PMC:7321036 / 101461-104155 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T14 269-276 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T15 461-468 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T16 864-871 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T17 1104-1111 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T18 1185-1192 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T19 2326-2333 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 2564-2571 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T18 257-264 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T19 547-549 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T20 628-635 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T21 1265-1272 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T22 1335-1336 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 1853-1860 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T24 2005-2012 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T25 2048-2049 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 2170-2178 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T27 2504-2511 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T28 2535-2536 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 2619-2624 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T97325 257-264 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T47608 269-276 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T4667 461-468 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T70590 628-635 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T91126 636-639 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T93339 864-871 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T33762 1104-1111 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T95034 1185-1192 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T79407 1265-1272 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T77426 1273-1276 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T12086 1853-1860 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T63067 1861-1864 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T78627 2005-2012 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T21246 2013-2017 Chemical denotes ions http://purl.obolibrary.org/obo/CHEBI_24870
T46488 2170-2178 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T47749 2326-2333 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T91743 2504-2511 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T25244 2512-2516 Chemical denotes ions http://purl.obolibrary.org/obo/CHEBI_24870
T71408 2564-2571 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T60486 2596-2601 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1892-1904 http://purl.obolibrary.org/obo/GO_0051179 denotes localization
T2 1908-1923 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T3 1980-1995 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T4 2269-2284 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T5 2564-2590 http://purl.obolibrary.org/obo/GO_0006468 denotes protein or phosphorylation
T6 2575-2590 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2305 918-926 Disease denotes infected MESH:D007239
2306 997-1005 Disease denotes infected MESH:D007239
2307 1077-1085 Disease denotes infected MESH:D007239
2309 1231-1239 Disease denotes infected MESH:D007239
2313 1853-1860 Chemical denotes peptide MESH:D010455
2314 2170-2178 Chemical denotes peptides MESH:D010455
2315 2661-2669 Disease denotes infected MESH:D007239

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T888 0-37 Sentence denotes Mass spectrometry data pre-processing
T889 38-144 Sentence denotes Quantitative analysis was performed in the R statistical programming language (version 3.6.1, 2019-07-05).
T890 145-356 Sentence denotes Initial quality control analyses, including inter-run clusterings, correlations, principal components analysis, peptide and protein counts and intensities were completed with the R package artMS (version 1.5.3).
T891 357-551 Sentence denotes Based on obvious outliers in intensities, correlations, and clusterings, 2 runs were discarded from the protein abundance data and 2 runs were discarded from the phosphopeptide data (Figure S1).
T892 552-828 Sentence denotes Additionally, the phosphopeptide data were filtered based on feature (i.e., peptide ion) intensity, removing any single feature with intensity less than 214—this decision was made based on apparent lack of correlation between runs for feature intensities below this intensity.
T893 829-1160 Sentence denotes Thus, for both phosphopeptides and protein abundance, we had 2 control time points and 6 infected time points, each with 3 biologically distinct replicates, except for infected at 0 and 2 hours in the phosphopeptide data and control at 0 hours and infected at 0 hours in the protein abundance data which only had 2 replicates each.
T894 1161-1799 Sentence denotes Statistical analysis of protein abundance changes between control and infected runs were computed using peptide ion fragment data output from Spectronaut and processed using a pipeline of three functions from the R package MSstats (version 3.19.5) (Choi et al., 2014): function MSstats::SpectronauttoMSstatsFormat with default settings other than setting “removeProtein_with1Feature = TRUE”; function MSstats::dataProcess with default settings other than setting “censoredInt = 0,” “featureSubset = highQuality,” “remove_uninformative_feature_outlier = TRUE,” “clusters=7”; and function MSstats::groupComparison with all default settings.
T895 1800-1961 Sentence denotes Phosphopeptide intensity data were summarized at the peptide ion level along with confident localization of phosphorylation as described in the previous section.
T896 1962-2165 Sentence denotes Quantification of phosphorylation based on peptide ions were processed using artMS as a wrapper around MSstats, via functions artMS::doSiteConversion and artMS::artmsQuantification with default settings.
T897 2166-2297 Sentence denotes All peptides containing the same set of phosphorylated sites were grouped and quantified together into phosphorylation site groups.
T898 2298-2694 Sentence denotes For both phosphopeptide and protein abundance MSstats pipelines, MSstats performs normalization by median equalization, imputation of missing values and median smoothing to combine intensities for multiple peptide ions or fragments into a single intensity for their protein or phosphorylation site group, and statistical tests of differences in intensity between infected and control time points.

2_test

Id Subject Object Predicate Lexical cue
32645325-24794931-20773114 1423-1427 24794931 denotes 2014