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LitCovid-PMC-OGER-BB

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T1495","span":{"begin":55,"end":65},"obj":"GO:0010467"},{"id":"T1496","span":{"begin":69,"end":75},"obj":"UBERON:0002405"},{"id":"T1497","span":{"begin":232,"end":242},"obj":"GO:0010467"},{"id":"T1498","span":{"begin":270,"end":280},"obj":"GO:0010467"},{"id":"T1499","span":{"begin":356,"end":366},"obj":"GO:0010467"},{"id":"T1500","span":{"begin":896,"end":906},"obj":"GO:0010467"},{"id":"T1501","span":{"begin":935,"end":945},"obj":"GO:0010467"},{"id":"T1502","span":{"begin":989,"end":999},"obj":"GO:0010467"},{"id":"T1503","span":{"begin":1054,"end":1064},"obj":"GO:0010467"},{"id":"T1504","span":{"begin":1189,"end":1193},"obj":"SO:0000704"},{"id":"T1505","span":{"begin":1443,"end":1453},"obj":"GO:0010467"}],"text":"Determination of cell-cell interaction\nWe employed the expression of immune-related ligands and receptors to assess the cell-cell interactions (Ma et al., 2020). The possible ligand-receptor interactions between one set of receptor-expressing cells and then next ligand-expressing cells were determined as the average of the product of receptor and ligand expression (respectively from set one and two) across all single-cell pairs:\n\\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$$I = \\mathop \\sum \\limits_{i}^{n} I_{i} \\times \\mathop \\sum \\limits_{j}^{m} r_{j} \\left(\\frac{1}{m*n}\\right)$$\\end{document}I=∑inIi×∑jmrj1m∗nwhere I refers to the interaction score between receptor expressing cells in set one and ligand-expressing cells in set two, Ii stands for the ligand expression of cell i in cell set one, rj represents the receptor expression of cell j in cell set two, n stands for the number of cells in set one and m denotes the number of cells in set two.\nIn the gene list, there were 168 pairs of well-annotated ligands and receptors, among which were co-stimulators, chemokines and cytokines. The possible interactions between two cell types were orchestrated by receptor-ligand pairs by the product of the average expression levels of the ligand in one cell type and the respective receptor in the other cell type."}

LitCovid-PD-FMA-UBERON

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1160","span":{"begin":17,"end":21},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1161","span":{"begin":22,"end":26},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1162","span":{"begin":120,"end":124},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1163","span":{"begin":125,"end":129},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1164","span":{"begin":243,"end":248},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1165","span":{"begin":281,"end":286},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1166","span":{"begin":421,"end":425},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1167","span":{"begin":767,"end":772},"obj":"http://purl.obolibrary.org/obo/CLO_0007029"},{"id":"T1168","span":{"begin":767,"end":772},"obj":"http://purl.obolibrary.org/obo/CLO_0050993"},{"id":"T1169","span":{"begin":907,"end":912},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1170","span":{"begin":946,"end":951},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1171","span":{"begin":1003,"end":1007},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1172","span":{"begin":1013,"end":1017},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1173","span":{"begin":1068,"end":1072},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1174","span":{"begin":1078,"end":1082},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1175","span":{"begin":1119,"end":1124},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1176","span":{"begin":1164,"end":1169},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1177","span":{"begin":1189,"end":1193},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T1178","span":{"begin":1359,"end":1369},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T1179","span":{"begin":1482,"end":1491},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T1180","span":{"begin":1533,"end":1542},"obj":"http://purl.obolibrary.org/obo/CL_0000000"}],"text":"Determination of cell-cell interaction\nWe employed the expression of immune-related ligands and receptors to assess the cell-cell interactions (Ma et al., 2020). The possible ligand-receptor interactions between one set of receptor-expressing cells and then next ligand-expressing cells were determined as the average of the product of receptor and ligand expression (respectively from set one and two) across all single-cell pairs:\n\\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$$I = \\mathop \\sum \\limits_{i}^{n} I_{i} \\times \\mathop \\sum \\limits_{j}^{m} r_{j} \\left(\\frac{1}{m*n}\\right)$$\\end{document}I=∑inIi×∑jmrj1m∗nwhere I refers to the interaction score between receptor expressing cells in set one and ligand-expressing cells in set two, Ii stands for the ligand expression of cell i in cell set one, rj represents the receptor expression of cell j in cell set two, n stands for the number of cells in set one and m denotes the number of cells in set two.\nIn the gene list, there were 168 pairs of well-annotated ligands and receptors, among which were co-stimulators, chemokines and cytokines. The possible interactions between two cell types were orchestrated by receptor-ligand pairs by the product of the average expression levels of the ligand in one cell type and the respective receptor in the other cell type."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T4789","span":{"begin":84,"end":91},"obj":"Chemical"},{"id":"T88562","span":{"begin":175,"end":181},"obj":"Chemical"},{"id":"T154","span":{"begin":263,"end":269},"obj":"Chemical"},{"id":"T28709","span":{"begin":349,"end":355},"obj":"Chemical"},{"id":"T14279","span":{"begin":928,"end":934},"obj":"Chemical"},{"id":"T157","span":{"begin":982,"end":988},"obj":"Chemical"},{"id":"T73358","span":{"begin":1239,"end":1246},"obj":"Chemical"},{"id":"T54318","span":{"begin":1400,"end":1406},"obj":"Chemical"},{"id":"T160","span":{"begin":1468,"end":1474},"obj":"Chemical"}],"attributes":[{"id":"A56055","pred":"chebi_id","subj":"T4789","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A75152","pred":"chebi_id","subj":"T88562","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A90104","pred":"chebi_id","subj":"T154","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A75201","pred":"chebi_id","subj":"T28709","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A27179","pred":"chebi_id","subj":"T14279","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A15867","pred":"chebi_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A66365","pred":"chebi_id","subj":"T73358","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A92138","pred":"chebi_id","subj":"T54318","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A29712","pred":"chebi_id","subj":"T160","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"}],"text":"Determination of cell-cell interaction\nWe employed the expression of immune-related ligands and receptors to assess the cell-cell interactions (Ma et al., 2020). The possible ligand-receptor interactions between one set of receptor-expressing cells and then next ligand-expressing cells were determined as the average of the product of receptor and ligand expression (respectively from set one and two) across all single-cell pairs:\n\\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$$I = \\mathop \\sum \\limits_{i}^{n} I_{i} \\times \\mathop \\sum \\limits_{j}^{m} r_{j} \\left(\\frac{1}{m*n}\\right)$$\\end{document}I=∑inIi×∑jmrj1m∗nwhere I refers to the interaction score between receptor expressing cells in set one and ligand-expressing cells in set two, Ii stands for the ligand expression of cell i in cell set one, rj represents the receptor expression of cell j in cell set two, n stands for the number of cells in set one and m denotes the number of cells in set two.\nIn the gene list, there were 168 pairs of well-annotated ligands and receptors, among which were co-stimulators, chemokines and cytokines. The possible interactions between two cell types were orchestrated by receptor-ligand pairs by the product of the average expression levels of the ligand in one cell type and the respective receptor in the other cell type."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T399","span":{"begin":0,"end":38},"obj":"Sentence"},{"id":"T400","span":{"begin":39,"end":161},"obj":"Sentence"},{"id":"T401","span":{"begin":162,"end":432},"obj":"Sentence"},{"id":"T402","span":{"begin":433,"end":1181},"obj":"Sentence"},{"id":"T403","span":{"begin":1182,"end":1320},"obj":"Sentence"},{"id":"T404","span":{"begin":1321,"end":1543},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Determination of cell-cell interaction\nWe employed the expression of immune-related ligands and receptors to assess the cell-cell interactions (Ma et al., 2020). The possible ligand-receptor interactions between one set of receptor-expressing cells and then next ligand-expressing cells were determined as the average of the product of receptor and ligand expression (respectively from set one and two) across all single-cell pairs:\n\\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$$I = \\mathop \\sum \\limits_{i}^{n} I_{i} \\times \\mathop \\sum \\limits_{j}^{m} r_{j} \\left(\\frac{1}{m*n}\\right)$$\\end{document}I=∑inIi×∑jmrj1m∗nwhere I refers to the interaction score between receptor expressing cells in set one and ligand-expressing cells in set two, Ii stands for the ligand expression of cell i in cell set one, rj represents the receptor expression of cell j in cell set two, n stands for the number of cells in set one and m denotes the number of cells in set two.\nIn the gene list, there were 168 pairs of well-annotated ligands and receptors, among which were co-stimulators, chemokines and cytokines. The possible interactions between two cell types were orchestrated by receptor-ligand pairs by the product of the average expression levels of the ligand in one cell type and the respective receptor in the other cell type."}

2_test

{"project":"2_test","denotations":[{"id":"32780218-29706550-132718732","span":{"begin":155,"end":159},"obj":"29706550"}],"text":"Determination of cell-cell interaction\nWe employed the expression of immune-related ligands and receptors to assess the cell-cell interactions (Ma et al., 2020). The possible ligand-receptor interactions between one set of receptor-expressing cells and then next ligand-expressing cells were determined as the average of the product of receptor and ligand expression (respectively from set one and two) across all single-cell pairs:\n\\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$$I = \\mathop \\sum \\limits_{i}^{n} I_{i} \\times \\mathop \\sum \\limits_{j}^{m} r_{j} \\left(\\frac{1}{m*n}\\right)$$\\end{document}I=∑inIi×∑jmrj1m∗nwhere I refers to the interaction score between receptor expressing cells in set one and ligand-expressing cells in set two, Ii stands for the ligand expression of cell i in cell set one, rj represents the receptor expression of cell j in cell set two, n stands for the number of cells in set one and m denotes the number of cells in set two.\nIn the gene list, there were 168 pairs of well-annotated ligands and receptors, among which were co-stimulators, chemokines and cytokines. The possible interactions between two cell types were orchestrated by receptor-ligand pairs by the product of the average expression levels of the ligand in one cell type and the respective receptor in the other cell type."}