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PMC:7258756 / 79-2159 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
6 46-93 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
7 95-105 Species denotes SARS-CoV-2 Tax:2697049
8 188-198 Species denotes SARS-CoV-2 Tax:2697049
9 313-323 Species denotes SARS-CoV-2 Tax:2697049
15 515-519 Gene denotes RdRp Gene:43740578
16 525-529 Gene denotes RdRp Gene:43740578
17 538-539 Gene denotes N Gene:43740575
18 491-492 Gene denotes E Gene:43740570
19 738-748 Species denotes SARS-CoV-2 Tax:2697049
25 1322-1327 Gene denotes spike Gene:43740568
26 867-877 Species denotes SARS-CoV-2 Tax:2697049
27 1016-1026 Species denotes SARS-CoV-2 Tax:2697049
28 1084-1120 Species denotes Wuhan seafood market pneumonia virus Tax:2697049
29 1456-1461 Species denotes human Tax:9606
32 1595-1605 Species denotes SARS-CoV-2 Tax:2697049
33 2069-2079 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T2 406-412 Body_part denotes Throat http://purl.org/sig/ont/fma/fma228738
T3 493-497 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T4 540-544 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T5 713-717 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T6 903-914 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T7 916-923 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T8 959-965 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T9 1258-1262 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T10 1328-1335 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T11 1429-1433 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T12 1462-1471 Body_part denotes leucocyte http://purl.org/sig/ont/fma/fma62852
T13 1764-1768 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 406-412 Body_part denotes Throat http://purl.obolibrary.org/obo/UBERON_0000341

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T3 46-93 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 46-79 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T5 95-103 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 95-99 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T7 188-196 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 188-192 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T9 313-321 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 313-317 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T11 738-746 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T12 738-742 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T13 867-875 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 867-871 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T15 1016-1024 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 1016-1020 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T17 1105-1114 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T18 1595-1603 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 1595-1599 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T20 2069-2077 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 2069-2073 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 13-23 http://purl.obolibrary.org/obo/BFO_0000030 denotes objectives
T3 107-110 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T4 269-278 http://purl.obolibrary.org/obo/BFO_0000030 denotes objective
T5 443-444 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 493-497 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T7 540-544 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T8 704-705 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T9 711-717 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T10 803-804 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 946-947 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1115-1120 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T13 1256-1262 http://purl.obolibrary.org/obo/CL_0000236 denotes B-cell
T14 1309-1311 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T15 1341-1342 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 1427-1433 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T17 1456-1461 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T18 1462-1471 http://purl.obolibrary.org/obo/CL_0000738 denotes leucocyte
T19 1499-1500 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T20 1505-1506 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T21 1755-1756 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T22 1762-1768 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 903-914 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T2 1328-1335 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T3 1358-1365 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T4 1472-1479 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 555-576 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T2 563-576 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T3 0-24 Sentence denotes Background & objectives:
T4 25-143 Sentence denotes Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries.
T5 144-264 Sentence denotes In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare.
T6 265-395 Sentence denotes The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.
T7 397-405 Sentence denotes Methods:
T8 406-635 Sentence denotes Throat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing.
T9 636-775 Sentence denotes Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken.
T10 777-785 Sentence denotes Results:
T11 786-878 Sentence denotes Three cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2.
T12 879-991 Sentence denotes Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained.
T13 992-1151 Sentence denotes The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512).
T14 1152-1238 Sentence denotes Phylogenetic analysis showed that the Indian sequences belonged to different clusters.
T15 1239-1412 Sentence denotes Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain.
T16 1413-1555 Sentence denotes The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population.
T17 1557-1586 Sentence denotes Interpretation & conclusions:
T18 1587-1691 Sentence denotes The two SARS-CoV-2 sequences obtained from India represent two different introductions into the country.
T19 1692-1739 Sentence denotes The genetic heterogeneity is as noted globally.
T20 1740-1875 Sentence denotes The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics.
T21 1876-2080 Sentence denotes Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1105-1114 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090