | 2134-2186 | Sentence | denotes | N (2708) → S Wuhan/IPBCAMS-WH-01/2019/EPI_ISL_402123 |
| T55 | 2187-2239 | Sentence | denotes | F (2908) → I Wuhan/IPBCAMS-WH-01/2019/EPI_ISL_402123 |
| T56 | 2240-2287 | Sentence | denotes | T (3058) → I France/IDF0515/2020/EPI_ISL_408430 |
| T57 | 2288-2340 | Sentence | denotes | S (3099) → L Shenzhen/HKU-SZ-005/2020/EPI_ISL_405839 |
| T58 | 2341-2565 | Sentence | denotes | L (3606) → F Yunnan/IVDC-YN-003/2020/EPI_ISL_408480Shandong/IVDC-SD-001/2020/EPI_ISL_408482Chongqing/IVDC-CQ-001/2020/EPI_ISL_408481Singapore/3/2020/EPI_ISL_407988France/IDF0515/2020/EPI_ISL_408430USA/AZ1/2020/EPI_ISL_406223 |
| T59 | 2566-2613 | Sentence | denotes | E (3764) → D Japan/KY-V-029/2020/EPI_ISL_408669 |
| T60 | 2614-2657 | Sentence | denotes | N (3833) → K Wuhan/WH01/2019/EPI_ISL_406798 |
| T61 | 2658-2699 | Sentence | denotes | W (5308) → C Taiwan/2/2020/EPI_ISL_406031 |
| T62 | 2700-2740 | Sentence | denotes | T (5579) → I USA/CA2/2020/EPI_ISL_406036 |
| T63 | 2741-2814 | Sentence | denotes | I (6075) → T England/02/2020/EPI_ISL_407073England/01/2020/EPI_ISL_407071 |
| T64 | 2815-2862 | Sentence | denotes | P (6083) → L Japan/AI/I-004/2020/EPI_ISL_407084 |
| T65 | 2863-2915 | Sentence | denotes | F (6309) → Y Sichuan/IVDC-SC-001/2020/EPI_ISL_408484 |
| T66 | 2916-2966 | Sentence | denotes | E (6565) → D Shenzhen/SZTH-004/2020/EPI_ISL_406595 |
| T67 | 2967-3011 | Sentence | denotes | K (6958) → R Wuhan/WIV05/2019/EPI_ISL_402128 |
| T68 | 3012-3056 | Sentence | denotes | D (7018) → N Wuhan/WIV02/2019/EPI_ISL_402127 |
| T69 | 3057-3079 | Sentence | denotes | Spike polyprotein 14 8 |
| T70 | 3080-3128 | Sentence | denotes | F (32) → I Wuhan/HBCDC-HB-01/2019/EPI_ISL_402132 |
| T71 | 3129-3251 | Sentence | denotes | H (49) → Y Guangdong/20SF174/2020/EPI_ISL_406531Guangdong/20SF040/2020/EPI_ISL_403937Guangdong/20SF028/2020/EPI_ISL_403936 |
| T72 | 3252-3299 | Sentence | denotes | S (247) → R Australia/VIC01/2020/EPI_ISL_406844 |
| T73 | 3300-3349 | Sentence | denotes | N (354) → D Shenzhen/SZTH-004/2020/EPI_ISL_406595 |
| T74 | 3350-3399 | Sentence | denotes | D (364) → Y Shenzhen/SZTH-004/2020/EPI_ISL_406595 |
| T75 | 3400-3480 | Sentence | denotes | V (367) → F France/IDF0372/2020/EPI_ISL_406596France/IDF0373/2020/EPI_ISL_406597 |
| T76 | 3481-3528 | Sentence | denotes | D (614) → G Germany/BavPat1/2020/EPI_ISL_406862 |
| T77 | 3529-3577 | Sentence | denotes | P (1143) → L Australia/QLD02/2020/EPI_ISL_407896 |
| T78 | 3578-3601 | Sentence | denotes | Intergenic region 5 N/A |
| T79 | 3602-3622 | Sentence | denotes | Envelope protein 0 0 |
| T80 | 3623-3641 | Sentence | denotes | Matrix protein 2 1 |
| T81 | 3642-3685 | Sentence | denotes | D (209) → H Singapore/2/2020/EPI_ISL_407987 |
| T82 | 3686-3709 | Sentence | denotes | Intergenic region 6 N/A |
| T83 | 3710-3734 | Sentence | denotes | Nucleocapsid protein 7 4 |
| T84 | 3735-3784 | Sentence | denotes | T (148) → I Shenzhen/SZTH-004/2020/EPI_ISL_406595 |
| T85 | 3785-3922 | Sentence | denotes | S (194) → L Shenzhen/SZTH-003/2020/EPI_ISL_406594Foshan/20SF207/2020/EPI_ISL_406534USA/CA3/2020/EPI_ISL_408008USA/CA4/2020/EPI_ISL_408009 |
| T86 | 3923-3970 | Sentence | denotes | S (202) → N Australia/QLD02/2020/EPI_ISL_407896 |
| T87 | 3971-4020 | Sentence | denotes | P (344) → S Guangzhou/20SF206/2020/EPI_ISL_406533 |
| T88 | 4021-4032 | Sentence | denotes | 3′UTR 3 N/A |
| T89 | 4033-4054 | Sentence | denotes | Complete genome 93 42 |