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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T512","span":{"begin":599,"end":604},"obj":"Body_part"},{"id":"T513","span":{"begin":729,"end":734},"obj":"Body_part"},{"id":"T514","span":{"begin":1033,"end":1038},"obj":"Body_part"},{"id":"T515","span":{"begin":1307,"end":1312},"obj":"Body_part"}],"attributes":[{"id":"A512","pred":"fma_id","subj":"T512","obj":"http://purl.org/sig/ont/fma/fma49184"},{"id":"A513","pred":"fma_id","subj":"T513","obj":"http://purl.org/sig/ont/fma/fma9670"},{"id":"A514","pred":"fma_id","subj":"T514","obj":"http://purl.org/sig/ont/fma/fma9576"},{"id":"A515","pred":"fma_id","subj":"T515","obj":"http://purl.org/sig/ont/fma/fma9670"}],"text":"Patients admitted to the Hospital of the University of Pennsylvania with a positive SARS-CoV2 PCR test were screened and approached for informed consent within 3 days of hospitalization. Healthy donors (HD) were adults with no prior diagnosis of or recent symptoms consistent with COVID-19. Normal reference ranges for HDs were the UPenn clinical laboratory values shaded in green. Recovered COVID-19 subjects (RD) were adults with a prior positive COVID-19 PCR test by self-report who met the definition of recovery by the Centers for Disease Control. HD and RD were recruited initially by word of mouth and subsequently through a centralized University of Pennsylvania resource website for COVID-19-related studies. Peripheral blood was collected from all subjects. For inpatients, clinical data were abstracted from the electronic medical record into standardized case report forms. ARDS was categorized in accordance with the Berlin definition reflecting each subject’s worst oxygenation level and with physician adjudication of chest radiographs. APACHE III scoring was based on data collected in the first 24 hours of ICU admission or the first 24 hours of hospital admission for subjects admitted to general inpatient units. Clinical laboratory data were abstracted from the date closest to research blood collection. HD and RD completed a survey about symptoms. After enrollment, the clinical team determined three patients to be COVID-negative and/or PCR false positive. Two of these patients were classified as Immunotype 3. In keeping with inclusion criteria, these subjects were maintained in the analysis. The statistical significance reported in Fig. 6K did not change when analysis was repeated without the three patients. All participants or their surrogates provided informed consent in accordance with protocols approved by the regional ethical research boards and the Declaration of Helsinki."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T30","span":{"begin":599,"end":604},"obj":"Body_part"},{"id":"T31","span":{"begin":729,"end":734},"obj":"Body_part"},{"id":"T32","span":{"begin":1033,"end":1038},"obj":"Body_part"},{"id":"T33","span":{"begin":1307,"end":1312},"obj":"Body_part"}],"attributes":[{"id":"A30","pred":"uberon_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/UBERON_0000165"},{"id":"A31","pred":"uberon_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"A32","pred":"uberon_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A33","pred":"uberon_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"}],"text":"Patients admitted to the Hospital of the University of Pennsylvania with a positive SARS-CoV2 PCR test were screened and approached for informed consent within 3 days of hospitalization. Healthy donors (HD) were adults with no prior diagnosis of or recent symptoms consistent with COVID-19. Normal reference ranges for HDs were the UPenn clinical laboratory values shaded in green. Recovered COVID-19 subjects (RD) were adults with a prior positive COVID-19 PCR test by self-report who met the definition of recovery by the Centers for Disease Control. HD and RD were recruited initially by word of mouth and subsequently through a centralized University of Pennsylvania resource website for COVID-19-related studies. Peripheral blood was collected from all subjects. For inpatients, clinical data were abstracted from the electronic medical record into standardized case report forms. ARDS was categorized in accordance with the Berlin definition reflecting each subject’s worst oxygenation level and with physician adjudication of chest radiographs. APACHE III scoring was based on data collected in the first 24 hours of ICU admission or the first 24 hours of hospital admission for subjects admitted to general inpatient units. Clinical laboratory data were abstracted from the date closest to research blood collection. HD and RD completed a survey about symptoms. After enrollment, the clinical team determined three patients to be COVID-negative and/or PCR false positive. Two of these patients were classified as Immunotype 3. In keeping with inclusion criteria, these subjects were maintained in the analysis. The statistical significance reported in Fig. 6K did not change when analysis was repeated without the three patients. All participants or their surrogates provided informed consent in accordance with protocols approved by the regional ethical research boards and the Declaration of Helsinki."}

LitCovid-PubTator

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T408","span":{"begin":84,"end":88},"obj":"Disease"},{"id":"T409","span":{"begin":203,"end":205},"obj":"Disease"},{"id":"T410","span":{"begin":281,"end":289},"obj":"Disease"},{"id":"T411","span":{"begin":392,"end":400},"obj":"Disease"},{"id":"T412","span":{"begin":411,"end":413},"obj":"Disease"},{"id":"T413","span":{"begin":449,"end":457},"obj":"Disease"},{"id":"T414","span":{"begin":553,"end":555},"obj":"Disease"},{"id":"T415","span":{"begin":560,"end":562},"obj":"Disease"},{"id":"T416","span":{"begin":692,"end":700},"obj":"Disease"},{"id":"T417","span":{"begin":886,"end":890},"obj":"Disease"},{"id":"T418","span":{"begin":1325,"end":1327},"obj":"Disease"},{"id":"T419","span":{"begin":1332,"end":1334},"obj":"Disease"}],"attributes":[{"id":"A408","pred":"mondo_id","subj":"T408","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A409","pred":"mondo_id","subj":"T409","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A410","pred":"mondo_id","subj":"T410","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A411","pred":"mondo_id","subj":"T411","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A412","pred":"mondo_id","subj":"T412","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A413","pred":"mondo_id","subj":"T413","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A414","pred":"mondo_id","subj":"T414","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A415","pred":"mondo_id","subj":"T415","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A416","pred":"mondo_id","subj":"T416","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A417","pred":"mondo_id","subj":"T417","obj":"http://purl.obolibrary.org/obo/MONDO_0006502"},{"id":"A418","pred":"mondo_id","subj":"T418","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A419","pred":"mondo_id","subj":"T419","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"}],"text":"Patients admitted to the Hospital of the University of Pennsylvania with a positive SARS-CoV2 PCR test were screened and approached for informed consent within 3 days of hospitalization. Healthy donors (HD) were adults with no prior diagnosis of or recent symptoms consistent with COVID-19. Normal reference ranges for HDs were the UPenn clinical laboratory values shaded in green. Recovered COVID-19 subjects (RD) were adults with a prior positive COVID-19 PCR test by self-report who met the definition of recovery by the Centers for Disease Control. HD and RD were recruited initially by word of mouth and subsequently through a centralized University of Pennsylvania resource website for COVID-19-related studies. Peripheral blood was collected from all subjects. For inpatients, clinical data were abstracted from the electronic medical record into standardized case report forms. ARDS was categorized in accordance with the Berlin definition reflecting each subject’s worst oxygenation level and with physician adjudication of chest radiographs. APACHE III scoring was based on data collected in the first 24 hours of ICU admission or the first 24 hours of hospital admission for subjects admitted to general inpatient units. Clinical laboratory data were abstracted from the date closest to research blood collection. HD and RD completed a survey about symptoms. After enrollment, the clinical team determined three patients to be COVID-negative and/or PCR false positive. Two of these patients were classified as Immunotype 3. In keeping with inclusion criteria, these subjects were maintained in the analysis. The statistical significance reported in Fig. 6K did not change when analysis was repeated without the three patients. All participants or their surrogates provided informed consent in accordance with protocols approved by the regional ethical research boards and the Declaration of Helsinki."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T925","span":{"begin":73,"end":74},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T926","span":{"begin":98,"end":102},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T927","span":{"begin":411,"end":413},"obj":"http://purl.obolibrary.org/obo/CLO_0008770"},{"id":"T928","span":{"begin":432,"end":433},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T929","span":{"begin":462,"end":466},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T930","span":{"begin":560,"end":562},"obj":"http://purl.obolibrary.org/obo/CLO_0008770"},{"id":"T931","span":{"begin":599,"end":604},"obj":"http://www.ebi.ac.uk/efo/EFO_0000825"},{"id":"T932","span":{"begin":630,"end":631},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T933","span":{"begin":729,"end":734},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T934","span":{"begin":729,"end":734},"obj":"http://www.ebi.ac.uk/efo/EFO_0000296"},{"id":"T935","span":{"begin":930,"end":936},"obj":"http://purl.obolibrary.org/obo/CLO_0001929"},{"id":"T936","span":{"begin":1033,"end":1038},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T937","span":{"begin":1307,"end":1312},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T938","span":{"begin":1307,"end":1312},"obj":"http://www.ebi.ac.uk/efo/EFO_0000296"},{"id":"T939","span":{"begin":1332,"end":1334},"obj":"http://purl.obolibrary.org/obo/CLO_0008770"},{"id":"T940","span":{"begin":1345,"end":1346},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Patients admitted to the Hospital of the University of Pennsylvania with a positive SARS-CoV2 PCR test were screened and approached for informed consent within 3 days of hospitalization. Healthy donors (HD) were adults with no prior diagnosis of or recent symptoms consistent with COVID-19. Normal reference ranges for HDs were the UPenn clinical laboratory values shaded in green. Recovered COVID-19 subjects (RD) were adults with a prior positive COVID-19 PCR test by self-report who met the definition of recovery by the Centers for Disease Control. HD and RD were recruited initially by word of mouth and subsequently through a centralized University of Pennsylvania resource website for COVID-19-related studies. Peripheral blood was collected from all subjects. For inpatients, clinical data were abstracted from the electronic medical record into standardized case report forms. ARDS was categorized in accordance with the Berlin definition reflecting each subject’s worst oxygenation level and with physician adjudication of chest radiographs. APACHE III scoring was based on data collected in the first 24 hours of ICU admission or the first 24 hours of hospital admission for subjects admitted to general inpatient units. Clinical laboratory data were abstracted from the date closest to research blood collection. HD and RD completed a survey about symptoms. After enrollment, the clinical team determined three patients to be COVID-negative and/or PCR false positive. Two of these patients were classified as Immunotype 3. In keeping with inclusion criteria, these subjects were maintained in the analysis. The statistical significance reported in Fig. 6K did not change when analysis was repeated without the three patients. All participants or their surrogates provided informed consent in accordance with protocols approved by the regional ethical research boards and the Declaration of Helsinki."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T65195","span":{"begin":203,"end":205},"obj":"Chemical"},{"id":"T61322","span":{"begin":411,"end":413},"obj":"Chemical"},{"id":"T94286","span":{"begin":553,"end":555},"obj":"Chemical"},{"id":"T21414","span":{"begin":560,"end":562},"obj":"Chemical"},{"id":"T1354","span":{"begin":1325,"end":1327},"obj":"Chemical"},{"id":"T46546","span":{"begin":1332,"end":1334},"obj":"Chemical"}],"attributes":[{"id":"A66603","pred":"chebi_id","subj":"T65195","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A36615","pred":"chebi_id","subj":"T61322","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"},{"id":"A93470","pred":"chebi_id","subj":"T94286","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A95361","pred":"chebi_id","subj":"T21414","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"},{"id":"A18148","pred":"chebi_id","subj":"T1354","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A37350","pred":"chebi_id","subj":"T46546","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"}],"text":"Patients admitted to the Hospital of the University of Pennsylvania with a positive SARS-CoV2 PCR test were screened and approached for informed consent within 3 days of hospitalization. Healthy donors (HD) were adults with no prior diagnosis of or recent symptoms consistent with COVID-19. Normal reference ranges for HDs were the UPenn clinical laboratory values shaded in green. Recovered COVID-19 subjects (RD) were adults with a prior positive COVID-19 PCR test by self-report who met the definition of recovery by the Centers for Disease Control. HD and RD were recruited initially by word of mouth and subsequently through a centralized University of Pennsylvania resource website for COVID-19-related studies. Peripheral blood was collected from all subjects. For inpatients, clinical data were abstracted from the electronic medical record into standardized case report forms. ARDS was categorized in accordance with the Berlin definition reflecting each subject’s worst oxygenation level and with physician adjudication of chest radiographs. APACHE III scoring was based on data collected in the first 24 hours of ICU admission or the first 24 hours of hospital admission for subjects admitted to general inpatient units. Clinical laboratory data were abstracted from the date closest to research blood collection. HD and RD completed a survey about symptoms. After enrollment, the clinical team determined three patients to be COVID-negative and/or PCR false positive. Two of these patients were classified as Immunotype 3. In keeping with inclusion criteria, these subjects were maintained in the analysis. The statistical significance reported in Fig. 6K did not change when analysis was repeated without the three patients. All participants or their surrogates provided informed consent in accordance with protocols approved by the regional ethical research boards and the Declaration of Helsinki."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T357","span":{"begin":0,"end":186},"obj":"Sentence"},{"id":"T358","span":{"begin":187,"end":290},"obj":"Sentence"},{"id":"T359","span":{"begin":291,"end":381},"obj":"Sentence"},{"id":"T360","span":{"begin":382,"end":552},"obj":"Sentence"},{"id":"T361","span":{"begin":553,"end":717},"obj":"Sentence"},{"id":"T362","span":{"begin":718,"end":767},"obj":"Sentence"},{"id":"T363","span":{"begin":768,"end":885},"obj":"Sentence"},{"id":"T364","span":{"begin":886,"end":1051},"obj":"Sentence"},{"id":"T365","span":{"begin":1052,"end":1231},"obj":"Sentence"},{"id":"T366","span":{"begin":1232,"end":1324},"obj":"Sentence"},{"id":"T367","span":{"begin":1325,"end":1369},"obj":"Sentence"},{"id":"T368","span":{"begin":1370,"end":1479},"obj":"Sentence"},{"id":"T369","span":{"begin":1480,"end":1534},"obj":"Sentence"},{"id":"T370","span":{"begin":1535,"end":1618},"obj":"Sentence"},{"id":"T371","span":{"begin":1619,"end":1737},"obj":"Sentence"},{"id":"T372","span":{"begin":1738,"end":1911},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Patients admitted to the Hospital of the University of Pennsylvania with a positive SARS-CoV2 PCR test were screened and approached for informed consent within 3 days of hospitalization. Healthy donors (HD) were adults with no prior diagnosis of or recent symptoms consistent with COVID-19. Normal reference ranges for HDs were the UPenn clinical laboratory values shaded in green. Recovered COVID-19 subjects (RD) were adults with a prior positive COVID-19 PCR test by self-report who met the definition of recovery by the Centers for Disease Control. HD and RD were recruited initially by word of mouth and subsequently through a centralized University of Pennsylvania resource website for COVID-19-related studies. Peripheral blood was collected from all subjects. For inpatients, clinical data were abstracted from the electronic medical record into standardized case report forms. ARDS was categorized in accordance with the Berlin definition reflecting each subject’s worst oxygenation level and with physician adjudication of chest radiographs. APACHE III scoring was based on data collected in the first 24 hours of ICU admission or the first 24 hours of hospital admission for subjects admitted to general inpatient units. Clinical laboratory data were abstracted from the date closest to research blood collection. HD and RD completed a survey about symptoms. After enrollment, the clinical team determined three patients to be COVID-negative and/or PCR false positive. Two of these patients were classified as Immunotype 3. In keeping with inclusion criteria, these subjects were maintained in the analysis. The statistical significance reported in Fig. 6K did not change when analysis was repeated without the three patients. All participants or their surrogates provided informed consent in accordance with protocols approved by the regional ethical research boards and the Declaration of Helsinki."}