PMC:7443692 / 58217-60073
Annnotations
LitCovid-sample-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T381 | 38-45 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T382 | 252-255 | Chemical | denotes | Asp | http://purl.obolibrary.org/obo/CHEBI_17053|http://purl.obolibrary.org/obo/CHEBI_22660|http://purl.obolibrary.org/obo/CHEBI_29958 |
| T385 | 291-294 | Chemical | denotes | Glu | http://purl.obolibrary.org/obo/CHEBI_16015|http://purl.obolibrary.org/obo/CHEBI_18237|http://purl.obolibrary.org/obo/CHEBI_29972 |
| T388 | 325-332 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T389 | 569-572 | Chemical | denotes | Lys | http://purl.obolibrary.org/obo/CHEBI_133538|http://purl.obolibrary.org/obo/CHEBI_18019|http://purl.obolibrary.org/obo/CHEBI_29967 |
| T392 | 601-609 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T393 | 704-709 | Chemical | denotes | water | http://purl.obolibrary.org/obo/CHEBI_15377 |
| T394 | 725-733 | Chemical | denotes | peptides | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T395 | 840-843 | Chemical | denotes | ion | http://purl.obolibrary.org/obo/CHEBI_24870 |
| T396 | 975-987 | Chemical | denotes | acetonitrile | http://purl.obolibrary.org/obo/CHEBI_38472 |
| T397 | 996-1007 | Chemical | denotes | formic acid | http://purl.obolibrary.org/obo/CHEBI_30751 |
| T398 | 1047-1059 | Chemical | denotes | acetonitrile | http://purl.obolibrary.org/obo/CHEBI_38472 |
| T399 | 1068-1079 | Chemical | denotes | formic acid | http://purl.obolibrary.org/obo/CHEBI_30751 |
| T400 | 1356-1359 | Chemical | denotes | ion | http://purl.obolibrary.org/obo/CHEBI_24870 |
| T401 | 1598-1605 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T402 | 1623-1630 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T403 | 1741-1744 | Chemical | denotes | Asp | http://purl.obolibrary.org/obo/CHEBI_17053|http://purl.obolibrary.org/obo/CHEBI_22660|http://purl.obolibrary.org/obo/CHEBI_29958 |
| T406 | 1813-1821 | Chemical | denotes | peptides | http://purl.obolibrary.org/obo/CHEBI_16670 |
LitCovid-sample-PD-NCBITaxon
| Id | Subject | Object | Predicate | Lexical cue | ncbi_taxonomy_id |
|---|---|---|---|---|---|
| T157 | 25-35 | Species | denotes | SARS-CoV-2 | NCBItxid:2697049 |
LitCovid-sample-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T393 | 0-180 | Sentence | denotes | Three 3.5-μg aliquots of SARS-CoV-2 S protein were reduced by incubating with 10 mM of dithiothreitol at 56°C and alkylated by 27.5 mM of iodoacetamide at room temperature in dark. |
| T394 | 181-297 | Sentence | denotes | The three aliquots were then digested respectively using chymotrypsin, Asp-N, or a combination of trypsin and Glu-C. |
| T395 | 298-467 | Sentence | denotes | Two 10-μg aliquots of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark. |
| T396 | 468-575 | Sentence | denotes | The two aliquots were then digested respectively using chymotrypsin, or a combination of trypsin and Lys-C. |
| T397 | 576-710 | Sentence | denotes | Following digestion, the proteins were deglycosylated by Endoglycosidase H followed by PNGaseF treatment in the presence of 18O water. |
| T398 | 711-934 | Sentence | denotes | The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min. |
| T399 | 935-1080 | Sentence | denotes | The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid. |
| T400 | 1081-1178 | Sentence | denotes | The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. |
| T401 | 1179-1365 | Sentence | denotes | Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following collision-induced dissociation (CID) at 38% collision energy were collected in the ion trap. |
| T402 | 1366-1506 | Sentence | denotes | The spectra were analyzed using SEQUEST (Proteome Discoverer 1.4) with mass tolerance set as 20 ppm for precursors and 0.5 Da for fragments. |
| T403 | 1507-1637 | Sentence | denotes | The search output was filtered using ProteoIQ (v2.7) to reach a 1% false discovery rate at protein level and 10% at peptide level. |
| T404 | 1638-1856 | Sentence | denotes | Occupancy of each N-linked glycosylation site was calculated using spectral counts assigned to the 18O-Asp-containing (PNGaseF-cleaved) and/or HexNAc-modified (EndoH-cleaved) peptides and their unmodified counterparts. |
LitCovid-sample-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T10 | 1151-1160 | Body_part | denotes | capillary | http://purl.obolibrary.org/obo/UBERON_0001982 |
LitCovid-sample-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T96 | 25-35 | Disease | denotes | SARS-CoV-2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-sample-UniProt
| Id | Subject | Object | Predicate | Lexical cue | uniprot_id |
|---|---|---|---|---|---|
| T4717 | 36-45 | Protein | denotes | S protein | https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9 |
| T4750 | 238-250 | Protein | denotes | chymotrypsin | https://www.uniprot.org/uniprot/P81521|https://www.uniprot.org/uniprot/P35002|https://www.uniprot.org/uniprot/O97398 |
| T4753 | 279-286 | Protein | denotes | trypsin | https://www.uniprot.org/uniprot/P83348|https://www.uniprot.org/uniprot/P81524|https://www.uniprot.org/uniprot/P81071|https://www.uniprot.org/uniprot/P70059|https://www.uniprot.org/uniprot/P51588|https://www.uniprot.org/uniprot/P35051|https://www.uniprot.org/uniprot/P35050|https://www.uniprot.org/uniprot/P35048|https://www.uniprot.org/uniprot/P35034|https://www.uniprot.org/uniprot/P19799|https://www.uniprot.org/uniprot/P00764|https://www.uniprot.org/uniprot/P00761|https://www.uniprot.org/uniprot/O97399 |
| T4766 | 320-324 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T4767 | 523-535 | Protein | denotes | chymotrypsin | https://www.uniprot.org/uniprot/P81521|https://www.uniprot.org/uniprot/P35002|https://www.uniprot.org/uniprot/O97398 |
| T4770 | 557-564 | Protein | denotes | trypsin | https://www.uniprot.org/uniprot/P83348|https://www.uniprot.org/uniprot/P81524|https://www.uniprot.org/uniprot/P81071|https://www.uniprot.org/uniprot/P70059|https://www.uniprot.org/uniprot/P51588|https://www.uniprot.org/uniprot/P35051|https://www.uniprot.org/uniprot/P35050|https://www.uniprot.org/uniprot/P35048|https://www.uniprot.org/uniprot/P35034|https://www.uniprot.org/uniprot/P19799|https://www.uniprot.org/uniprot/P00764|https://www.uniprot.org/uniprot/P00761|https://www.uniprot.org/uniprot/O97399 |
| T4783 | 1179-1183 | Protein | denotes | Full | https://www.uniprot.org/uniprot/Q8N1N2 |
| T4784 | 1360-1364 | Protein | denotes | trap | https://www.uniprot.org/uniprot/Q9Y2M3|https://www.uniprot.org/uniprot/Q9UFF0|https://www.uniprot.org/uniprot/Q9R1R4|https://www.uniprot.org/uniprot/Q96JT1|https://www.uniprot.org/uniprot/Q8R181|https://www.uniprot.org/uniprot/Q8NHU6|https://www.uniprot.org/uniprot/Q8K1H1|https://www.uniprot.org/uniprot/Q5VV27|https://www.uniprot.org/uniprot/Q5FVD0|https://www.uniprot.org/uniprot/E7EQD4|https://www.uniprot.org/uniprot/B4DXF7|https://www.uniprot.org/uniprot/B4DG99|https://www.uniprot.org/uniprot/B2RBX3|https://www.uniprot.org/uniprot/B1AWH5|https://www.uniprot.org/uniprot/B1AWG7|https://www.uniprot.org/uniprot/A6NCI6 |
LitCovid-sample-PD-IDO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T157 | 1679-1683 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | site |
LitCovid-sample-PD-FMA
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T191 | 38-45 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T192 | 325-332 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T193 | 601-609 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T194 | 1151-1160 | Body_part | denotes | capillary | http://purl.org/sig/ont/fma/fma63194 |
| T195 | 1598-1605 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-sample-PD-GO-BP-0
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T121 | 586-595 | http://purl.obolibrary.org/obo/GO_0007586 | denotes | digestion |
| T122 | 663-670 | http://purl.obolibrary.org/obo/GO_0000224 | denotes | PNGaseF |
| T123 | 1665-1678 | http://purl.obolibrary.org/obo/GO_0070085 | denotes | glycosylation |
| T124 | 1757-1764 | http://purl.obolibrary.org/obo/GO_0000224 | denotes | PNGaseF |
LitCovid-sample-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T114 | 586-595 | http://purl.obolibrary.org/obo/GO_0007586 | denotes | digestion |
| T115 | 1574-1579 | http://purl.obolibrary.org/obo/GO_0071878 | denotes | false |
| T116 | 1574-1579 | http://purl.obolibrary.org/obo/GO_0071877 | denotes | false |
| T117 | 1665-1678 | http://purl.obolibrary.org/obo/GO_0070085 | denotes | glycosylation |
LitCovid-sample-Glycan
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T2869 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G30059ZJ | denotes | HexNAc |
| T2870 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G46412HK | denotes | HexNAc |
| T2871 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G37373JE | denotes | HexNAc |
| T2872 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G80366GS | denotes | HexNAc |
| T2873 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G92326AT | denotes | HexNAc |
| T2874 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G06461TM | denotes | HexNAc |
| T2875 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G08775HA | denotes | HexNAc |
| T2876 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G14893NV | denotes | HexNAc |
| T2877 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G03646SE | denotes | HexNAc |
| T2878 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G14093GS | denotes | HexNAc |
| T2879 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G68384AJ | denotes | HexNAc |
| T2880 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G87935EZ | denotes | HexNAc |
| T2881 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G03811WP | denotes | HexNAc |
| T2882 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G88386LN | denotes | HexNAc |
| T2883 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G88431DQ | denotes | HexNAc |
| T2884 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G31282CB | denotes | HexNAc |
| T2885 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G23331KR | denotes | HexNAc |
| T2886 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G81363VR | denotes | HexNAc |
| T2887 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G80364TX | denotes | HexNAc |
| T2888 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G68910GL | denotes | HexNAc |
| T2889 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G60562UB | denotes | HexNAc |
| T2890 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G15814MG | denotes | HexNAc |
| T2891 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G58082FV | denotes | HexNAc |
| T2892 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G55084SZ | denotes | HexNAc |
| T2893 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G76017CU | denotes | HexNAc |
| T2894 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G63748FT | denotes | HexNAc |
| T2895 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G39298OQ | denotes | HexNAc |
| T2896 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G55196OZ | denotes | HexNAc |
| T2897 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G90088PE | denotes | HexNAc |
| T2898 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G04505NJ | denotes | HexNAc |
| T2899 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G84289JA | denotes | HexNAc |
| T2900 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G64769SU | denotes | HexNAc |
| T2901 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G99324LT | denotes | HexNAc |
| T2902 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G18156HN | denotes | HexNAc |
| T2903 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G48853ER | denotes | HexNAc |
| T2904 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G17057LD | denotes | HexNAc |
| T2905 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G54482BE | denotes | HexNAc |
| T2906 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G42038AH | denotes | HexNAc |
| T2907 | 1781-1787 | https://glytoucan.org/Structures/Glycans/G20606OJ | denotes | HexNAc |