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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1","span":{"begin":344,"end":350},"obj":"Body_part"},{"id":"T2","span":{"begin":549,"end":556},"obj":"Body_part"},{"id":"T3","span":{"begin":689,"end":695},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"Introduction\nAccording to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown aetiology in Wuhan City, Hubei Province, on 31 December 2019 [1]. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. A viral genome sequence was released for immediate public health support via the community online resource virological.org on 10 January (Wuhan-Hu-1, GenBank accession number MN908947 [2]), followed by four other genomes deposited on 12 January in the viral sequence database curated by the Global Initiative on Sharing All Influenza Data (GISAID). The genome sequences suggest presence of a virus closely related to the members of a viral species termed severe acute respiratory syndrome (SARS)-related CoV, a species defined by the agent of the 2002/03 outbreak of SARS in humans [3,4]. The species also comprises a large number of viruses mostly detected in rhinolophid bats in Asia and Europe.\nAs at 20 January 2019, 282 laboratory-confirmed human cases have been notified to WHO [5]. Confirmed cases in travellers from Wuhan were announced on 13 and 17 January in Thailand as well as on 15 January in Japan and 19 January in Korea. The extent of human-to-human transmission of 2019-nCoV is unclear at the time of writing of this report but there is evidence of some human-to-human transmission.\nAmong the foremost priorities to facilitate public health interventions is reliable laboratory diagnosis. In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from respiratory secretions. We have previously demonstrated the feasibility of introducing robust detection technology based on real-time RT-PCR in public health laboratories during international health emergencies by coordination between public and academic laboratories [6-12]. In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.\nIn the present case of 2019-nCoV, virus isolates or samples from infected patients have so far not become available to the international public health community. We report here on the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T4","span":{"begin":117,"end":126},"obj":"Disease"},{"id":"T5","span":{"begin":660,"end":669},"obj":"Disease"},{"id":"T6","span":{"begin":791,"end":824},"obj":"Disease"},{"id":"T7","span":{"begin":826,"end":830},"obj":"Disease"},{"id":"T8","span":{"begin":903,"end":907},"obj":"Disease"},{"id":"T9","span":{"begin":1551,"end":1572},"obj":"Disease"},{"id":"T10","span":{"begin":1563,"end":1572},"obj":"Disease"},{"id":"T11","span":{"begin":2502,"end":2510},"obj":"Disease"},{"id":"T12","span":{"begin":2502,"end":2506},"obj":"Disease"}],"attributes":[{"id":"A4","pred":"mondo_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A5","pred":"mondo_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A6","pred":"mondo_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0024355"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A12","pred":"mondo_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Introduction\nAccording to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown aetiology in Wuhan City, Hubei Province, on 31 December 2019 [1]. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. A viral genome sequence was released for immediate public health support via the community online resource virological.org on 10 January (Wuhan-Hu-1, GenBank accession number MN908947 [2]), followed by four other genomes deposited on 12 January in the viral sequence database curated by the Global Initiative on Sharing All Influenza Data (GISAID). The genome sequences suggest presence of a virus closely related to the members of a viral species termed severe acute respiratory syndrome (SARS)-related CoV, a species defined by the agent of the 2002/03 outbreak of SARS in humans [3,4]. The species also comprises a large number of viruses mostly detected in rhinolophid bats in Asia and Europe.\nAs at 20 January 2019, 282 laboratory-confirmed human cases have been notified to WHO [5]. Confirmed cases in travellers from Wuhan were announced on 13 and 17 January in Thailand as well as on 15 January in Japan and 19 January in Korea. The extent of human-to-human transmission of 2019-nCoV is unclear at the time of writing of this report but there is evidence of some human-to-human transmission.\nAmong the foremost priorities to facilitate public health interventions is reliable laboratory diagnosis. In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from respiratory secretions. We have previously demonstrated the feasibility of introducing robust detection technology based on real-time RT-PCR in public health laboratories during international health emergencies by coordination between public and academic laboratories [6-12]. In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.\nIn the present case of 2019-nCoV, virus isolates or samples from infected patients have so far not become available to the international public health community. We report here on the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T3","span":{"begin":2546,"end":2558},"obj":"Chemical"},{"id":"T4","span":{"begin":2554,"end":2558},"obj":"Chemical"}],"attributes":[{"id":"A3","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_33696"},{"id":"A4","pred":"chebi_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"}],"text":"Introduction\nAccording to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown aetiology in Wuhan City, Hubei Province, on 31 December 2019 [1]. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. A viral genome sequence was released for immediate public health support via the community online resource virological.org on 10 January (Wuhan-Hu-1, GenBank accession number MN908947 [2]), followed by four other genomes deposited on 12 January in the viral sequence database curated by the Global Initiative on Sharing All Influenza Data (GISAID). The genome sequences suggest presence of a virus closely related to the members of a viral species termed severe acute respiratory syndrome (SARS)-related CoV, a species defined by the agent of the 2002/03 outbreak of SARS in humans [3,4]. The species also comprises a large number of viruses mostly detected in rhinolophid bats in Asia and Europe.\nAs at 20 January 2019, 282 laboratory-confirmed human cases have been notified to WHO [5]. Confirmed cases in travellers from Wuhan were announced on 13 and 17 January in Thailand as well as on 15 January in Japan and 19 January in Korea. The extent of human-to-human transmission of 2019-nCoV is unclear at the time of writing of this report but there is evidence of some human-to-human transmission.\nAmong the foremost priorities to facilitate public health interventions is reliable laboratory diagnosis. In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from respiratory secretions. We have previously demonstrated the feasibility of introducing robust detection technology based on real-time RT-PCR in public health laboratories during international health emergencies by coordination between public and academic laboratories [6-12]. In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.\nIn the present case of 2019-nCoV, virus isolates or samples from infected patients have so far not become available to the international public health community. We report here on the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T1","span":{"begin":1644,"end":1654},"obj":"http://purl.obolibrary.org/obo/GO_0046903"}],"text":"Introduction\nAccording to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown aetiology in Wuhan City, Hubei Province, on 31 December 2019 [1]. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. A viral genome sequence was released for immediate public health support via the community online resource virological.org on 10 January (Wuhan-Hu-1, GenBank accession number MN908947 [2]), followed by four other genomes deposited on 12 January in the viral sequence database curated by the Global Initiative on Sharing All Influenza Data (GISAID). The genome sequences suggest presence of a virus closely related to the members of a viral species termed severe acute respiratory syndrome (SARS)-related CoV, a species defined by the agent of the 2002/03 outbreak of SARS in humans [3,4]. The species also comprises a large number of viruses mostly detected in rhinolophid bats in Asia and Europe.\nAs at 20 January 2019, 282 laboratory-confirmed human cases have been notified to WHO [5]. Confirmed cases in travellers from Wuhan were announced on 13 and 17 January in Thailand as well as on 15 January in Japan and 19 January in Korea. The extent of human-to-human transmission of 2019-nCoV is unclear at the time of writing of this report but there is evidence of some human-to-human transmission.\nAmong the foremost priorities to facilitate public health interventions is reliable laboratory diagnosis. In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from respiratory secretions. We have previously demonstrated the feasibility of introducing robust detection technology based on real-time RT-PCR in public health laboratories during international health emergencies by coordination between public and academic laboratories [6-12]. In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.\nIn the present case of 2019-nCoV, virus isolates or samples from infected patients have so far not become available to the international public health community. We report here on the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T15","span":{"begin":0,"end":12},"obj":"Sentence"},{"id":"T16","span":{"begin":13,"end":203},"obj":"Sentence"},{"id":"T17","span":{"begin":204,"end":335},"obj":"Sentence"},{"id":"T18","span":{"begin":336,"end":684},"obj":"Sentence"},{"id":"T19","span":{"begin":685,"end":924},"obj":"Sentence"},{"id":"T20","span":{"begin":925,"end":1033},"obj":"Sentence"},{"id":"T21","span":{"begin":1034,"end":1124},"obj":"Sentence"},{"id":"T22","span":{"begin":1125,"end":1272},"obj":"Sentence"},{"id":"T23","span":{"begin":1273,"end":1435},"obj":"Sentence"},{"id":"T24","span":{"begin":1436,"end":1541},"obj":"Sentence"},{"id":"T25","span":{"begin":1542,"end":1655},"obj":"Sentence"},{"id":"T26","span":{"begin":1656,"end":1907},"obj":"Sentence"},{"id":"T27","span":{"begin":1908,"end":2053},"obj":"Sentence"},{"id":"T28","span":{"begin":2054,"end":2215},"obj":"Sentence"},{"id":"T29","span":{"begin":2216,"end":2421},"obj":"Sentence"},{"id":"T30","span":{"begin":2422,"end":2570},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Introduction\nAccording to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown aetiology in Wuhan City, Hubei Province, on 31 December 2019 [1]. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. A viral genome sequence was released for immediate public health support via the community online resource virological.org on 10 January (Wuhan-Hu-1, GenBank accession number MN908947 [2]), followed by four other genomes deposited on 12 January in the viral sequence database curated by the Global Initiative on Sharing All Influenza Data (GISAID). The genome sequences suggest presence of a virus closely related to the members of a viral species termed severe acute respiratory syndrome (SARS)-related CoV, a species defined by the agent of the 2002/03 outbreak of SARS in humans [3,4]. The species also comprises a large number of viruses mostly detected in rhinolophid bats in Asia and Europe.\nAs at 20 January 2019, 282 laboratory-confirmed human cases have been notified to WHO [5]. Confirmed cases in travellers from Wuhan were announced on 13 and 17 January in Thailand as well as on 15 January in Japan and 19 January in Korea. The extent of human-to-human transmission of 2019-nCoV is unclear at the time of writing of this report but there is evidence of some human-to-human transmission.\nAmong the foremost priorities to facilitate public health interventions is reliable laboratory diagnosis. In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from respiratory secretions. We have previously demonstrated the feasibility of introducing robust detection technology based on real-time RT-PCR in public health laboratories during international health emergencies by coordination between public and academic laboratories [6-12]. In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.\nIn the present case of 2019-nCoV, virus isolates or samples from infected patients have so far not become available to the international public health community. We report here on the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T1","span":{"begin":117,"end":126},"obj":"Phenotype"},{"id":"T2","span":{"begin":1551,"end":1572},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A2","pred":"hp_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/HP_0011947"}],"text":"Introduction\nAccording to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown aetiology in Wuhan City, Hubei Province, on 31 December 2019 [1]. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. A viral genome sequence was released for immediate public health support via the community online resource virological.org on 10 January (Wuhan-Hu-1, GenBank accession number MN908947 [2]), followed by four other genomes deposited on 12 January in the viral sequence database curated by the Global Initiative on Sharing All Influenza Data (GISAID). The genome sequences suggest presence of a virus closely related to the members of a viral species termed severe acute respiratory syndrome (SARS)-related CoV, a species defined by the agent of the 2002/03 outbreak of SARS in humans [3,4]. The species also comprises a large number of viruses mostly detected in rhinolophid bats in Asia and Europe.\nAs at 20 January 2019, 282 laboratory-confirmed human cases have been notified to WHO [5]. Confirmed cases in travellers from Wuhan were announced on 13 and 17 January in Thailand as well as on 15 January in Japan and 19 January in Korea. The extent of human-to-human transmission of 2019-nCoV is unclear at the time of writing of this report but there is evidence of some human-to-human transmission.\nAmong the foremost priorities to facilitate public health interventions is reliable laboratory diagnosis. In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from respiratory secretions. We have previously demonstrated the feasibility of introducing robust detection technology based on real-time RT-PCR in public health laboratories during international health emergencies by coordination between public and academic laboratories [6-12]. In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.\nIn the present case of 2019-nCoV, virus isolates or samples from infected patients have so far not become available to the international public health community. We report here on the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology."}

2_test

{"project":"2_test","denotations":[{"id":"31992387-14681510-29325737","span":{"begin":921,"end":922},"obj":"14681510"},{"id":"31992387-12736651-29325738","span":{"begin":1901,"end":1902},"obj":"12736651"},{"id":"31992387-23231891-29325738","span":{"begin":1901,"end":1902},"obj":"23231891"},{"id":"31992387-12690091-29325738","span":{"begin":1901,"end":1902},"obj":"12690091"},{"id":"31992387-23611031-29325738","span":{"begin":1901,"end":1902},"obj":"23611031"},{"id":"31992387-23041020-29325738","span":{"begin":1901,"end":1902},"obj":"23041020"},{"id":"31992387-19239767-29325738","span":{"begin":1901,"end":1902},"obj":"19239767"},{"id":"31992387-27994281-29325738","span":{"begin":1901,"end":1902},"obj":"27994281"}],"text":"Introduction\nAccording to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown aetiology in Wuhan City, Hubei Province, on 31 December 2019 [1]. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. A viral genome sequence was released for immediate public health support via the community online resource virological.org on 10 January (Wuhan-Hu-1, GenBank accession number MN908947 [2]), followed by four other genomes deposited on 12 January in the viral sequence database curated by the Global Initiative on Sharing All Influenza Data (GISAID). The genome sequences suggest presence of a virus closely related to the members of a viral species termed severe acute respiratory syndrome (SARS)-related CoV, a species defined by the agent of the 2002/03 outbreak of SARS in humans [3,4]. The species also comprises a large number of viruses mostly detected in rhinolophid bats in Asia and Europe.\nAs at 20 January 2019, 282 laboratory-confirmed human cases have been notified to WHO [5]. Confirmed cases in travellers from Wuhan were announced on 13 and 17 January in Thailand as well as on 15 January in Japan and 19 January in Korea. The extent of human-to-human transmission of 2019-nCoV is unclear at the time of writing of this report but there is evidence of some human-to-human transmission.\nAmong the foremost priorities to facilitate public health interventions is reliable laboratory diagnosis. In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from respiratory secretions. We have previously demonstrated the feasibility of introducing robust detection technology based on real-time RT-PCR in public health laboratories during international health emergencies by coordination between public and academic laboratories [6-12]. In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.\nIn the present case of 2019-nCoV, virus isolates or samples from infected patients have so far not become available to the international public health community. We report here on the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology."}

LitCovid-PubTator

MyTest

{"project":"MyTest","denotations":[{"id":"31992387-14681510-29325737","span":{"begin":921,"end":922},"obj":"14681510"},{"id":"31992387-12736651-29325738","span":{"begin":1901,"end":1902},"obj":"12736651"},{"id":"31992387-23231891-29325738","span":{"begin":1901,"end":1902},"obj":"23231891"},{"id":"31992387-12690091-29325738","span":{"begin":1901,"end":1902},"obj":"12690091"},{"id":"31992387-23611031-29325738","span":{"begin":1901,"end":1902},"obj":"23611031"},{"id":"31992387-23041020-29325738","span":{"begin":1901,"end":1902},"obj":"23041020"},{"id":"31992387-19239767-29325738","span":{"begin":1901,"end":1902},"obj":"19239767"},{"id":"31992387-27994281-29325738","span":{"begin":1901,"end":1902},"obj":"27994281"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Introduction\nAccording to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown aetiology in Wuhan City, Hubei Province, on 31 December 2019 [1]. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. A viral genome sequence was released for immediate public health support via the community online resource virological.org on 10 January (Wuhan-Hu-1, GenBank accession number MN908947 [2]), followed by four other genomes deposited on 12 January in the viral sequence database curated by the Global Initiative on Sharing All Influenza Data (GISAID). The genome sequences suggest presence of a virus closely related to the members of a viral species termed severe acute respiratory syndrome (SARS)-related CoV, a species defined by the agent of the 2002/03 outbreak of SARS in humans [3,4]. The species also comprises a large number of viruses mostly detected in rhinolophid bats in Asia and Europe.\nAs at 20 January 2019, 282 laboratory-confirmed human cases have been notified to WHO [5]. Confirmed cases in travellers from Wuhan were announced on 13 and 17 January in Thailand as well as on 15 January in Japan and 19 January in Korea. The extent of human-to-human transmission of 2019-nCoV is unclear at the time of writing of this report but there is evidence of some human-to-human transmission.\nAmong the foremost priorities to facilitate public health interventions is reliable laboratory diagnosis. In acute respiratory infection, RT-PCR is routinely used to detect causative viruses from respiratory secretions. We have previously demonstrated the feasibility of introducing robust detection technology based on real-time RT-PCR in public health laboratories during international health emergencies by coordination between public and academic laboratories [6-12]. In all of these situations, virus isolates were available as the primary substrate for establishing and controlling assays and assay performance.\nIn the present case of 2019-nCoV, virus isolates or samples from infected patients have so far not become available to the international public health community. We report here on the establishment and validation of a diagnostic workflow for 2019-nCoV screening and specific confirmation, designed in absence of available virus isolates or original patient specimens. Design and validation were enabled by the close genetic relatedness to the 2003 SARS-CoV, and aided by the use of synthetic nucleic acid technology."}

PMC:6988269 / 1363-3933 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:6988269 / 1363-3933 JSON TXT