PMC:7354481 / 5845-9095
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T29 | 67-78 | Body_part | denotes | nucleotides | http://purl.org/sig/ont/fma/fma82740 |
| T30 | 117-121 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T31 | 297-301 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T32 | 321-325 | Body_part | denotes | mRNA | http://purl.org/sig/ont/fma/fma67122 |
| T33 | 630-633 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T34 | 634-641 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T35 | 1063-1067 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T36 | 1235-1240 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T37 | 1291-1298 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T38 | 1387-1393 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T39 | 1516-1519 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T40 | 1526-1533 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T41 | 1541-1544 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T42 | 1664-1667 | Body_part | denotes | HIV | http://purl.org/sig/ont/fma/fma278683 |
| T43 | 1678-1681 | Body_part | denotes | HIV | http://purl.org/sig/ont/fma/fma278683 |
| T44 | 1688-1691 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T45 | 1933-1944 | Body_part | denotes | cytoplasmic | http://purl.org/sig/ont/fma/fma66835 |
| T46 | 1962-1967 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T47 | 2037-2042 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T48 | 2097-2100 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T49 | 2101-2107 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T50 | 2289-2294 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T51 | 2448-2452 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T52 | 2573-2578 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T53 | 2708-2716 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T54 | 2858-2863 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T55 | 2965-2969 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T56 | 3077-3081 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T57 | 3168-3172 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T58 | 3173-3177 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T8 | 3077-3081 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T9 | 3168-3172 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T37 | 1684-1687 | Disease | denotes | TAR | http://purl.obolibrary.org/obo/MONDO_0010121 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T47 | 64-66 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
| T48 | 117-121 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T49 | 289-290 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T50 | 297-306 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell type |
| T51 | 312-313 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T52 | 390-395 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T53 | 617-624 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T54 | 824-827 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T55 | 854-859 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T56 | 900-905 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T57 | 1063-1067 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T58 | 1122-1123 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T59 | 1150-1155 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T60 | 1235-1240 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T61 | 1299-1302 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T62 | 1468-1473 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T63 | 1693-1694 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T64 | 1735-1736 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T65 | 1861-1870 | http://purl.obolibrary.org/obo/OBI_0100026 | denotes | organisms |
| T66 | 1861-1870 | http://purl.obolibrary.org/obo/UBERON_0000468 | denotes | organisms |
| T67 | 1962-1967 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T68 | 2037-2042 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T69 | 2214-2219 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T70 | 2289-2294 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T71 | 2448-2452 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T72 | 2497-2504 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T73 | 2540-2547 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T74 | 2573-2578 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T75 | 2603-2608 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T76 | 2663-2665 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T77 | 2725-2735 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signalling |
| T78 | 2796-2797 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T79 | 2858-2863 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T80 | 2965-2969 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T81 | 3077-3081 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T82 | 3077-3081 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T83 | 3157-3162 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T84 | 3168-3172 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T85 | 3168-3172 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T86 | 3173-3177 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T15 | 67-78 | Chemical | denotes | nucleotides | http://purl.obolibrary.org/obo/CHEBI_36976 |
| T16 | 630-633 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T17 | 2708-2716 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T19 | 890-899 | Phenotype | denotes | leukaemia | http://purl.obolibrary.org/obo/HP_0001909 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T10 | 85-132 | http://purl.obolibrary.org/obo/GO_0010608 | denotes | post-transcriptionally regulate gene expression |
| T11 | 117-132 | http://purl.obolibrary.org/obo/GO_0010467 | denotes | gene expression |
| T12 | 203-214 | http://purl.obolibrary.org/obo/GO_0009056 | denotes | degradation |
| T13 | 218-231 | http://purl.obolibrary.org/obo/GO_0006412 | denotes | translational |
| T14 | 439-449 | http://purl.obolibrary.org/obo/GO_0065007 | denotes | regulation |
| T15 | 471-494 | http://purl.obolibrary.org/obo/GO_0006355 | denotes | transcriptional control |
| T16 | 764-776 | http://purl.obolibrary.org/obo/GO_0009405 | denotes | pathogenesis |
| T17 | 1004-1018 | http://purl.obolibrary.org/obo/GO_0042783 | denotes | immune evasion |
| T18 | 1068-1078 | http://purl.obolibrary.org/obo/GO_0065007 | denotes | regulation |
| T19 | 2725-2744 | http://purl.obolibrary.org/obo/GO_0007165 | denotes | signalling pathways |
| T20 | 2725-2735 | http://purl.obolibrary.org/obo/GO_0023052 | denotes | signalling |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T38 | 0-243 | Sentence | denotes | MicroRNAs (miRs) are non-coding RNAs of length approximately 20–22 nucleotides; they post-transcriptionally regulate gene expression by binding to the 3′-untranslated regions of target mRNAs, leading to degradation or translational inhibition. |
| T39 | 244-548 | Sentence | denotes | Each miR can target hundreds of mRNAs within a given cell type, and a single mRNA is often the target of multiple miRs, and thus over half of the human transcriptome is predicted to be under miR regulation, embedding this post-transcriptional control pathway within nearly every biological process [4,5]. |
| T40 | 549-642 | Sentence | denotes | Virally expressed miRs have recently been discovered, especially in viruses with DNA genomes. |
| T41 | 643-806 | Sentence | denotes | The best-known viral miRs are found mostly in herpesvirus families, where they enhance bilateral crosstalk between viral pathogenesis and host response mechanisms. |
| T42 | 807-951 | Sentence | denotes | Additionally, it has been shown that different virus families such as delta bovine leukaemia virus and foamy retroviruses could encode miRs [6]. |
| T43 | 952-1088 | Sentence | denotes | As previously shown, viral miRs are critical in the immune evasion mechanisms, affecting host immunity-related gene regulation networks. |
| T44 | 1089-1245 | Sentence | denotes | This bilateral effect results in a rapid increase during the virus resistance against host defence mechanisms and leads to their survival in host cells [7]. |
| T45 | 1246-1484 | Sentence | denotes | The scope of miR generation from ssRNA viral genomes has been controversial, mainly due to the potentially deleterious effect of ssRNA viral genome cleavage into pre-/pri-miRs, making it unavailable for packaging into new virus particles. |
| T46 | 1485-1607 | Sentence | denotes | However, predictive studies on RNA viral genomes reveal RNA structures, which are conceivable Drosha and Dicer substrates. |
| T47 | 1608-1794 | Sentence | denotes | One of the well-described annotations was performed for HIV to define HIV-1 TAR RNA, a 59-nt long sequence that could generate a stem-loop structure similar to the pre-miR structure [8]. |
| T48 | 1795-1871 | Sentence | denotes | The identified numbers of viral miRs are not as many as for other organisms. |
| T49 | 1872-2043 | Sentence | denotes | One of the reasons for this is that viral miRs, due to their cytoplasmic location in host cells, render interaction with nuclear miR biogenesis elements of the host cells. |
| T50 | 2044-2132 | Sentence | denotes | Another hypothesis is that the cleavage of the viral RNA genome could generate miRs [9]. |
| T51 | 2133-2318 | Sentence | denotes | According to data obtained using in silico screening, there are fewer identified virus miRs compared with other species, and their functional roles in host cells are not well described. |
| T52 | 2319-2430 | Sentence | denotes | Therefore, greater effort is required to identify novel virally encoded miRs and to predict their host targets. |
| T53 | 2431-2510 | Sentence | denotes | Conversely, host cell miRs may alter the biological effect of the viruses [10]. |
| T54 | 2511-2930 | Sentence | denotes | Several interactions between viruses and the miRs in the host cells have been reported: the virus may either avoid being targeted by the cellular miRs [11]; block the cellular miRs to regulate key proteins in main signalling pathways [12,13]; synthesize their own viral miRs to create a more favourable cellular environment to survive in the host cells [14], or simply use the cellular miRs to their own advantage [15]. |
| T55 | 2931-3038 | Sentence | denotes | It should also be noted that host cell miR repertoires change dramatically in response to various diseases. |
| T56 | 3039-3250 | Sentence | denotes | Several underlying cardiovascular and lung conditions may significantly alter host miR expression, which would affect virus-host lung cell interactions, and may significantly determine the course of the disease. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32512929-32222466-144200693 | 543-544 | 32222466 | denotes | 4 |
| 32512929-15211354-144200694 | 545-546 | 15211354 | denotes | 5 |
| 32512929-14744438-144200695 | 948-949 | 14744438 | denotes | 6 |
| 32512929-24522910-144200696 | 1242-1243 | 24522910 | denotes | 7 |
| 32512929-21277611-144200697 | 1791-1792 | 21277611 | denotes | 8 |
| 32512929-26984525-144200698 | 2129-2130 | 26984525 | denotes | 9 |
| 32512929-28555130-144200699 | 2506-2508 | 28555130 | denotes | 10 |
| 32512929-30888610-144200700 | 2663-2665 | 30888610 | denotes | 11 |
| 32512929-23416678-144200701 | 2746-2748 | 23416678 | denotes | 12 |
| 32512929-15542639-144200702 | 2749-2751 | 15542639 | denotes | 13 |
| 32512929-16887810-144200703 | 2865-2867 | 16887810 | denotes | 14 |
| 32512929-24769093-144200704 | 2926-2928 | 24769093 | denotes | 15 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 142 | 1579-1585 | Gene | denotes | Drosha | Gene:29102 |
| 143 | 1590-1595 | Gene | denotes | Dicer | Gene:23405 |
| 144 | 1684-1687 | Gene | denotes | TAR | Gene:9939 |
| 145 | 390-395 | Species | denotes | human | Tax:9606 |
| 146 | 689-700 | Species | denotes | herpesvirus | Tax:39059 |
| 147 | 883-889 | Species | denotes | bovine | Tax:9913 |
| 148 | 1678-1683 | Species | denotes | HIV-1 | Tax:11676 |
| 149 | 890-905 | Disease | denotes | leukaemia virus | MESH:D015459 |