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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T924 528-532 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T925 535-539 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T926 766-770 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T927 773-777 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T928 934-938 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T929 1061-1065 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T930 1068-1072 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T931 1115-1119 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T932 1122-1126 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T933 1389-1394 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T934 1446-1450 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T935 1509-1514 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T936 1522-1538 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T937 1533-1538 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T938 1551-1562 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T939 1607-1612 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T940 1729-1734 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T941 1799-1804 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T942 2537-2541 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T169 2537-2541 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T338 939-947 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T339 1885-1893 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T340 2338-2346 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T341 2338-2342 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T342 2533-2536 Disease denotes HCA http://purl.obolibrary.org/obo/MONDO_0018902

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1352 36-38 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T1353 52-53 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1354 358-359 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1355 393-394 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1356 528-532 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T1357 535-539 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T1358 766-770 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T1359 773-777 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T1360 934-938 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T1361 1061-1065 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T1362 1068-1072 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T1363 1115-1119 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T1364 1122-1126 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T1365 1140-1145 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T1366 1389-1394 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1367 1446-1450 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T1368 1509-1514 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1369 1522-1532 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T1370 1533-1547 http://purl.obolibrary.org/obo/CL_0000000 denotes cells for type
T1371 1607-1612 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1372 1729-1734 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1373 1799-1804 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1374 1808-1817 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes are
T1375 2314-2318 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T1376 2537-2541 http://purl.obolibrary.org/obo/UBERON_0002048 denotes Lung
T1377 2537-2541 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lung

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T26285 1548-1550 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T120 2561-2566 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T566 0-26 Sentence denotes Data and Code Availability
T567 27-268 Sentence denotes In Table S9 , we provide a guide to all datasets analyzed in this paper as well as links to each individual dataset for download with the main landing page here: https://singlecell.broadinstitute.org/single_cell?scpbr=the-alexandria-project.
T568 269-473 Sentence denotes To download the data from the portal, follow the link to the visualization page, sign in a free account in the portal using a Google apps enabled email address, and select the ‘Download’ tab in the study.
T569 474-579 Sentence denotes Downloadable datasets include both raw and normalized cell x gene matrices, as well as relevant metadata.
T570 580-739 Sentence denotes These datasets are additionally available here to facilitate downloading: https://drive.google.com/drive/folders/1bxCIqNeZ7wLuVOT16gphwj98_cc9KhrV?usp=sharing.
T571 740-1044 Sentence denotes We have also posted these cell x gene matrices to Chan Zuckerberg Initiative cellxgene (https://chanzuckerberg.github.io/cellxgene/posts/cellxgene_cziscience_com) and the Broad Institute Single Cell COVID-19 portal (https://singlecell.broadinstitute.org/single_cell/covid19) as leading community efforts.
T572 1045-1188 Sentence denotes FASTQ files and cell x gene matrices for NHP and murine datasets, and cell x gene matrices for human datasets, are available at GEO: GSE148829.
T573 1189-1248 Sentence denotes In this same table, we further highlight four access types.
T574 1249-1736 Sentence denotes 1. published datasets where everything is available (1 study); 2. unpublished datasets where everything is available (2 studies, 19,670 new cells for download), 3. unpublished datasets where ACE2+ cell subsets, and the necessary subsets to contextualize those cells (i.e., epithelial cells for type II pneumocytes) are fully available (5 studies, 17,986 new cells for download); and, 4. those unpublished datasets where expression is shared for ACE2/TMPRSS2 (2 studies, 9,112 new cells).
T575 1737-1912 Sentence denotes For those unpublished datasets where only specific subsets of cells or genes are available, full expression matrices are available upon request for COVID-19 related questions.
T576 1913-2001 Sentence denotes All data included in the present study can be visualized using the following web viewer:
T577 2002-2081 Sentence denotes https://singlecell.broadinstitute.org/single_cell?scpbr=the-alexandria-project.
T578 2082-2451 Sentence denotes As we gain further insight and feedback from our own groups, collaborators, and investigators, we will continue to provide updates on our resource websites, including the utility of in vitro systems, such as organoids (Mead et al., 2018), for the study of SARS-CoV-2: http://shaleklab.com/resource/covid-19-resources/ and www.ordovasmontaneslab.com/covid-19-resources/.
T579 2452-2641 Sentence denotes We also note that there are several ongoing efforts unified together through the HCA Lung Biological Network group that we will reference and to which we will link as they become available.
T580 2642-2762 Sentence denotes No custom code was used to analyze these data and all methods and packages used are cited in the Method Details section.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2335 1094-1100 Species denotes murine Tax:10090
2336 1140-1145 Species denotes human Tax:9606
2337 939-947 Disease denotes COVID-19 MESH:C000657245
2342 1440-1444 Gene denotes ACE2 Gene:59272
2343 1694-1698 Gene denotes ACE2 Gene:59272
2344 1699-1706 Gene denotes TMPRSS2 Gene:7113
2345 1885-1893 Disease denotes COVID-19 MESH:C000657245
2349 2338-2348 Species denotes SARS-CoV-2 Tax:2697049
2350 2380-2388 Disease denotes covid-19 MESH:C000657245
2351 2431-2439 Disease denotes covid-19 MESH:C000657245

2_test

Id Subject Object Predicate Lexical cue
32413319-29871632-20790564 2314-2318 29871632 denotes 2018