PMC:7252096 / 120735-122458 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T180 142-146 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T181 208-215 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T182 235-240 Body_part denotes ileum http://purl.org/sig/ont/fma/fma7208
T183 245-249 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T184 390-395 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T185 412-416 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T186 502-507 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T187 591-595 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T188 661-665 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T189 824-830 Body_part denotes cell’s http://purl.org/sig/ont/fma/fma68646
T190 1125-1129 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T191 1261-1267 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T192 1530-1535 Body_part denotes ileum http://purl.org/sig/ont/fma/fma7208
T193 1544-1548 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T194 1606-1610 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T195 1619-1623 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T196 1704-1709 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T256 235-240 Body_part denotes ileum http://purl.obolibrary.org/obo/UBERON_0002116
T257 245-249 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T258 1261-1267 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T259 1530-1535 Body_part denotes ileum http://purl.obolibrary.org/obo/UBERON_0002116
T260 1606-1610 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T262 70-71 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T263 142-146 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T264 221-226 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T265 227-234 http://purl.obolibrary.org/obo/NCBITaxon_9443 denotes primate
T266 235-240 http://purl.obolibrary.org/obo/UBERON_0002116 denotes ileum
T267 245-249 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T268 245-249 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T269 264-265 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T270 390-395 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T271 412-416 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T272 458-459 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T273 502-507 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T274 591-595 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T275 645-646 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T276 659-665 http://purl.obolibrary.org/obo/CLO_0001020 denotes a cell
T277 681-682 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T278 824-830 http://purl.obolibrary.org/obo/GO_0005623 denotes cell’s
T279 861-862 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T280 926-927 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T281 1125-1129 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T282 1314-1319 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T283 1507-1508 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T284 1530-1535 http://purl.obolibrary.org/obo/UBERON_0002116 denotes ileum
T285 1544-1548 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T286 1582-1583 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T287 1606-1610 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T288 1606-1610 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T289 1619-1623 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T290 1704-1709 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T18549 367-376 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T76325 690-698 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T9827 789-798 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T1128 1393-1401 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T15833 1430-1439 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T21 56-66 http://purl.obolibrary.org/obo/GO_0006351 denotes transcript

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T855 0-179 Sentence denotes Next, we examined the probability of sequencing an ACE2 transcript as a function of read depth and ACE2’s fractional abundance in each single cell within our sequencing libraries.
T856 180-720 Sentence denotes First, across two different tissues (non-human primate ileum and lung, representing a high expresser of ACE2 and low expresser, respectively), we calculated the proportion of unique ACE2 molecules in our ACE2+ cells (defined as any cell with at least 1 UMI aligning to ACE2) as a fraction of total reads within individual cells to provide an order-of-magnitude estimate for average ACE2 abundance in our single-cell sequencing libraries (i.e., the probability that a read within a cell corresponds to a unique molecule of ACE2, Figure S6B).
T857 721-1062 Sentence denotes We highlight that by calculating probabilities based on ACE2 unique molecules divided by an individual cell’s total reads, we are providing a conservative estimate for the probability of observing ACE2 as a function of sequencing depth (e.g., as compared to basing these probabilities on ACE2 non-UMI-collapsed reads divided by total reads).
T858 1063-1205 Sentence denotes Next, we obtained information on the number of reads in these cell populations to provide estimates of average sequencing depths (Figure S6C).
T859 1206-1490 Sentence denotes Using the mean fractional abundances of ACE2 from each tissue (Figure S6B) and the mean read depths for all genes (Figure S6C), we calculated the probability of detecting at least 1 ACE2 molecule (i.e., P(detecting > 0 ACE2 molecules) = 1 - (1 - ACE2 fractional abundance)Read depth).
T860 1491-1723 Sentence denotes This results in a 93.7% probability in ileum-derived cell libraries that contain ACE2, and a 76.0% probability for lung-derived cell libraries, indicating that our sequencing depths are sufficient to detect ACE2+ cells (Figure S6D).

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2852 51-55 Gene denotes ACE2 Gene:59272
2853 99-103 Gene denotes ACE2 Gene:59272
2854 284-288 Gene denotes ACE2 Gene:59272
2855 362-366 Gene denotes ACE2 Gene:59272
2856 384-388 Gene denotes ACE2 Gene:59272
2857 449-453 Gene denotes ACE2 Gene:59272
2858 562-566 Gene denotes ACE2 Gene:59272
2859 702-706 Gene denotes ACE2 Gene:59272
2860 777-781 Gene denotes ACE2 Gene:59272
2861 918-922 Gene denotes ACE2 Gene:59272
2862 1009-1013 Gene denotes ACE2 Gene:59272
2863 1246-1250 Gene denotes ACE2 Gene:59272
2864 1388-1392 Gene denotes ACE2 Gene:59272
2865 1425-1429 Gene denotes ACE2 Gene:59272
2866 1452-1456 Gene denotes ACE2 Gene:59272
2867 1572-1576 Gene denotes ACE2 Gene:59272
2868 1698-1702 Gene denotes ACE2 Gene:59272
2869 221-226 Species denotes human Tax:9606