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PMC:7033698 / 2861-6004 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T21 98-101 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T22 215-218 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T23 284-287 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T24 551-554 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T25 810-813 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T26 959-962 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T27 1055-1058 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T28 1184-1187 Body_part denotes gag http://purl.org/sig/ont/fma/fma63011
T29 1209-1212 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T30 1215-1221 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T31 1355-1358 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T32 1425-1428 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T33 1560-1563 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T34 1694-1697 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T35 1731-1734 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T36 1746-1758 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T37 1888-1891 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T38 1903-1915 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T39 1999-2002 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T40 2111-2114 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T41 2231-2234 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T42 2237-2244 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T43 2306-2309 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T44 2323-2326 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T45 2400-2406 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T46 2503-2507 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T47 2638-2641 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T48 2781-2784 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T49 3080-3083 Body_part denotes Gag http://purl.org/sig/ont/fma/fma63011

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T6 699-708 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T33 86-93 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T34 247-254 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T35 435-440 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T36 501-502 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 671-678 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T38 719-729 http://purl.obolibrary.org/obo/NCBITaxon_2759 denotes eukaryotic
T39 730-737 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T40 792-793 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 1177-1182 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T42 1657-1666 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T43 1657-1666 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T44 1677-1684 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T45 1993-1994 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 2503-2507 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T47 2618-2623 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 (2)
T48 2632-2637 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 (2)
T49 2664-2666 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T50 2668-2670 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T51 2692-2702 http://purl.obolibrary.org/obo/NCBITaxon_2759 denotes Eukaryotic
T52 2703-2705 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T53 2707-2709 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T54 2765-2770 http://purl.obolibrary.org/obo/CLO_0001000 denotes (3) 5
T55 2787-2789 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T56 2790-2796 http://purl.obolibrary.org/obo/CLO_0054057 denotes (18) 1
T57 2791-2793 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T58 2822-2832 http://purl.obolibrary.org/obo/NCBITaxon_2759 denotes Eukaryotic
T59 2833-2840 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T60 2881-2888 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T61 2900-2906 http://purl.obolibrary.org/obo/CLO_0001053 denotes (1) 21
T62 2931-2936 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T63 2937-2942 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 (1)

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T5 1746-1758 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T6 1903-1915 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T7 3085-3088 Chemical denotes Pro http://purl.obolibrary.org/obo/CHEBI_50342

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T24 0-132 Sentence denotes Current report conducted careful examination of the sequences of 2019-nCoV, other CoV viruses and HIV-1 as well as GenBank database.
T25 133-290 Sentence denotes Our results demonstrated no evidence that the sequences of these four inserts are HIV-1 specific or the 2019-nCoV viruses obtain these insertions from HIV-1.
T26 291-485 Sentence denotes First, the results of blast search of these motifs against GenBank shows that the top 100 identical or highly homologous hits are all from host genes of mammalian, insects, bacterial and others.
T27 486-565 Sentence denotes There are only a few hits on coronaviruses, but none of them are HIV-1 related.
T28 566-748 Sentence denotes Blast against viral sequence database also showed these insertion sequences widely exist in all kinds of viruses from bacteriophage, influenza, to giant eukaryotic viruses (Table 1).
T29 749-880 Sentence denotes More hits were found for coronaviruses and a few also hit on HIV-1 sequences than the search against the entire database (Table 1).
T30 881-1106 Sentence denotes However, while the 100% match between the insertion 1 and 2 sequences and the HIV sequences were found in 19 entries, the matches between the insertion 3 and 4 sequences and HIV-1 sequences were rather poor (from 42% to 88%).
T31 1107-1308 Sentence denotes Moreover, the insertion 4 sequence ambiguously hit multiple different genes (gag, pol and env) in the HIV-1 genome, suggesting that similarities (as low as 42%) between them are too low to be reliable.
T32 1309-1473 Sentence denotes Search these four insertion sequences against HIV-1 Sequence Database (https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html) yielded similar results.
T33 1474-1576 Sentence denotes Sequences that completely match the insertion 3 and 4 sequences were not found in any HIV-1 sequences.
T34 1577-1709 Sentence denotes This clearly shows that these insertioin sequences are widely present in living organisms including viruses, but not HIV-1 specific.
T35 1710-1916 Sentence denotes All these regions in HIV-1 envelope glycoprotein are highly variable with many large insertions and deletions, indicating that they are not essential for biological functions of HIV-1 envelope glycoprotein.
T36 1917-2127 Sentence denotes The detection of completely matched sequences of 1 and 2 insertions in only a few HIV-1 strains demonstrated that four insertions are very rare or not present among tens of thousands of natural HIV-1 sequences.
T37 2128-2249 Sentence denotes This also explains why four insertion homolog sequences could only be independently found in different HIV-1 genomes [8].
T38 2250-2407 Sentence denotes Because of their poor identities to and rareness in the HIV-1 sequences, HIV-1 could not be the source for those insertion sequences in the 2019-nCoV genome.
T39 2408-2416 Sentence denotes Table 1.
T40 2417-2493 Sentence denotes Blast search results of four insertion sequences against sequence databases.
T41 2494-2598 Sentence denotes Database Gene source Insertion 1 TNGTKR Insertion 2 HKNNKS Insertion 3 RSYLTPGDSSSG Insertion 4 QTNSPRRA
T42 2599-2637 Sentence denotes Whole database CoV 2 (2) 0 3 (3) 2 (2)
T43 2638-2651 Sentence denotes HIV-1 0 0 0 0
T44 2652-2691 Sentence denotes Prokaryotic 27 (27) 3 (3) 74 (0) 66 (1)
T45 2692-2732 Sentence denotes Eukaryotic 71 (71) 97 (97) 23 (0) 32 (1)
T46 2733-2780 Sentence denotes Only viral database CoV 3 (3) 3 (3) 5 (3) 3 (2)
T47 2781-2815 Sentence denotes HIV-1 18 (18) 1 (1) 4 (0)* 6 (0)**
T48 2816-2868 Sentence denotes Other Eukaryotic viruses 49 (2) 66 (8) 69 (0) 62 (0)
T49 2869-2917 Sentence denotes Prokaryotic viruses 29 (13) 30 (1) 21 (0) 28 (0)
T50 2918-2956 Sentence denotes Unclassified virus 1 (1) 0 1 (0) 1 (0)
T51 2957-3143 Sentence denotes Top 100 hits are analyzed and the numbers of 100% matches are shown in parentheses. * Similarity at 67%; ** Random hits in Gag, Pro and Env sequences with similarity between 42% and 88%.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
74 2614-2619 Species denotes CoV 2 Tax:2697049
75 2638-2643 Species denotes HIV-1 Tax:11676
76 2515-2524 Species denotes Insertion Tax:2673
77 2534-2543 Species denotes Insertion Tax:2673
78 2553-2562 Species denotes Insertion Tax:2673
79 2578-2587 Species denotes Insertion Tax:2673
81 2446-2465 Species denotes insertion sequences Tax:2673
85 3080-3083 Gene denotes Gag Gene:155030
86 3093-3096 Gene denotes Env Gene:100616444
87 3085-3088 Chemical denotes Pro MESH:D011392
123 1197-1200 Gene denotes env Gene:100616444
124 1184-1187 Gene denotes gag Gene:155030
125 65-74 Species denotes 2019-nCoV Tax:2697049
126 82-85 Species denotes CoV Tax:11118
127 98-103 Species denotes HIV-1 Tax:11676
128 215-220 Species denotes HIV-1 Tax:11676
129 237-246 Species denotes 2019-nCoV Tax:2697049
130 284-289 Species denotes HIV-1 Tax:11676
131 444-453 Species denotes mammalian Tax:9606
132 515-528 Species denotes coronaviruses Tax:11118
133 551-556 Species denotes HIV-1 Tax:11676
134 622-641 Species denotes insertion sequences Tax:2673
135 684-697 Species denotes bacteriophage Tax:38018
136 774-787 Species denotes coronaviruses Tax:11118
137 810-815 Species denotes HIV-1 Tax:11676
138 1055-1060 Species denotes HIV-1 Tax:11676
139 1209-1214 Species denotes HIV-1 Tax:11676
140 1327-1346 Species denotes insertion sequences Tax:2673
141 1355-1360 Species denotes HIV-1 Tax:11676
142 1560-1565 Species denotes HIV-1 Tax:11676
143 1694-1699 Species denotes HIV-1 Tax:11676
144 1731-1736 Species denotes HIV-1 Tax:11676
145 1888-1893 Species denotes HIV-1 Tax:11676
146 1999-2004 Species denotes HIV-1 Tax:11676
147 2111-2116 Species denotes HIV-1 Tax:11676
148 2231-2236 Species denotes HIV-1 Tax:11676
149 2306-2311 Species denotes HIV-1 Tax:11676
150 2323-2328 Species denotes HIV-1 Tax:11676
151 2363-2382 Species denotes insertion sequences Tax:2673
152 2390-2399 Species denotes 2019-nCoV Tax:2697049
153 923-932 Species denotes insertion Tax:2673
154 1023-1032 Species denotes insertion Tax:2673
155 1121-1130 Species denotes insertion Tax:2673
156 1510-1519 Species denotes insertion Tax:2673
157 2156-2165 Species denotes insertion Tax:2673