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PMC:7321036 / 79618-81672 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T606 0-4 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T607 25-30 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T608 247-255 Body_part denotes Proteins http://purl.org/sig/ont/fma/fma67257
T609 273-277 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T610 404-411 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T611 455-463 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T612 726-729 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T613 899-906 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T614 1920-1927 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1113 0-4 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T1114 25-30 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T1115 144-149 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T1116 218-223 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T1117 273-277 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T1118 695-696 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1119 853-854 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1120 1006-1007 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1121 1304-1305 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1122 1370-1371 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1123 1531-1532 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1124 1640-1649 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T1125 1678-1681 http://purl.obolibrary.org/obo/CLO_0001655 denotes ACN
T1126 1792-1797 http://purl.obolibrary.org/obo/CLO_0053794 denotes 4 × 1
T1127 1858-1861 http://purl.obolibrary.org/obo/CLO_0001655 denotes ACN

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T356 330-338 Chemical denotes methanol http://purl.obolibrary.org/obo/CHEBI_17790
T357 404-411 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T358 455-463 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T359 490-496 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T360 502-506 Chemical denotes urea http://purl.obolibrary.org/obo/CHEBI_16199
T361 515-523 Chemical denotes ammonium http://purl.obolibrary.org/obo/CHEBI_28938
T362 537-540 Chemical denotes ABC http://purl.obolibrary.org/obo/CHEBI_421707
T363 550-554 Chemical denotes NaCl http://purl.obolibrary.org/obo/CHEBI_26710
T364 556-574 Chemical denotes protease inhibitor http://purl.obolibrary.org/obo/CHEBI_37670|http://purl.obolibrary.org/obo/CHEBI_60258
T366 565-574 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T367 614-624 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T368 644-648 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T369 650-664 Chemical denotes 2-carboxyethyl http://purl.obolibrary.org/obo/CHEBI_50329
T370 665-674 Chemical denotes phosphine http://purl.obolibrary.org/obo/CHEBI_30278|http://purl.obolibrary.org/obo/CHEBI_35883
T372 676-680 Chemical denotes TCEP http://purl.obolibrary.org/obo/CHEBI_63213
T373 726-729 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T374 746-751 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T375 899-906 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T376 973-976 Chemical denotes IAA http://purl.obolibrary.org/obo/CHEBI_16411
T377 1125-1128 Chemical denotes IAA http://purl.obolibrary.org/obo/CHEBI_16411
T378 1177-1180 Chemical denotes DTT http://purl.obolibrary.org/obo/CHEBI_18320
T379 1286-1289 Chemical denotes ABC http://purl.obolibrary.org/obo/CHEBI_421707
T380 1312-1316 Chemical denotes urea http://purl.obolibrary.org/obo/CHEBI_16199
T381 1339-1346 Chemical denotes Trypsin http://purl.obolibrary.org/obo/CHEBI_9765
T382 1476-1496 Chemical denotes trifluoroacetic acid http://purl.obolibrary.org/obo/CHEBI_45892
T383 1492-1496 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T384 1498-1501 Chemical denotes TFA http://purl.obolibrary.org/obo/CHEBI_45892
T385 1664-1676 Chemical denotes acetonitrile http://purl.obolibrary.org/obo/CHEBI_38472
T386 1678-1681 Chemical denotes ACN http://purl.obolibrary.org/obo/CHEBI_38472
T387 1688-1691 Chemical denotes TFA http://purl.obolibrary.org/obo/CHEBI_45892
T388 1733-1736 Chemical denotes TFA http://purl.obolibrary.org/obo/CHEBI_45892
T389 1809-1812 Chemical denotes TFA http://purl.obolibrary.org/obo/CHEBI_45892
T390 1858-1861 Chemical denotes ACN http://purl.obolibrary.org/obo/CHEBI_38472
T391 1868-1879 Chemical denotes formic acid http://purl.obolibrary.org/obo/CHEBI_30751
T392 1875-1879 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T393 1881-1883 Chemical denotes FA http://purl.obolibrary.org/obo/CHEBI_39002|http://purl.obolibrary.org/obo/CHEBI_73630|http://purl.obolibrary.org/obo/CHEBI_30751
T396 1920-1927 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T451 5-10 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis
T452 15-24 http://purl.obolibrary.org/obo/GO_0007586 denotes digestion
T453 166-171 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis
T454 484-489 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis
T455 602-613 http://purl.obolibrary.org/obo/GO_0016791 denotes phosphatase
T456 1461-1470 http://purl.obolibrary.org/obo/GO_0007586 denotes digestion

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1810 1336-1337 Gene denotes M Gene:43740571
1811 1284-1285 Gene denotes M Gene:43740571
1812 500-501 Gene denotes M Gene:43740571
1813 1539-1541 Gene denotes pH Gene:5053
1814 1291-1293 Gene denotes pH Gene:5053
1815 1591-1594 Gene denotes Pak
1816 69-72 Chemical denotes PBS MESH:D007854
1817 330-338 Chemical denotes methanol MESH:D000432
1818 502-506 Chemical denotes urea MESH:D014508
1819 515-535 Chemical denotes ammonium bicarbonate MESH:C027043
1820 550-554 Chemical denotes NaCl MESH:D012965
1821 644-674 Chemical denotes Tris-(2-carboxyethyl)phosphine MESH:C080938
1822 676-680 Chemical denotes TCEP MESH:C080938
1823 958-971 Chemical denotes Iodoacetamide MESH:D007460
1824 973-976 Chemical denotes IAA MESH:D007460
1825 1125-1128 Chemical denotes IAA MESH:D007460
1826 1161-1175 Chemical denotes dithiothreitol MESH:D004229
1827 1177-1180 Chemical denotes DTT MESH:D004229
1828 1312-1316 Chemical denotes urea MESH:D014508
1829 1476-1496 Chemical denotes trifluoroacetic acid MESH:D014269
1830 1498-1501 Chemical denotes TFA MESH:D014269
1831 1664-1676 Chemical denotes acetonitrile MESH:C032159
1832 1678-1681 Chemical denotes ACN MESH:C032159
1833 1688-1691 Chemical denotes TFA MESH:D014269
1834 1733-1736 Chemical denotes TFA MESH:D014269
1835 1809-1812 Chemical denotes TFA MESH:D014269
1836 1858-1861 Chemical denotes ACN MESH:C032159
1837 1868-1879 Chemical denotes formic acid MESH:C030544

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T724 0-24 Sentence denotes Cell lysis and digestion
T725 25-150 Sentence denotes Cells were lysed using 1% IGEPAL (Sigma) in PBS (Invitrogen) for 20 minutes at room temperature (RT) to inactivate the virus.
T726 151-246 Sentence denotes These specific lysis conditions were used as this was the approved virus inactivation protocol.
T727 247-399 Sentence denotes Proteins contained in the cell lysate were then immediately precipitated using 90% methanol (v/v) (Sigma) by centrifugation at 20,000x g for 10 minutes.
T728 400-441 Sentence denotes The protein pellets were frozen at −80°C.
T729 442-643 Sentence denotes Precipitated proteins were resuspended in lysis buffer (8 M urea, 100 mM ammonium bicarbonate (ABC), 150 mM NaCl, protease inhibitor (mini-cOmplete, Roche) and phosphatase inhibitors (phosSTOP, Roche).
T730 644-725 Sentence denotes Tris-(2-carboxyethyl)phosphine (TCEP) was added to a final concentration of 4 mM.
T731 726-825 Sentence denotes DNA was sheared via probe sonication, on ice, at 20% amplitude for 20 s., followed by 10 s of rest.
T732 826-876 Sentence denotes This process was performed a total of three times.
T733 877-957 Sentence denotes Following sonication, protein concentration was determined using Bradford assay.
T734 958-1117 Sentence denotes Iodoacetamide (IAA) was added to each sample to a final concentration of 10 mM, and samples were incubated in the dark at room temperature (RT) for 30 minutes.
T735 1118-1248 Sentence denotes Excess IAA was quenched by the addition of dithiothreitol (DTT) to 10 mM, followed by incubation in the dark at RT for 30 minutes.
T736 1249-1338 Sentence denotes Samples were then diluted with 0.1 M ABC (pH = 8.0) to a final urea concentration of 2 M.
T737 1339-1450 Sentence denotes Trypsin (Promega) was added at a 1:100 (enzyme:protein w:w) ratio and digested overnight at 37°C with rotation.
T738 1451-1545 Sentence denotes Following digestion, 10% trifluoroacetic acid (TFA) was added to each sample to a final pH ∼2.
T739 1546-1620 Sentence denotes Samples were desalted under vacuum using Sep Pak tC18 cartridges (Waters).
T740 1621-1737 Sentence denotes Each cartridge was activated with 1 mL 80% acetonitrile (ACN)/0.1% TFA, then equilibrated with 3 × 1 mL of 0.1% TFA.
T741 1738-1885 Sentence denotes Following sample loading, cartridges were washed with 4 × 1 mL of 0.1% TFA, and samples were eluted with 4 × 0.5 mL 50% ACN/0.25% formic acid (FA).
T742 1886-2009 Sentence denotes 20 μg of each sample was kept for protein abundance measurements, and the remainder was used for phosphopeptide enrichment.
T743 2010-2054 Sentence denotes Samples were dried by vacuum centrifugation.