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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T11","span":{"begin":420,"end":424},"obj":"Body_part"},{"id":"T12","span":{"begin":695,"end":699},"obj":"Body_part"},{"id":"T13","span":{"begin":813,"end":816},"obj":"Body_part"},{"id":"T14","span":{"begin":827,"end":830},"obj":"Body_part"},{"id":"T15","span":{"begin":849,"end":853},"obj":"Body_part"},{"id":"T16","span":{"begin":881,"end":885},"obj":"Body_part"},{"id":"T17","span":{"begin":2187,"end":2191},"obj":"Body_part"},{"id":"T18","span":{"begin":2202,"end":2205},"obj":"Body_part"},{"id":"T19","span":{"begin":2251,"end":2254},"obj":"Body_part"},{"id":"T20","span":{"begin":2272,"end":2275},"obj":"Body_part"}],"attributes":[{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma24728"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma67095"}],"text":"Implementation of molecular diagnostics for novel coronavirus\n\nBiosafety level\nFor the biosafety-level (BSL) applied for inactivation of clinical samples suspected of 2019-nCoV, 22 laboratories of the 47 EU/EEA laboratories indicated to do this at BSL2. Twenty-one laboratories indicated to do so at BSL3. Four laboratories indicated an intermediate level BSL2 + (BSL2 with extra precautions such as wearing a filtering face piece (FFP)2 mask). Different approaches were observed between laboratories within some countries.\n\nTest specifics\nAs of 14 January 2020, protocols for RT-PCR of 2019-nCoV are being published on the WHO website [7]. At survey closure (29 January 2020), the envelope (E)-gene screening test as published by Corman et al. [6,7], had been implemented by 35 laboratories and the confirmatory RNA-dependent RNA polymerase (RdRp)-gene test and nucleoprotein (N)-gene test by respectively 33 and 21 laboratories. Sixteen laboratories indicated to have additional tests, i.e. in house tests (n = 5), pan-CoV tests (n = 12) or an assay based on Poon et al. (n = 1) [7]. Two laboratories indicated to base 2019-nCoV testing solely on previously published pan-CoV tests [8].\n\nLevel of specificity validation\nOnly 11 laboratories of the 38 laboratories that had implemented testing indicated having validated the specificity of the implemented test against the six additionally known HCoVs and other common respiratory pathogens. For 15 laboratories, specificity validation was still in progress at the time of data submission. Seven laboratories indicated to have only partially validated the implemented test(s) while five laboratories had not (yet) performed any validation. The questionnaire was send out before the first 2019-nCoV cases appeared in Europe (Figure 1) and positive clinical specimens were assumed to be not available to the European laboratories. Therefore, the level of validation for clinical sensitivity was not assessed.\n\nPositive control\nThree of 38 laboratories that had implemented diagnostics did the implementation without a positive control. Indicated sources for positive controls were the European Virus Archive (EVAg) (synthetic 2019-nCoV E-gene, SARS-CoV RNA) (n = 23) [9], or own stocks, i.e. SARS-HCoV RNA and/or synthetic RNA (n = 15)."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T5","span":{"begin":420,"end":424},"obj":"Body_part"}],"attributes":[{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_0001456"}],"text":"Implementation of molecular diagnostics for novel coronavirus\n\nBiosafety level\nFor the biosafety-level (BSL) applied for inactivation of clinical samples suspected of 2019-nCoV, 22 laboratories of the 47 EU/EEA laboratories indicated to do this at BSL2. Twenty-one laboratories indicated to do so at BSL3. Four laboratories indicated an intermediate level BSL2 + (BSL2 with extra precautions such as wearing a filtering face piece (FFP)2 mask). Different approaches were observed between laboratories within some countries.\n\nTest specifics\nAs of 14 January 2020, protocols for RT-PCR of 2019-nCoV are being published on the WHO website [7]. At survey closure (29 January 2020), the envelope (E)-gene screening test as published by Corman et al. [6,7], had been implemented by 35 laboratories and the confirmatory RNA-dependent RNA polymerase (RdRp)-gene test and nucleoprotein (N)-gene test by respectively 33 and 21 laboratories. Sixteen laboratories indicated to have additional tests, i.e. in house tests (n = 5), pan-CoV tests (n = 12) or an assay based on Poon et al. (n = 1) [7]. Two laboratories indicated to base 2019-nCoV testing solely on previously published pan-CoV tests [8].\n\nLevel of specificity validation\nOnly 11 laboratories of the 38 laboratories that had implemented testing indicated having validated the specificity of the implemented test against the six additionally known HCoVs and other common respiratory pathogens. For 15 laboratories, specificity validation was still in progress at the time of data submission. Seven laboratories indicated to have only partially validated the implemented test(s) while five laboratories had not (yet) performed any validation. The questionnaire was send out before the first 2019-nCoV cases appeared in Europe (Figure 1) and positive clinical specimens were assumed to be not available to the European laboratories. Therefore, the level of validation for clinical sensitivity was not assessed.\n\nPositive control\nThree of 38 laboratories that had implemented diagnostics did the implementation without a positive control. Indicated sources for positive controls were the European Virus Archive (EVAg) (synthetic 2019-nCoV E-gene, SARS-CoV RNA) (n = 23) [9], or own stocks, i.e. SARS-HCoV RNA and/or synthetic RNA (n = 15)."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T14","span":{"begin":2193,"end":2201},"obj":"Disease"},{"id":"T15","span":{"begin":2241,"end":2245},"obj":"Disease"}],"attributes":[{"id":"A14","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Implementation of molecular diagnostics for novel coronavirus\n\nBiosafety level\nFor the biosafety-level (BSL) applied for inactivation of clinical samples suspected of 2019-nCoV, 22 laboratories of the 47 EU/EEA laboratories indicated to do this at BSL2. Twenty-one laboratories indicated to do so at BSL3. Four laboratories indicated an intermediate level BSL2 + (BSL2 with extra precautions such as wearing a filtering face piece (FFP)2 mask). Different approaches were observed between laboratories within some countries.\n\nTest specifics\nAs of 14 January 2020, protocols for RT-PCR of 2019-nCoV are being published on the WHO website [7]. At survey closure (29 January 2020), the envelope (E)-gene screening test as published by Corman et al. [6,7], had been implemented by 35 laboratories and the confirmatory RNA-dependent RNA polymerase (RdRp)-gene test and nucleoprotein (N)-gene test by respectively 33 and 21 laboratories. Sixteen laboratories indicated to have additional tests, i.e. in house tests (n = 5), pan-CoV tests (n = 12) or an assay based on Poon et al. (n = 1) [7]. Two laboratories indicated to base 2019-nCoV testing solely on previously published pan-CoV tests [8].\n\nLevel of specificity validation\nOnly 11 laboratories of the 38 laboratories that had implemented testing indicated having validated the specificity of the implemented test against the six additionally known HCoVs and other common respiratory pathogens. For 15 laboratories, specificity validation was still in progress at the time of data submission. Seven laboratories indicated to have only partially validated the implemented test(s) while five laboratories had not (yet) performed any validation. The questionnaire was send out before the first 2019-nCoV cases appeared in Europe (Figure 1) and positive clinical specimens were assumed to be not available to the European laboratories. Therefore, the level of validation for clinical sensitivity was not assessed.\n\nPositive control\nThree of 38 laboratories that had implemented diagnostics did the implementation without a positive control. Indicated sources for positive controls were the European Virus Archive (EVAg) (synthetic 2019-nCoV E-gene, SARS-CoV RNA) (n = 23) [9], or own stocks, i.e. SARS-HCoV RNA and/or synthetic RNA (n = 15)."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T6","span":{"begin":1116,"end":1120},"obj":"Chemical"}],"attributes":[{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_22695"}],"text":"Implementation of molecular diagnostics for novel coronavirus\n\nBiosafety level\nFor the biosafety-level (BSL) applied for inactivation of clinical samples suspected of 2019-nCoV, 22 laboratories of the 47 EU/EEA laboratories indicated to do this at BSL2. Twenty-one laboratories indicated to do so at BSL3. Four laboratories indicated an intermediate level BSL2 + (BSL2 with extra precautions such as wearing a filtering face piece (FFP)2 mask). Different approaches were observed between laboratories within some countries.\n\nTest specifics\nAs of 14 January 2020, protocols for RT-PCR of 2019-nCoV are being published on the WHO website [7]. At survey closure (29 January 2020), the envelope (E)-gene screening test as published by Corman et al. [6,7], had been implemented by 35 laboratories and the confirmatory RNA-dependent RNA polymerase (RdRp)-gene test and nucleoprotein (N)-gene test by respectively 33 and 21 laboratories. Sixteen laboratories indicated to have additional tests, i.e. in house tests (n = 5), pan-CoV tests (n = 12) or an assay based on Poon et al. (n = 1) [7]. Two laboratories indicated to base 2019-nCoV testing solely on previously published pan-CoV tests [8].\n\nLevel of specificity validation\nOnly 11 laboratories of the 38 laboratories that had implemented testing indicated having validated the specificity of the implemented test against the six additionally known HCoVs and other common respiratory pathogens. For 15 laboratories, specificity validation was still in progress at the time of data submission. Seven laboratories indicated to have only partially validated the implemented test(s) while five laboratories had not (yet) performed any validation. The questionnaire was send out before the first 2019-nCoV cases appeared in Europe (Figure 1) and positive clinical specimens were assumed to be not available to the European laboratories. Therefore, the level of validation for clinical sensitivity was not assessed.\n\nPositive control\nThree of 38 laboratories that had implemented diagnostics did the implementation without a positive control. Indicated sources for positive controls were the European Virus Archive (EVAg) (synthetic 2019-nCoV E-gene, SARS-CoV RNA) (n = 23) [9], or own stocks, i.e. SARS-HCoV RNA and/or synthetic RNA (n = 15)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T56","span":{"begin":0,"end":61},"obj":"Sentence"},{"id":"T57","span":{"begin":63,"end":78},"obj":"Sentence"},{"id":"T58","span":{"begin":79,"end":253},"obj":"Sentence"},{"id":"T59","span":{"begin":254,"end":305},"obj":"Sentence"},{"id":"T60","span":{"begin":306,"end":444},"obj":"Sentence"},{"id":"T61","span":{"begin":445,"end":523},"obj":"Sentence"},{"id":"T62","span":{"begin":525,"end":539},"obj":"Sentence"},{"id":"T63","span":{"begin":540,"end":640},"obj":"Sentence"},{"id":"T64","span":{"begin":641,"end":930},"obj":"Sentence"},{"id":"T65","span":{"begin":931,"end":1085},"obj":"Sentence"},{"id":"T66","span":{"begin":1086,"end":1188},"obj":"Sentence"},{"id":"T67","span":{"begin":1190,"end":1221},"obj":"Sentence"},{"id":"T68","span":{"begin":1222,"end":1442},"obj":"Sentence"},{"id":"T69","span":{"begin":1443,"end":1540},"obj":"Sentence"},{"id":"T70","span":{"begin":1541,"end":1690},"obj":"Sentence"},{"id":"T71","span":{"begin":1691,"end":1879},"obj":"Sentence"},{"id":"T72","span":{"begin":1880,"end":1957},"obj":"Sentence"},{"id":"T73","span":{"begin":1959,"end":1975},"obj":"Sentence"},{"id":"T74","span":{"begin":1976,"end":2084},"obj":"Sentence"},{"id":"T75","span":{"begin":2085,"end":2285},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Implementation of molecular diagnostics for novel coronavirus\n\nBiosafety level\nFor the biosafety-level (BSL) applied for inactivation of clinical samples suspected of 2019-nCoV, 22 laboratories of the 47 EU/EEA laboratories indicated to do this at BSL2. Twenty-one laboratories indicated to do so at BSL3. Four laboratories indicated an intermediate level BSL2 + (BSL2 with extra precautions such as wearing a filtering face piece (FFP)2 mask). Different approaches were observed between laboratories within some countries.\n\nTest specifics\nAs of 14 January 2020, protocols for RT-PCR of 2019-nCoV are being published on the WHO website [7]. At survey closure (29 January 2020), the envelope (E)-gene screening test as published by Corman et al. [6,7], had been implemented by 35 laboratories and the confirmatory RNA-dependent RNA polymerase (RdRp)-gene test and nucleoprotein (N)-gene test by respectively 33 and 21 laboratories. Sixteen laboratories indicated to have additional tests, i.e. in house tests (n = 5), pan-CoV tests (n = 12) or an assay based on Poon et al. (n = 1) [7]. Two laboratories indicated to base 2019-nCoV testing solely on previously published pan-CoV tests [8].\n\nLevel of specificity validation\nOnly 11 laboratories of the 38 laboratories that had implemented testing indicated having validated the specificity of the implemented test against the six additionally known HCoVs and other common respiratory pathogens. For 15 laboratories, specificity validation was still in progress at the time of data submission. Seven laboratories indicated to have only partially validated the implemented test(s) while five laboratories had not (yet) performed any validation. The questionnaire was send out before the first 2019-nCoV cases appeared in Europe (Figure 1) and positive clinical specimens were assumed to be not available to the European laboratories. Therefore, the level of validation for clinical sensitivity was not assessed.\n\nPositive control\nThree of 38 laboratories that had implemented diagnostics did the implementation without a positive control. Indicated sources for positive controls were the European Virus Archive (EVAg) (synthetic 2019-nCoV E-gene, SARS-CoV RNA) (n = 23) [9], or own stocks, i.e. SARS-HCoV RNA and/or synthetic RNA (n = 15)."}