PMC:7321036 / 85216-86613
Annnotations
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T186 | 232-268 | NCBITaxon:9606 | denotes | st a database of Uniprot Chlorocebus |
| T187 | 375-425 | SP_6;NCBITaxon:9606 | denotes | genomic sequence downloaded from GISAID (accession |
| T188 | 488-549 | SO:0000704 | denotes | G22661T Spike V367F and G26144T ORF3a G251V) detected by RNAS |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T619 | 287-295 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T620 | 341-348 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T621 | 582-589 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T622 | 685-695 | Body_part | denotes | methionine | http://purl.org/sig/ont/fma/fma82759 |
| T623 | 746-754 | Body_part | denotes | cysteine | http://purl.org/sig/ont/fma/fma82751 |
| T624 | 861-868 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T625 | 1101-1108 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T343 | 91-94 | Disease | denotes | DIA | http://purl.obolibrary.org/obo/MONDO_0022963 |
| T344 | 330-338 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T345 | 646-649 | Disease | denotes | BGS | http://purl.obolibrary.org/obo/MONDO_0009039 |
| T346 | 935-938 | Disease | denotes | BGS | http://purl.obolibrary.org/obo/MONDO_0009039 |
| T347 | 1087-1090 | Disease | denotes | DIA | http://purl.obolibrary.org/obo/MONDO_0022963 |
| T348 | 1136-1139 | Disease | denotes | BGS | http://purl.obolibrary.org/obo/MONDO_0009039 |
| T349 | 1329-1332 | Disease | denotes | DIA | http://purl.obolibrary.org/obo/MONDO_0022963 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1188 | 235-236 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1189 | 564-569 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T1190 | 773-774 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1191 | 818-825 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
| T1192 | 827-834 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
| T1193 | 851-854 | http://purl.obolibrary.org/obo/UBERON_0003059 | denotes | PSM |
| T1194 | 992-996 | http://purl.obolibrary.org/obo/CLO_0009141 | denotes | S, T |
| T1195 | 992-996 | http://purl.obolibrary.org/obo/CLO_0050980 | denotes | S, T |
| T1196 | 1007-1008 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T458 | 37-40 | Chemical | denotes | DDA | http://purl.obolibrary.org/obo/CHEBI_28139|http://purl.obolibrary.org/obo/CHEBI_91207 |
| T460 | 287-295 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T461 | 341-348 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T462 | 582-589 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T463 | 685-695 | Chemical | denotes | methionine | http://purl.obolibrary.org/obo/CHEBI_16811|http://purl.obolibrary.org/obo/CHEBI_64558 |
| T465 | 746-754 | Chemical | denotes | cysteine | http://purl.obolibrary.org/obo/CHEBI_15356 |
| T466 | 818-825 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T467 | 827-834 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T468 | 861-868 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T469 | 1101-1108 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T457 | 973-988 | http://purl.obolibrary.org/obo/GO_0016310 | denotes | phosphorylation |
| T458 | 1351-1363 | http://purl.obolibrary.org/obo/GO_0051179 | denotes | localization |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id | tao:has_standard_notation |
|---|---|---|---|---|---|---|
| 1892 | 520-525 | Gene | denotes | ORF3a | Gene:43740569 | |
| 1893 | 992-993 | Gene | denotes | S | Gene:43740568 | |
| 1894 | 496-501 | Gene | denotes | Spike | Gene:43740568 | |
| 1895 | 330-340 | Species | denotes | SARS-CoV-2 | Tax:2697049 | |
| 1896 | 570-576 | Species | denotes | stocks | Tax:3724 | |
| 1897 | 257-268 | Species | denotes | Chlorocebus | Tax:60711 | |
| 1898 | 685-695 | Chemical | denotes | methionine | MESH:D008715 | |
| 1899 | 730-754 | Chemical | denotes | carbamidomethyl cysteine | MESH:C034636 | |
| 1900 | 902-916 | Chemical | denotes | phosphopeptide | MESH:D010748 | |
| 1901 | 1202-1216 | Chemical | denotes | phosphopeptide | MESH:D010748 | |
| 1902 | 488-495 | Mutation | denotes | G22661T | g.22661G>T | |
| 1903 | 502-507 | Mutation | denotes | V367F | p.V367F | |
| 1904 | 512-519 | Mutation | denotes | G26144T | g.26144G>T | |
| 1905 | 526-531 | Mutation | denotes | G251V | p.G251V |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T769 | 0-577 | Sentence | denotes | Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks. |
| T770 | 578-897 | Sentence | denotes | For protein abundance samples, data were searched using the default BGS settings, variable modification of methionine oxidation, static modification of carbamidomethyl cysteine, and filtering to a final 1% false discovery rate (FDR) at the peptide, peptide spectrum match (PSM), and protein level (Elias and Gygi 2007). |
| T771 | 898-1031 | Sentence | denotes | For phosphopeptide enriched samples, BGS settings were modified to include phosphorylation of S, T, and Y as a variable modification. |
| T772 | 1032-1096 | Sentence | denotes | The generated search libraries were used to search the DIA data. |
| T773 | 1097-1197 | Sentence | denotes | For protein abundance samples, default BGS settings were used, with no data normalization performed. |
| T774 | 1198-1397 | Sentence | denotes | For phosphopeptide enriched samples, the Significant PTM default settings were used, with no data normalization performed, and the DIA-specific PTM site localization score in Spectronaut was applied. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32645325-25724911-20773110 | 208-212 | 25724911 | denotes | 2015 |
| 32645325-17327847-20773111 | 891-895 | 17327847 | denotes | 2007 |