PMC:7321036 / 104202-105527 JSONTXT

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LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T30 144-148 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T31 482-489 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T32 561-562 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 788-796 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T34 922-924 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T35 976-977 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 1246-1251 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T37 1269-1271 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T38 1307-1315 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T76109 482-489 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T16401 490-494 Chemical denotes ions http://purl.obolibrary.org/obo/CHEBI_24870
T97754 788-796 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T7 241-256 http://purl.obolibrary.org/obo/GO_0016310 denotes Phosphorylation
T8 605-620 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T9 744-759 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T10 805-820 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T11 883-898 http://purl.obolibrary.org/obo/GO_0016310 denotes phosphorylation
T12 1300-1315 http://purl.obolibrary.org/obo/GO_0016301 denotes kinase activity

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2319 100-101 Gene denotes N Gene:43740575
2320 1246-1251 Species denotes human Tax:9606
2321 597-604 Chemical denotes MSstats

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T900 0-106 Sentence denotes When not explicitly indicated, we used defaults for MSstats for adjusted p values, even in cases of N = 2.
T901 107-240 Sentence denotes By default, MSstats uses Student’s t test for p value calculation and Benjamini-Hochberg method of FDR estimation to adjust p values.
T902 241-433 Sentence denotes Phosphorylation fold change data were filtered for quality based on consistency of observations between treatment and controls by requiring the MSstats reported value missingPercentage < 0.60.
T903 434-596 Sentence denotes This value is the proportion of features (i.e., peptide ions) that are missing across the treatment and control replicates for a specific fold change computation.
T904 597-685 Sentence denotes MSstats phosphorylation results had to be further simplified to effects at single sites.
T905 686-939 Sentence denotes The results of artMS/MSstats are fold changes of specific phosphorylation site groups detected within peptides, so one phosphorylation site can have multiple measurements if it occurs in different phosphorylation site groups (see Table S1 for examples).
T906 940-1189 Sentence denotes This complex dataset was reduced to a single fold change per site and time point by choosing (per time point) the fold change with the lowest p value, favoring those detected in both treatment and control, i.e., non-infinite log2 fold change values.
T907 1190-1325 Sentence denotes This single-site dataset, further reduced to those with human orthology (Table S1), was used as the input for kinase activity analysis.