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PMC:7321036 / 6932-9388 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T149 64-74 SP_7 denotes SARS-CoV-2
T150 89-93 CL_6 denotes Vero
T151 122-132 SP_7 denotes SARS-CoV-2
T152 157-162 NCBITaxon:10239 denotes viral
T153 258-262 CL_6 denotes Vero
T154 471-476 GO:0019835 denotes lysed
T155 922-927 SP_6;NCBITaxon:9606 denotes human
T156 936-945 SO:0000855 denotes orthologs
T157 1406-1416 SP_7 denotes SARS-CoV-2
T158 1486-1495 GO:0065007 denotes regulated
T159 1638-1647 GO:0065007 denotes regulated
T160 1763-1767 SO:0000704 denotes Gene
T161 1950-1959 GO:0065007 denotes regulated
T162 2238-2247 GO:0065007 denotes regulated

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T39940 97-102 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T68158 171-176 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T52662 266-271 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T6256 446-450 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T95345 460-465 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T75308 482-490 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T16865 606-613 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T73440 870-877 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T71250 928-935 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T90884 1080-1087 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T10395 1417-1425 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T82515 1433-1440 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T16496 1648-1656 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T52527 1711-1718 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T14696 1763-1767 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T80093 1827-1835 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T24339 2125-2132 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T23973 2248-2256 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T60 64-72 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 75-84 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T62 122-130 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 369-378 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T64 629-638 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T65 787-790 Disease denotes DIA http://purl.obolibrary.org/obo/MONDO_0022963
T66 1406-1414 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 1517-1526 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T68 1595-1604 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T69 1668-1677 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T70 1748-1757 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T71 2153-2162 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T72 2202-2211 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T73 2296-2305 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T74 2422-2426 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T71578 86-87 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T69924 89-102 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T67115 171-176 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T3201 225-229 http://purl.obolibrary.org/obo/CLO_0001382 denotes 4, 8
T66033 247-248 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14454 258-271 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T7941 446-450 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T78869 460-465 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T14567 510-518 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T22339 580-582 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T38966 701-709 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T47323 774-783 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T20014 785-786 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T1296 817-819 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T57282 922-935 http://purl.obolibrary.org/obo/PR_000029067 denotes human protein
T69937 948-949 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T17836 1057-1059 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T99358 1161-1162 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18957 1763-1767 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T9146 1975-1976 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47093 2403-2405 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T35469 2453-2455 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T29 482-490 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T30 510-518 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T31 580-582 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T32 606-613 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T33 701-709 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T34 817-819 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T35 870-877 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T36 928-935 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T37 981-984 Chemical denotes PCA http://purl.obolibrary.org/obo/CHEBI_36751|http://purl.obolibrary.org/obo/CHEBI_62248
T39 1080-1087 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T40 1417-1425 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T41 1433-1440 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T42 1563-1568 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T43 1648-1656 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T44 1711-1718 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T45 1827-1835 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T46 2125-2132 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T47 2248-2256 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T48 2403-2405 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T12240 21-36 http://purl.obolibrary.org/obo/GO_0016310 denotes Phosphorylation
T60087 163-169 http://purl.obolibrary.org/obo/GO_0098739 denotes uptake
T26491 163-169 http://purl.obolibrary.org/obo/GO_0098657 denotes uptake
T13196 758-773 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T28719 774-783 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T63425 844-859 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T20969 989-1004 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T62569 1107-1122 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
137 69-84 Disease denotes CoV-2 Infection MESH:C000657245
147 122-132 Species denotes SARS-CoV-2 Tax:2697049
148 922-927 Species denotes human Tax:9606
149 701-709 Chemical denotes peptides MESH:D010455
150 108-116 Disease denotes infected MESH:D007239
151 287-295 Disease denotes infected MESH:D007239
152 369-378 Disease denotes infection MESH:D007239
153 629-638 Disease denotes infection MESH:D007239
154 94-96 CellLine denotes E6 CVCL:4582
155 263-265 CellLine denotes E6 CVCL:4582
157 1406-1416 Species denotes SARS-CoV-2 Tax:2697049
160 1496-1498 Gene denotes PH Gene:5053
161 1517-1526 Disease denotes infection MESH:D007239
164 1541-1551 Species denotes F) Volcano Tax:707972
165 1595-1604 Disease denotes infection MESH:D007239
167 1668-1677 Disease denotes infection MESH:D007239
169 1748-1757 Disease denotes infection MESH:D007239
171 1960-1962 Gene denotes PH Gene:5053
176 2153-2162 Disease denotes infection MESH:D007239
177 2202-2211 Disease denotes infection MESH:D007239
178 2296-2305 Disease denotes infection MESH:D007239
179 2363-2371 Disease denotes infected MESH:D007239

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T44 85-143 Sentence denotes (A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0).
T45 144-243 Sentence denotes After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h.
T46 244-379 Sentence denotes As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection.
T47 380-435 Sentence denotes All conditions were performed in biological triplicate.
T48 436-519 Sentence denotes Following cell harvest, cells were lysed, and proteins were digested into peptides.
T49 520-784 Sentence denotes Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling.
T50 785-833 Sentence denotes A DIA approach was used for all MS acquisitions.
T51 834-946 Sentence denotes Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs.
T52 947-1040 Sentence denotes (B) Principal-component analysis (PCA) of phosphorylation replicates after removing outliers.
T53 1041-1060 Sentence denotes See also Figure S1.
T54 1061-1231 Sentence denotes (C) Correlation of protein abundance (AB) and phosphorylation sites (PHs) between replicates within a biological condition (red) and across biological conditions (black).
T55 1232-1377 Sentence denotes Boxplots depict median (horizonal lines), interquartile range (boxes), maximum and minimum values (vertical lines), and outliers (solid circles).
T56 1378-1453 Sentence denotes (D) Median AB of individual SARS-CoV-2 proteins in the protein AB analysis.
T57 1454-1539 Sentence denotes (E) The number of significantly regulated PH groups across the infection time course.
T58 1540-1605 Sentence denotes (F) Volcano plot of PH group quantification 24 h after infection.
T59 1606-1690 Sentence denotes (G) The number of significantly regulated proteins across the infection time course.
T60 1691-1758 Sentence denotes (H) Volcano plot of protein AB quantification 24 h after infection.
T61 1759-1917 Sentence denotes (I) Gene Ontology enrichment analysis of all significantly changing proteins in terms of AB divided into two sets: downregulated (blue) and upregulated (red).
T62 1918-2136 Sentence denotes (J) Proportion of significantly regulated PH groups with a correlated (i.e., same direction, AB match) or anticorrelated (i.e., opposite direction, AB mismatch) significant or insignificant (gray) change in protein AB.
T63 2137-2436 Sentence denotes In (E)–(H), all infection time points are compared with the mock infection at 0 h, and significantly regulated proteins are defined as (absolute value of log2(infection/mock) > 1 and adjusted p < 0.05 or when only detected in infected or mock based on replicate and MS feature counts; STAR Methods).
T64 2437-2456 Sentence denotes See also Figure S1.