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PMC:7402624 / 74109-75186 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2163 61-65 Chemical denotes UMAP
2169 149-157 Species denotes patients Tax:9606
2170 415-422 Species denotes patient Tax:9606
2171 751-755 Chemical denotes UMAP
2172 140-148 Disease denotes COVID-19 MESH:C000657245
2173 406-414 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T438 140-148 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T439 406-414 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1053 82-83 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T1054 180-181 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1055 217-218 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T1056 826-827 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T1057 914-915 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T50300 213-215 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T64153 284-288 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T67801 357-361 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T2551 888-892 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T460 0-81 Sentence denotes Visualizing variation of flow cytometric features across the UMAP embedding space
T461 82-225 Sentence denotes A feature-weighted kernel density was computed across all COVID-19 patients, and was displayed as a contour plot (Fig. 6G and fig. S8, A to D).
T462 226-612 Sentence denotes Whereas traditional kernel density methods apply the same base kernel function to every point to visualize point density, here the base kernel function centered at each individual COVID-19 patient sample was instead weighted (multiplied) by the Z-transform (mean-centered and standard deviation-scaled) of the log-transformed input feature prior to computing the overall kernel density.
T463 613-825 Sentence denotes This weighting procedure facilitated visualization of the overall feature gradients (going from relatively low-to-high expression) across UMAP coordinates independent of the different range of each input feature.
T464 826-1077 Sentence denotes A radially symmetric two-dimensional Gaussian was used as the base kernel function with a variance parameter equal to one-half, which was tuned to be sufficiently broad in order to smooth out local discontinuities and best visualize feature gradients.