PMC:7073332 / 40615-41937 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"1111","span":{"begin":13,"end":18},"obj":"Species"},{"id":"1115","span":{"begin":80,"end":85},"obj":"Species"},{"id":"1116","span":{"begin":987,"end":992},"obj":"Species"},{"id":"1117","span":{"begin":1240,"end":1245},"obj":"Species"}],"attributes":[{"id":"A1111","pred":"tao:has_database_id","subj":"1111","obj":"Tax:9606"},{"id":"A1115","pred":"tao:has_database_id","subj":"1115","obj":"Tax:9606"},{"id":"A1116","pred":"tao:has_database_id","subj":"1116","obj":"Tax:9606"},{"id":"A1117","pred":"tao:has_database_id","subj":"1117","obj":"Tax:9606"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Building the human protein–protein interactome\nTo build a comprehensive list of human PPIs, we assembled data from a total of 18 bioinformatics and systems biology databases with five types of experimental evidence: (i) binary PPIs tested by high-throughput yeast-two-hybrid (Y2H) systems; (ii) binary, physical PPIs from protein 3D structures; (iii) kinase-substrate interactions by literature-derived low-throughput or high-throughput experiments; (iv) signaling network by literature-derived low-throughput experiments; and (v) literature-curated PPIs identified by affinity purification followed by mass spectrometry (AP-MS), Y2H, or by literature-derived low-throughput experiments. All inferred data, including evolutionary analysis, gene expression data, and metabolic associations, were excluded. The genes were mapped to their Entrez ID based on the NCBI database92 as well as their official gene symbols based on GeneCards (https://www.genecards.org/). In total, the resulting human protein–protein interactome used in this study includes 351,444 unique PPIs (edges or links) connecting 17,706 proteins (nodes), representing a 50% increase in the number of the PPIs we have used previously. Detailed descriptions for building the human protein–protein interactome are provided in our previous studies13,23,28,93."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T197","span":{"begin":19,"end":26},"obj":"Body_part"},{"id":"T198","span":{"begin":27,"end":34},"obj":"Body_part"},{"id":"T199","span":{"begin":322,"end":329},"obj":"Body_part"},{"id":"T200","span":{"begin":740,"end":744},"obj":"Body_part"},{"id":"T201","span":{"begin":901,"end":905},"obj":"Body_part"},{"id":"T202","span":{"begin":993,"end":1000},"obj":"Body_part"},{"id":"T203","span":{"begin":1001,"end":1008},"obj":"Body_part"},{"id":"T204","span":{"begin":1104,"end":1112},"obj":"Body_part"},{"id":"T205","span":{"begin":1246,"end":1253},"obj":"Body_part"},{"id":"T206","span":{"begin":1254,"end":1261},"obj":"Body_part"}],"attributes":[{"id":"A197","pred":"fma_id","subj":"T197","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A198","pred":"fma_id","subj":"T198","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A199","pred":"fma_id","subj":"T199","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A200","pred":"fma_id","subj":"T200","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A201","pred":"fma_id","subj":"T201","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A202","pred":"fma_id","subj":"T202","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A203","pred":"fma_id","subj":"T203","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A204","pred":"fma_id","subj":"T204","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A205","pred":"fma_id","subj":"T205","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A206","pred":"fma_id","subj":"T206","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Building the human protein–protein interactome\nTo build a comprehensive list of human PPIs, we assembled data from a total of 18 bioinformatics and systems biology databases with five types of experimental evidence: (i) binary PPIs tested by high-throughput yeast-two-hybrid (Y2H) systems; (ii) binary, physical PPIs from protein 3D structures; (iii) kinase-substrate interactions by literature-derived low-throughput or high-throughput experiments; (iv) signaling network by literature-derived low-throughput experiments; and (v) literature-curated PPIs identified by affinity purification followed by mass spectrometry (AP-MS), Y2H, or by literature-derived low-throughput experiments. All inferred data, including evolutionary analysis, gene expression data, and metabolic associations, were excluded. The genes were mapped to their Entrez ID based on the NCBI database92 as well as their official gene symbols based on GeneCards (https://www.genecards.org/). In total, the resulting human protein–protein interactome used in this study includes 351,444 unique PPIs (edges or links) connecting 17,706 proteins (nodes), representing a 50% increase in the number of the PPIs we have used previously. Detailed descriptions for building the human protein–protein interactome are provided in our previous studies13,23,28,93."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T278","span":{"begin":13,"end":26},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T279","span":{"begin":56,"end":57},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T280","span":{"begin":80,"end":85},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T281","span":{"begin":115,"end":116},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T282","span":{"begin":126,"end":128},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T283","span":{"begin":232,"end":238},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T284","span":{"begin":455,"end":464},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T285","span":{"begin":622,"end":624},"obj":"http://purl.obolibrary.org/obo/CLO_0001547"},{"id":"T286","span":{"begin":625,"end":627},"obj":"http://purl.obolibrary.org/obo/CLO_0007874"},{"id":"T287","span":{"begin":740,"end":744},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T288","span":{"begin":809,"end":814},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T289","span":{"begin":901,"end":905},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T290","span":{"begin":987,"end":1000},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T291","span":{"begin":1135,"end":1136},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T292","span":{"begin":1240,"end":1253},"obj":"http://purl.obolibrary.org/obo/PR_000029067"}],"text":"Building the human protein–protein interactome\nTo build a comprehensive list of human PPIs, we assembled data from a total of 18 bioinformatics and systems biology databases with five types of experimental evidence: (i) binary PPIs tested by high-throughput yeast-two-hybrid (Y2H) systems; (ii) binary, physical PPIs from protein 3D structures; (iii) kinase-substrate interactions by literature-derived low-throughput or high-throughput experiments; (iv) signaling network by literature-derived low-throughput experiments; and (v) literature-curated PPIs identified by affinity purification followed by mass spectrometry (AP-MS), Y2H, or by literature-derived low-throughput experiments. All inferred data, including evolutionary analysis, gene expression data, and metabolic associations, were excluded. The genes were mapped to their Entrez ID based on the NCBI database92 as well as their official gene symbols based on GeneCards (https://www.genecards.org/). In total, the resulting human protein–protein interactome used in this study includes 351,444 unique PPIs (edges or links) connecting 17,706 proteins (nodes), representing a 50% increase in the number of the PPIs we have used previously. Detailed descriptions for building the human protein–protein interactome are provided in our previous studies13,23,28,93."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T451","span":{"begin":19,"end":26},"obj":"Chemical"},{"id":"T452","span":{"begin":27,"end":34},"obj":"Chemical"},{"id":"T453","span":{"begin":322,"end":329},"obj":"Chemical"},{"id":"T454","span":{"begin":622,"end":624},"obj":"Chemical"},{"id":"T457","span":{"begin":625,"end":627},"obj":"Chemical"},{"id":"T458","span":{"begin":843,"end":845},"obj":"Chemical"},{"id":"T459","span":{"begin":993,"end":1000},"obj":"Chemical"},{"id":"T460","span":{"begin":1001,"end":1008},"obj":"Chemical"},{"id":"T461","span":{"begin":1104,"end":1112},"obj":"Chemical"},{"id":"T462","span":{"begin":1246,"end":1253},"obj":"Chemical"},{"id":"T463","span":{"begin":1254,"end":1261},"obj":"Chemical"}],"attributes":[{"id":"A451","pred":"chebi_id","subj":"T451","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A452","pred":"chebi_id","subj":"T452","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A453","pred":"chebi_id","subj":"T453","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A454","pred":"chebi_id","subj":"T454","obj":"http://purl.obolibrary.org/obo/CHEBI_28971"},{"id":"A455","pred":"chebi_id","subj":"T454","obj":"http://purl.obolibrary.org/obo/CHEBI_73393"},{"id":"A456","pred":"chebi_id","subj":"T454","obj":"http://purl.obolibrary.org/obo/CHEBI_81686"},{"id":"A457","pred":"chebi_id","subj":"T457","obj":"http://purl.obolibrary.org/obo/CHEBI_73613"},{"id":"A458","pred":"chebi_id","subj":"T458","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"},{"id":"A459","pred":"chebi_id","subj":"T459","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A460","pred":"chebi_id","subj":"T460","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A461","pred":"chebi_id","subj":"T461","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A462","pred":"chebi_id","subj":"T462","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A463","pred":"chebi_id","subj":"T463","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"Building the human protein–protein interactome\nTo build a comprehensive list of human PPIs, we assembled data from a total of 18 bioinformatics and systems biology databases with five types of experimental evidence: (i) binary PPIs tested by high-throughput yeast-two-hybrid (Y2H) systems; (ii) binary, physical PPIs from protein 3D structures; (iii) kinase-substrate interactions by literature-derived low-throughput or high-throughput experiments; (iv) signaling network by literature-derived low-throughput experiments; and (v) literature-curated PPIs identified by affinity purification followed by mass spectrometry (AP-MS), Y2H, or by literature-derived low-throughput experiments. All inferred data, including evolutionary analysis, gene expression data, and metabolic associations, were excluded. The genes were mapped to their Entrez ID based on the NCBI database92 as well as their official gene symbols based on GeneCards (https://www.genecards.org/). In total, the resulting human protein–protein interactome used in this study includes 351,444 unique PPIs (edges or links) connecting 17,706 proteins (nodes), representing a 50% increase in the number of the PPIs we have used previously. Detailed descriptions for building the human protein–protein interactome are provided in our previous studies13,23,28,93."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T61","span":{"begin":455,"end":464},"obj":"http://purl.obolibrary.org/obo/GO_0023052"},{"id":"T62","span":{"begin":740,"end":755},"obj":"http://purl.obolibrary.org/obo/GO_0010467"}],"text":"Building the human protein–protein interactome\nTo build a comprehensive list of human PPIs, we assembled data from a total of 18 bioinformatics and systems biology databases with five types of experimental evidence: (i) binary PPIs tested by high-throughput yeast-two-hybrid (Y2H) systems; (ii) binary, physical PPIs from protein 3D structures; (iii) kinase-substrate interactions by literature-derived low-throughput or high-throughput experiments; (iv) signaling network by literature-derived low-throughput experiments; and (v) literature-curated PPIs identified by affinity purification followed by mass spectrometry (AP-MS), Y2H, or by literature-derived low-throughput experiments. All inferred data, including evolutionary analysis, gene expression data, and metabolic associations, were excluded. The genes were mapped to their Entrez ID based on the NCBI database92 as well as their official gene symbols based on GeneCards (https://www.genecards.org/). In total, the resulting human protein–protein interactome used in this study includes 351,444 unique PPIs (edges or links) connecting 17,706 proteins (nodes), representing a 50% increase in the number of the PPIs we have used previously. Detailed descriptions for building the human protein–protein interactome are provided in our previous studies13,23,28,93."}

{"project":"LitCovid-sentences","denotations":[{"id":"T253","span":{"begin":0,"end":46},"obj":"Sentence"},{"id":"T254","span":{"begin":47,"end":687},"obj":"Sentence"},{"id":"T255","span":{"begin":688,"end":804},"obj":"Sentence"},{"id":"T256","span":{"begin":805,"end":962},"obj":"Sentence"},{"id":"T257","span":{"begin":963,"end":1200},"obj":"Sentence"},{"id":"T258","span":{"begin":1201,"end":1322},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Building the human protein–protein interactome\nTo build a comprehensive list of human PPIs, we assembled data from a total of 18 bioinformatics and systems biology databases with five types of experimental evidence: (i) binary PPIs tested by high-throughput yeast-two-hybrid (Y2H) systems; (ii) binary, physical PPIs from protein 3D structures; (iii) kinase-substrate interactions by literature-derived low-throughput or high-throughput experiments; (iv) signaling network by literature-derived low-throughput experiments; and (v) literature-curated PPIs identified by affinity purification followed by mass spectrometry (AP-MS), Y2H, or by literature-derived low-throughput experiments. All inferred data, including evolutionary analysis, gene expression data, and metabolic associations, were excluded. The genes were mapped to their Entrez ID based on the NCBI database92 as well as their official gene symbols based on GeneCards (https://www.genecards.org/). In total, the resulting human protein–protein interactome used in this study includes 351,444 unique PPIs (edges or links) connecting 17,706 proteins (nodes), representing a 50% increase in the number of the PPIs we have used previously. Detailed descriptions for building the human protein–protein interactome are provided in our previous studies13,23,28,93."}

{"project":"2_test","denotations":[{"id":"32194980-26615191-19614261","span":{"begin":872,"end":874},"obj":"26615191"},{"id":"32194980-30002366-19614262","span":{"begin":1310,"end":1312},"obj":"30002366"},{"id":"32194980-31375661-19614263","span":{"begin":1313,"end":1315},"obj":"31375661"},{"id":"32194980-30867426-19614264","span":{"begin":1316,"end":1318},"obj":"30867426"},{"id":"32194980-31006514-19614265","span":{"begin":1319,"end":1321},"obj":"31006514"}],"text":"Building the human protein–protein interactome\nTo build a comprehensive list of human PPIs, we assembled data from a total of 18 bioinformatics and systems biology databases with five types of experimental evidence: (i) binary PPIs tested by high-throughput yeast-two-hybrid (Y2H) systems; (ii) binary, physical PPIs from protein 3D structures; (iii) kinase-substrate interactions by literature-derived low-throughput or high-throughput experiments; (iv) signaling network by literature-derived low-throughput experiments; and (v) literature-curated PPIs identified by affinity purification followed by mass spectrometry (AP-MS), Y2H, or by literature-derived low-throughput experiments. All inferred data, including evolutionary analysis, gene expression data, and metabolic associations, were excluded. The genes were mapped to their Entrez ID based on the NCBI database92 as well as their official gene symbols based on GeneCards (https://www.genecards.org/). In total, the resulting human protein–protein interactome used in this study includes 351,444 unique PPIs (edges or links) connecting 17,706 proteins (nodes), representing a 50% increase in the number of the PPIs we have used previously. Detailed descriptions for building the human protein–protein interactome are provided in our previous studies13,23,28,93."}